Contacts of the helix formed by residues 126 - 154 (chain A) in PDB entry 2RBD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 126 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO 3.2 15.4 + - - +
9A GLN* 3.6 24.0 + - - +
11A GLU* 2.9 51.2 + - + +
12A PRO 4.1 6.5 - - - +
13A LEU* 3.7 20.3 - - - +
17A GLU* 2.8 16.8 + - - +
68A LEU* 3.5 19.8 - - - +
72A ASN* 3.2 26.7 + - - +
124A SER* 4.1 3.8 - - - -
125A ILE* 1.3 76.8 - - - +
127A GLU* 1.3 65.5 + - - +
128A ASP* 2.8 38.0 + - - +
129A VAL* 3.1 17.4 + - + +
130A ALA* 3.4 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 4.4 20.0 - - + +
11A GLU* 5.0 0.4 + - - -
125A ILE 3.3 2.0 + - - +
126A ARG* 1.3 73.7 - - - +
128A ASP* 1.3 58.2 + - - +
130A ALA* 3.4 8.4 + - - +
131A LEU* 3.0 40.0 + - + +
148B LEU* 4.8 9.4 - - + +
149B LYS* 3.8 24.3 - - - +
152B LYS* 4.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PRO* 3.6 11.0 - - + +
9A GLN* 3.5 30.4 - - - +
68A LEU* 3.9 10.9 - - - +
126A ARG* 2.8 53.7 + - - +
127A GLU* 1.3 78.3 - - - +
129A VAL* 1.3 62.0 + - - +
131A LEU* 3.5 7.7 + - - +
132A MSE 3.0 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 3.6 31.4 - - + -
17A GLU* 4.4 12.6 - - + +
21A THR* 4.2 9.6 - - + -
68A LEU* 4.3 13.2 - - + -
120A ILE* 4.1 16.2 - - + -
124A SER* 3.4 16.8 - - - +
126A ARG* 3.1 12.2 + - + +
128A ASP* 1.3 86.6 - - - +
130A ALA* 1.3 65.7 + - - +
132A MSE 3.3 7.2 + - - +
133A PHE* 3.2 38.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.7 27.8 - - + +
124A SER* 3.7 22.9 + - - +
126A ARG 3.4 5.7 + - - +
127A GLU* 3.4 11.6 + - - +
129A VAL* 1.3 78.5 - - - +
131A LEU* 1.3 58.9 + - + +
133A PHE 3.4 0.3 + - - -
134A SER* 2.9 29.7 + - - -
141B VAL* 6.3 0.4 - - + -
148B LEU* 6.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 3.0 28.5 + - + +
128A ASP* 4.0 6.7 - - - +
130A ALA* 1.3 73.4 - - + +
132A MSE 1.3 66.3 + - - +
134A SER* 3.3 12.7 + - - +
135A GLN* 3.0 23.2 + - - +
141B VAL* 6.0 3.4 - - + -
142B GLN* 5.6 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.9 38.1 - - + +
65A LEU* 4.1 19.7 - - - -
68A LEU* 4.3 25.8 - - + -
128A ASP* 3.0 23.6 + - + +
129A VAL* 3.3 8.0 + - - +
131A LEU* 1.3 76.8 - - - +
133A PHE* 1.3 65.1 + - + +
135A GLN* 3.2 7.2 + - - +
136A PHE* 2.9 62.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.7 25.4 - - + -
24A TYR* 3.7 18.2 - + + -
65A LEU* 3.7 26.0 - - + -
117A CYS* 3.9 21.4 - - - +
120A ILE* 3.5 43.5 - - + -
121A ILE* 3.7 21.9 - - + +
129A VAL* 3.2 24.7 + - + +
132A MSE 1.3 87.7 - - + +
134A SER* 1.3 60.3 + - - +
136A PHE* 3.7 24.7 - + - +
137A HIS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ILE* 3.6 12.0 - - - +
130A ALA 2.9 18.3 + - - -
131A LEU* 3.4 15.5 - - - +
133A PHE* 1.3 77.0 - - - +
135A GLN* 1.3 60.8 + - - -
137A HIS* 3.3 4.6 + - - +
138A MSE 3.1 35.2 + - - +
137B HIS* 5.9 0.4 - - - -
138B MSE 4.6 7.3 - - - +
