Contacts of the helix formed by residues 137 - 153 (chain A) in PDB entry 3SJ5
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 MET 137 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.0 13.5 - - + -
9A TRP* 4.0 11.0 - - + -
67A TRP* 3.4 50.9 - - + -
131A TYR* 2.8 20.9 + - - +
135A ARG* 3.5 21.1 - - + +
136A LYS* 1.3 70.7 - - - +
138A TYR* 1.3 62.0 + - - +
139A ASP 3.4 2.2 - - - -
140A TYR* 3.4 17.3 + - + -
141A PHE* 3.0 22.3 + - - +
500A HEM 3.6 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 4.0 10.5 - + - -
136A LYS* 3.2 33.4 + - + +
137A MET* 1.3 75.9 - - - +
139A ASP* 1.3 62.5 + - - +
141A PHE* 3.4 5.9 + - - +
142A LEU* 3.0 32.5 + - - +
163A ARG* 3.4 41.7 - - + +
164A GLY* 3.5 24.4 + - - -
165A GLU* 4.2 4.2 - - - +
170A SER* 3.4 28.4 + - - -
171A ARG 3.7 19.1 - - - -
172A LEU* 3.7 29.0 - - + +
160B GLU 4.9 1.8 - - - -
161B VAL* 4.8 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN* 3.1 56.8 + - - +
67A TRP* 4.0 6.3 - - + -
68A ARG* 3.4 37.1 + - + +
137A MET 3.4 0.4 - - - -
138A TYR* 1.3 81.4 - - - +
140A TYR* 1.3 61.5 + - - +
142A LEU* 3.8 8.9 - - - +
143A GLY 2.9 23.7 + - - -
163A ARG* 5.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 3.3 13.0 - - - -
9A TRP* 3.1 28.8 + + - -
67A TRP* 3.7 36.0 - + + +
70A VAL* 4.0 4.0 - - + -
71A GLY* 3.6 31.6 - - - -
74A ASN* 2.7 24.2 + - - -
78A PHE* 3.7 4.3 - - - -
137A MET* 3.4 19.7 + - + +
138A TYR 3.4 0.4 - - - -
139A ASP* 1.3 76.8 - - - +
141A PHE* 1.3 63.6 + - - +
143A GLY* 3.3 0.9 + - - -
144A LEU* 2.9 48.1 + - + +
500A HEM 3.7 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.7 20.2 - - + -
129A MET* 4.3 12.6 - - + -
131A TYR* 3.7 44.6 - + + -
137A MET 3.0 14.1 + - - +
138A TYR 3.4 9.9 - - - +
140A TYR* 1.3 78.3 - - - +
142A LEU* 1.3 74.5 + - + +
144A LEU* 3.3 6.0 + - - +
145A ILE* 3.2 42.0 + - + +
172A LEU* 4.0 25.4 - - + -
174A VAL* 4.3 11.2 - - + -
500A HEM 3.7 41.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.8 36.3 - - - +
138A TYR 3.0 19.5 + - - +
139A ASP* 3.9 6.1 - - - +
141A PHE* 1.3 85.3 - - + +
143A GLY* 1.3 62.1 + - - +
145A ILE* 3.3 10.1 + - + +
146A GLU* 3.1 27.5 + - - +
158A VAL* 4.7 11.0 - - + -
160A GLU* 4.1 7.0 - - + +
163A ARG* 4.0 22.9 - - - +
172A LEU* 4.0 8.3 - - + -
174A VAL* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.4 25.3 - - - +
71A GLY 3.5 6.5 - - - -
72A ARG* 3.3 17.2 - - - +
139A ASP 2.9 13.9 + - - -
140A TYR 3.7 1.3 - - - -
142A LEU* 1.3 73.5 - - - +
144A LEU* 1.3 60.4 + - - +
146A GLU* 3.2 5.9 + - - -
147A GLY 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLY* 3.3 22.4 - - - +
74A ASN* 3.9 9.0 - - + -
75A ILE* 3.5 21.6 - - + +
78A PHE* 3.8 18.2 - - + -
140A TYR* 2.9 46.1 + - + +
141A PHE 3.3 4.0 + - - +
143A GLY* 1.3 76.1 - - - +
145A ILE* 1.3 62.9 + - - +
147A GLY 3.4 0.2 + - - -
