Contacts of the helix formed by residues 115 - 143 (chain A) in PDB entry 1B71
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 GLU 115 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.2 4.8 - - - +
110A ARG* 3.1 41.7 + - + +
113A GLY 3.5 5.6 + - - -
114A TYR* 1.3 76.0 - - - +
116A GLU* 1.3 57.2 + - - +
118A ALA* 3.1 10.2 - - - +
119A ARG* 2.8 50.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.6 18.0 - - + +
59A ARG* 3.3 29.3 + - - -
63A PHE* 3.9 22.3 - - + -
114A TYR 3.3 0.6 - - - -
115A GLU* 1.3 78.0 - - - +
117A ILE* 1.3 64.5 + - - +
119A ARG* 3.0 25.5 + - - +
120A VAL* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.6 7.6 - - - -
4A LEU* 3.9 22.4 - - + -
9A THR* 3.9 13.2 - - + -
13A ILE* 3.7 25.1 - - + -
60A LEU* 5.6 1.8 - - + -
63A PHE* 3.4 35.7 - - + -
109A ALA* 4.1 1.3 - - + -
114A TYR* 3.7 20.8 - - + +
115A GLU 3.3 0.2 - - - -
116A GLU* 1.3 75.8 - - - +
118A ALA* 1.3 58.4 + - - +
120A VAL* 3.0 9.1 + - + +
121A PHE* 2.9 58.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 3.5 29.2 - - - +
109A ALA* 3.9 7.2 - - - -
110A ARG* 3.8 19.5 + - + +
114A TYR 2.9 14.7 + - - +
115A GLU* 3.1 23.1 - - - +
117A ILE* 1.3 78.2 - - - +
119A ARG* 1.3 59.2 + - - +
121A PHE* 3.3 2.9 + - - +
122A ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU* 2.8 39.6 + - - +
116A GLU* 3.0 25.5 + - - +
118A ALA* 1.3 75.8 - - - +
120A VAL* 1.3 53.5 + - + +
122A ALA* 3.2 7.1 + - - +
123A SER* 2.7 44.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 3.4 55.2 - - + +
60A LEU* 4.2 13.2 - - + -
63A PHE* 4.2 10.8 - - + -
116A GLU* 3.0 21.6 + - - +
117A ILE* 3.4 9.4 - - - +
119A ARG* 1.3 75.8 - - + +
121A PHE* 1.3 61.0 + - - +
123A SER* 3.7 6.1 - - - -
124A ILE* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 4.3 4.9 - - + -
12A ASN* 4.3 2.0 - - + -
13A ILE* 3.9 30.5 - - + -
16A ALA* 4.2 6.1 - - + -
60A LEU* 3.9 20.6 - - + -
102A TYR* 3.3 48.3 - + + +
105A PHE* 3.6 45.8 - + + -
106A ALA* 3.9 13.7 - - + -
109A ALA* 4.2 3.6 - - + -
117A ILE* 2.9 38.2 + - + -
118A ALA 3.7 4.9 - - - +
120A VAL* 1.3 76.6 - - - +
122A ALA* 1.3 62.3 + - - +
124A ILE* 4.0 2.1 - - + +
125A ALA* 3.2 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 5.6 1.1 - - - -
103A PRO* 6.4 0.2 - - - -
106A ALA* 4.5 9.4 - - + +
110A ARG* 5.5 5.2 - - - +
118A ALA 3.0 13.1 + - - +
119A ARG* 3.7 8.7 - - - +
121A PHE* 1.3 75.1 - - - +
123A SER* 1.3 66.6 - - - +
125A ALA* 3.1 21.3 - - - +
126A VAL* 3.2 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ARG* 2.7 30.4 + - - +
120A VAL* 3.7 7.6 - - - -
122A ALA* 1.3 73.2 - - - +
124A ILE* 1.3 62.2 + - - +
126A VAL* 3.0 26.2 + - - +
127A ALA* 3.4 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.9 4.3 - - - +
56A HIS* 3.7 34.8 - - + +
59A ARG* 5.8 0.9 - - + -