141B VAL* 3.7 30.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 5.8 5.6 - - - +
131A LEU 3.0 13.1 + - - +
132A MSE 3.4 11.0 - - - +
134A SER* 1.3 74.5 - - - +
136A PHE* 1.3 71.7 + - + +
138A MSE 3.2 14.2 + - + +
139A ALA* 3.1 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.8 15.5 - + - -
61A GLU* 3.7 54.7 - - + +
64A GLN* 3.8 23.3 - - - -
65A LEU* 4.1 8.5 - - + -
117A CYS* 3.8 10.8 - - - -
132A MSE 2.9 45.7 + - + -
133A PHE* 3.7 38.6 - + - +
134A SER 3.4 0.2 - - - -
135A GLN* 1.3 82.2 - - + +
137A HIS* 1.3 63.4 + - - +
139A ALA* 3.3 5.7 + - - +
140A LYS* 2.9 25.1 + - - +
171A PG4 3.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.3 35.0 - - + +
117A CYS* 4.0 12.1 - - + -
118A SER* 3.5 7.6 - - - -
121A ILE* 4.7 1.1 - - + -
133A PHE 2.9 17.9 + - - +
134A SER* 3.6 6.5 - - - +
136A PHE* 1.3 77.2 - - - +
138A MSE 1.3 60.6 + - - +
140A LYS* 3.1 6.0 + - - +
141A VAL* 2.9 57.6 + - + +
118B SER* 2.7 24.2 + - - -
121B ILE* 4.2 8.3 - - + -
134B SER* 5.8 0.4 - - - -
137B HIS* 3.4 35.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER* 3.1 21.9 + - - +
135A GLN* 3.2 14.1 + - + +
137A HIS* 1.3 81.7 - - - +
139A ALA* 1.3 61.5 + - - +
141A VAL* 3.5 7.1 + - - +
142A GLN* 3.4 24.9 + - - +
138B MSE 4.4 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLN* 3.1 12.8 + - + +
136A PHE* 3.7 8.5 - - - +
138A MSE 1.3 76.7 - - - +
140A LYS* 1.3 58.0 + - - +
142A GLN* 3.2 9.1 + - - +
143A PHE* 3.1 25.6 + - - +
171A PG4 3.8 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.2 23.3 + - - -
58A MSE 5.2 0.8 - - - +
61A GLU* 3.5 8.4 + - - -
110A VAL* 3.8 21.8 - - + +
113A GLY* 3.7 26.5 - - - -
114A LEU* 3.6 16.6 - - + +
117A CYS* 4.2 9.4 - - - -
136A PHE 2.9 13.9 + - - +
137A HIS* 4.3 0.4 - - - -
139A ALA* 1.3 73.4 - - - +
141A VAL* 1.3 65.9 + - - +
143A PHE* 3.8 0.8 - - - +
144A GLY* 2.9 22.2 + - - -
171A PG4 2.8 77.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.6 12.3 - - + -
137A HIS* 2.9 47.0 + - + +
138A MSE 3.7 7.2 - - - +
140A LYS* 1.3 76.9 - - - +
142A GLN* 1.3 78.0 + - - +
144A GLY* 3.4 1.3 + - - -
145A GLY* 3.0 18.5 + - - -
121B ILE* 4.4 21.8 - - + +
130B ALA* 5.7 1.1 - - + +
134B SER* 4.1 22.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A MSE 3.4 12.9 + - - +
139A ALA* 3.2 10.3 + - - +
141A VAL* 1.3 91.5 - - - +
143A PHE* 1.3 62.7 + - - +
145A GLY* 3.1 3.9 + - - +
146A LYS* 3.1 27.4 + - + +
134B SER* 5.8 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.4 45.1 - - + -
53A GLU* 3.8 23.1 - - + +
54A ALA* 3.6 20.4 - - + -
57A ALA* 5.9 0.2 - - + -
106A ILE* 4.2 4.9 - - + -
110A VAL* 3.7 20.6 - - + -
139A ALA 3.1 15.4 + - - +
140A LYS 3.9 2.9 - - - +
142A GLN* 1.3 76.5 - - - +
144A GLY* 1.3 62.3 + - - +
146A LYS* 3.1 10.0 + - + +
147A MSE 3.0 50.9 + - + +
171A PG4 3.6 35.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A VAL* 3.7 18.9 - - - +
114A LEU* 6.2 1.3 - - - -