148A SER* 2.9 29.4 + - - -
500A HEM 3.3 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 5.5 0.2 - - - +
95A LEU* 4.8 8.4 - - + +
129A MET* 4.5 2.9 - - - -
141A PHE* 3.2 47.0 + - + +
142A LEU* 3.5 14.1 - - + +
143A GLY 3.2 0.2 - - - -
144A LEU* 1.3 76.8 - - - +
146A GLU* 1.3 64.0 + - + +
148A SER* 3.2 8.4 + - - -
149A SER* 3.1 19.9 + - - -
156A ILE* 3.8 22.9 - - + +
158A VAL* 4.1 16.2 - - + -
174A VAL* 4.1 15.7 - - + -
176A ILE* 4.2 16.6 - - + -
500A HEM 3.6 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 3.0 35.5 + - - +
72A ARG* 2.7 44.8 + - + +
142A LEU 3.1 12.4 + - - +
143A GLY* 3.2 6.1 + - - +
145A ILE* 1.3 79.4 - - + +
147A GLY* 1.3 61.6 + - - +
149A SER* 3.2 8.6 + - - -
150A LYS* 3.1 32.7 + - - +
156A ILE* 5.4 1.8 - - + -
158A VAL* 5.5 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 3.6 27.6 - - - +
75A ILE* 3.9 9.7 - - - +
143A GLY 2.8 14.2 + - - -
144A LEU 3.8 1.6 - - - -
146A GLU* 1.3 72.5 - - - +
148A SER* 1.3 60.1 + - - +
150A LYS* 3.4 10.6 + - - +
151A PHE* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 3.4 23.7 - - - +
91A LEU* 3.7 19.5 - - - -
94A PHE* 3.5 20.4 - - - -
95A LEU* 4.5 5.8 - - - -
144A LEU 2.9 22.0 + - - -
145A ILE 3.2 6.0 + - - -
147A GLY* 1.3 73.8 - - - +
149A SER* 1.3 67.6 + - - +
151A PHE* 3.3 0.4 + - - -
152A PHE* 3.0 31.5 + - - +
500A HEM 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.9 8.9 - - - +
145A ILE 3.1 6.9 + - - -
146A GLU* 3.2 10.5 + - - -
148A SER* 1.3 77.4 - - - +
150A LYS* 1.3 62.8 + - - +
152A PHE 3.8 0.2 - - - -
153A LYS* 3.0 18.2 + - - -
154A GLU 2.7 36.0 + - - -
155A GLU* 4.0 2.1 - - - -
156A ILE* 3.7 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 4.9 3.6 + - - -
72A ARG* 3.7 35.7 + - - +
73A GLN* 4.9 5.9 - - - +
76A LYS* 6.5 2.0 - - - -
146A GLU* 3.1 24.0 + - - +
147A GLY* 3.7 10.3 - - - +
149A SER* 1.3 78.4 - - - +
151A PHE* 1.3 62.7 + - - +
153A LYS* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 4.1 14.8 - - + -
76A LYS* 4.1 29.6 - - + -
79A SER* 3.3 33.9 - - - -
86A PHE* 3.6 31.6 - + + -
147A GLY 2.9 17.9 + - - +
148A SER 3.3 3.3 + - - +
150A LYS* 1.3 79.8 - - - +
152A PHE* 1.3 67.7 + + + +
153A LYS* 3.4 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 3.7 40.4 - + + -
89A ARG* 3.3 31.9 - - + -
90A ARG 4.1 3.6 - - - -
91A LEU* 3.8 24.5 - - + -
94A PHE* 3.6 44.6 - + + -
148A SER* 3.0 28.8 + - - +
149A SER 4.4 1.6 - - - +
151A PHE* 1.3 82.2 - + + +
153A LYS* 1.3 71.8 + - - +
154A GLU* 3.5 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A SER 3.0 8.0 + - - -
150A LYS* 3.2 14.6 + - - +
151A PHE 4.2 5.2 - - - +
152A PHE* 1.3 81.7 - - - +
154A GLU* 1.3 60.6 + - - +
155A GLU* 4.2 0.9 - - - -
----------------------------------------------------------
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