60A LEU* 4.1 26.5 - - + -
102A TYR* 4.0 15.5 - - + +
120A VAL* 2.9 44.1 + - + +
121A PHE* 4.0 7.2 - - - +
123A SER* 1.3 70.8 - - - +
125A ALA* 1.3 57.9 + - - +
127A ALA* 3.0 9.2 + - - +
128A GLU* 2.8 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.5 27.8 - - + +
102A TYR* 4.2 12.1 - - + -
103A PRO* 5.1 2.9 - - + -
121A PHE 3.2 13.0 + - - +
122A ALA* 3.1 15.4 + - - +
123A SER 3.2 0.4 - - - -
124A ILE* 1.3 76.6 - - - +
126A VAL* 1.3 65.2 + - + +
128A GLU* 3.0 10.6 + - - +
129A GLU* 2.8 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.2 11.4 + - - +
123A SER* 3.0 13.4 + - - +
125A ALA* 1.3 78.6 - - + +
127A ALA* 1.3 64.6 + - - +
129A GLU* 2.9 19.4 + - - +
130A PHE* 3.1 12.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.7 27.6 - - + +
123A SER 3.4 4.3 + - - +
124A ILE* 3.0 11.1 + - - +
126A VAL* 1.3 81.6 - - - +
128A GLU* 1.4 60.9 + - - +
130A PHE* 3.1 7.3 + - - +
131A HIS* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.0 12.3 - - - +
56A HIS* 3.4 1.0 - - - -
94A GLU* 3.1 21.2 - - - +
97A GLU* 3.4 11.8 - - - +
98A TYR* 4.0 12.2 - - + -
102A TYR* 4.0 7.5 - - + -
124A ILE* 2.8 39.2 + - + +
125A ALA* 3.0 8.7 + - - +
127A ALA* 1.4 79.9 - - - +
129A GLU* 1.3 62.1 + - - +
131A HIS* 2.9 15.9 + - - +
132A GLU* 2.9 22.3 + - - +
193A FE 2.0 29.1 - - - -
194A ZN 2.1 31.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.8 38.6 + - + -
125A ALA 2.8 12.3 + - - +
126A VAL* 2.9 12.1 + - - +
128A GLU* 1.3 79.1 - - - +
130A PHE* 1.3 57.5 + - - +
132A GLU* 3.1 3.5 + - - +
133A LYS* 2.8 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 6.1 0.2 - - - -
126A VAL* 3.1 8.5 + - + +
127A ALA* 3.1 9.5 + - - +
129A GLU* 1.3 76.7 - - - +
131A HIS* 1.3 73.6 + + - +
133A LYS* 3.1 13.8 + - + -
134A ARG* 2.8 65.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.7 20.2 - - + +
52A GLN* 3.0 31.5 + - + +
53A GLU* 3.1 12.0 + - - -
56A HIS* 3.7 17.3 - + - -
94A GLU* 3.2 14.3 + - + +
127A ALA* 2.8 22.4 + - - +
128A GLU* 2.9 13.2 + - - +
129A GLU 3.2 0.2 - - - -
130A PHE* 1.3 83.5 - + - +
132A GLU* 1.3 64.3 + - - +
134A ARG* 3.4 17.9 + - - +
135A PHE* 2.9 31.8 + - + -
193A FE 2.1 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 3.8 20.2 - - + +
94A GLU* 4.2 9.8 - - + +
95A HIS* 3.2 22.3 + - - +
98A TYR* 2.4 40.5 + - + -
128A GLU 2.9 13.5 + - - +
129A GLU 3.3 6.5 - - - +
131A HIS* 1.3 78.6 - - - +
133A LYS* 1.3 72.7 + - - +
135A PHE* 3.0 7.7 + - - +
136A LEU* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR* 3.8 9.7 + - - -
129A GLU* 2.8 51.6 + - + +
130A PHE* 3.4 21.1 - - + +
132A GLU* 1.3 83.1 + - - +
134A ARG* 1.3 59.4 + - - +
136A LEU* 3.1 11.5 + - + +
137A ASP* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.5 29.7 + - + +
48A GLU* 2.8 33.9 + - - -
49A THR* 2.9 26.9 + - - +