140A LYS 2.9 16.9 + - - -
141A VAL* 3.8 2.2 - - - -
143A PHE* 1.3 79.3 - - - +
145A GLY* 1.3 55.7 + - - +
147A MSE 3.3 8.4 + - - +
148A LEU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL 3.0 14.0 + - - -
142A GLN 3.1 5.1 + - - -
144A GLY* 1.3 76.4 - - - +
146A LYS* 1.3 54.8 + - - +
148A LEU* 3.4 10.7 + - - +
149A LYS* 3.0 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.0 25.8 - - + +
53A GLU* 2.5 40.8 + - - +
142A GLN* 3.1 16.7 + - + +
143A PHE* 3.1 12.3 + - - +
145A GLY* 1.3 73.6 - - - +
147A MSE 1.3 59.7 + - - +
149A LYS* 3.3 13.8 + - + +
150A LEU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.4 5.4 - - + -
50A LEU* 4.0 22.9 - - - -
103A SER* 3.2 44.9 - - - +
106A ILE* 4.0 17.9 - - + -
107A SER* 3.7 16.2 - - - +
110A VAL* 4.8 3.6 - - + -
143A PHE* 3.0 51.0 + - + +
144A GLY* 3.3 10.7 + - - +
146A LYS* 1.3 71.5 - - - +
148A LEU* 1.3 66.3 + - - +
150A LEU* 3.3 13.6 + - + +
151A ASN* 3.0 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 3.0 14.0 + - - +
145A GLY* 3.6 11.9 - - - +
146A LYS 3.3 0.2 - - - -
147A MSE 1.3 75.4 - - - +
149A LYS* 1.3 58.2 + - + +
151A ASN* 3.3 6.5 + - + +
152A LYS* 2.9 55.5 + - + +
157A LEU* 4.0 24.7 - - + -
124B SER 3.8 16.8 - - - +
125B ILE* 3.5 31.0 - - + +
127B GLU* 4.9 11.2 - - + +
130B ALA* 5.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY* 3.0 23.6 + - - +
146A LYS* 3.6 14.3 - - + +
147A MSE 3.3 0.2 - - - -
148A LEU* 1.3 76.6 - - + +
150A LEU* 1.3 56.8 + - - +
152A LYS* 3.3 9.5 + - + +
153A ASN* 2.8 46.6 + - - +
127B GLU* 4.2 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP* 3.8 28.5 - - + -
47A LEU* 3.7 34.3 - - + +
50A LEU* 3.8 23.8 - - + -
103A SER* 3.7 15.5 - - - +
146A LYS 3.0 13.8 + - - +
147A MSE 3.3 12.8 + - + +
149A LYS* 1.3 75.9 - - - +
151A ASN* 1.3 56.7 + - - +
153A ASN* 3.1 8.2 + - + +
154A LYS* 2.9 51.4 + - + +
156A TRP* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 2.6 32.4 + - - -
104A ALA* 4.8 1.6 + - - +
107A SER* 3.1 28.9 + - - -
147A MSE 3.0 19.7 + - - +
148A LEU* 3.7 7.3 - - - +
150A LEU* 1.3 76.8 - - - +
152A LYS* 1.3 62.0 + - - +
155A GLY* 3.1 2.6 + - - -
156A TRP* 2.9 43.7 + - - +
157A LEU* 3.4 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 2.9 32.5 + - + +
149A LYS* 3.6 8.5 - - + +
151A ASN* 1.3 76.1 - - - +
153A ASN* 1.3 65.6 + - - +
155A GLY* 3.2 12.9 + - - -
157A LEU* 3.8 17.3 - - + -
11B GLU* 4.0 13.8 + - - -
125B ILE* 2.8 45.7 + - - -
127B GLU* 4.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LYS* 2.8 38.5 + - - +
150A LEU* 3.6 7.7 - - + +
152A LYS* 1.3 75.6 - - - +
154A LYS* 1.3 67.9 + - + +
155A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 2.7 37.5 + - - +
46A ASP* 2.7 29.0 + - - -
150A LEU* 2.9 33.6 + - + +
153A ASN* 1.3 82.1 - - + +
155A GLY* 1.3 60.5 + - - +
156A TRP* 3.5 47.9 + - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il