52A GLN* 3.9 10.5 + - - -
130A PHE* 2.8 49.8 + - + +
131A HIS* 3.6 14.6 + - - +
133A LYS* 1.3 77.4 - - - +
135A PHE* 1.3 65.4 + - + +
137A ASP* 3.3 7.8 + - - +
138A PHE* 3.0 48.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 4.3 4.0 - + - -
45A ILE* 4.2 20.2 - - + -
46A PHE* 3.5 34.5 - + - -
49A THR* 3.5 35.7 - - + -
87A LEU* 3.3 43.4 - - + +
90A SER* 3.9 21.8 - - - -
91A ALA* 4.3 7.6 - - + -
94A GLU* 4.3 11.2 - - + -
131A HIS* 2.9 27.3 + - + +
132A GLU* 3.5 4.0 - - - +
134A ARG* 1.3 78.8 - - + +
136A LEU* 1.3 59.2 + - - +
138A PHE* 3.5 1.8 + + - +
139A ALA* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.1 19.5 - - + -
91A ALA* 3.3 26.0 - - + -
132A GLU* 2.9 44.1 + - + +
133A LYS* 3.4 9.9 - - + +
135A PHE* 1.3 76.0 - - - +
137A ASP* 1.3 62.3 + - - +
139A ALA* 3.2 2.2 + - - +
140A ARG* 2.8 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 2.9 22.3 + - - +
134A ARG* 3.9 7.2 - - - +
136A LEU* 1.3 75.2 - - - +
138A PHE* 1.3 62.1 - - + +
140A ARG* 3.3 18.4 + - - +
141A ASN* 2.9 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 3.7 36.3 - - - -
42A ILE* 3.5 35.8 - - + +
45A ILE* 3.8 30.5 - - + -
87A LEU* 3.9 11.7 - - + -
134A ARG* 3.0 47.0 + - + +
135A PHE* 3.8 4.5 - - - +
137A ASP* 1.3 78.8 - - + +
139A ALA* 1.3 65.2 + - - +
141A ASN* 3.4 16.4 + - + +
142A ILE* 3.0 26.7 + - - +
147A VAL* 6.2 3.1 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
84A HIS* 3.3 23.2 + - + +
87A LEU* 3.6 18.7 - - + +
88A ILE* 3.6 30.5 - - + -
135A PHE 2.9 18.6 + - - +
136A LEU* 3.2 5.8 + - + +
138A PHE* 1.3 75.2 - - - +
140A ARG* 1.3 51.7 + - - +
142A ILE* 3.2 2.2 + - - +
143A LYS* 2.7 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 2.8 44.0 + - - +
137A ASP* 3.5 16.7 + - - +
139A ALA* 1.3 76.6 - - - +
141A ASN* 1.3 55.4 + - - +
143A LYS* 2.9 8.9 + - + +
144A GLU* 2.6 65.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ASP* 2.9 28.6 + - - +
138A PHE* 3.9 19.2 - - + +
140A ARG* 1.3 74.9 - - - +
142A ILE* 1.3 64.4 + - - +
144A GLU* 4.3 4.0 - - - +
145A GLY* 2.9 4.9 + - - -
146A ARG* 2.8 50.7 + - - +
147A VAL* 3.8 15.9 + - + +
150A ARG* 4.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.1 19.5 - - + -
42A ILE* 3.9 10.8 - - + -
83A THR* 3.6 20.4 - - + -
84A HIS* 3.9 24.7 - - + +
87A LEU* 3.3 33.4 - - + -
138A PHE 3.0 12.6 + - - +
139A ALA* 3.5 6.1 - - - +
141A ASN* 1.3 78.4 - - - +
143A LYS* 1.3 66.8 + - - +
145A GLY* 3.3 8.0 + - - -
147A VAL* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A HIS* 3.6 25.1 + - + -
139A ALA 2.7 12.0 + - - +
140A ARG* 2.9 12.8 + - + +
142A ILE* 1.3 81.8 - - - +
144A GLU* 1.3 60.3 + - + +
145A GLY 3.2 2.9 + - - -
----------------------------------------------------------
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