Contacts of the strand formed by residues 136 - 143 (chain B) in PDB entry 5GJQ
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 CYS 136 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 4.0 3.5 - - - +
80B MET* 4.0 5.6 - - + -
81B THR 3.3 7.6 - - - +
86B ASP 3.8 16.6 - - - -
87B SER* 3.4 28.3 - - - +
90B GLN* 3.5 29.7 + - - +
134B LEU* 2.9 27.2 + - - +
135B GLY* 1.3 79.2 - - - +
137B CYS* 1.3 62.1 + - - +
154B CYS 4.7 0.2 - - - +
155B ASP 4.6 1.4 - - - -
156B PRO* 3.4 24.8 - - - +
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Residues in contact with CYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.7 16.6 - - + -
79B VAL 3.6 1.7 - - - +
80B MET* 3.3 7.7 - - - +
81B THR* 2.8 41.6 + - - +
90B GLN* 4.9 0.2 - - - -
136B CYS* 1.3 77.0 - - - +
138B MET* 1.3 63.0 + - - +
139B ILE* 4.8 1.3 - - - -
153B LYS* 3.6 36.6 - - - -
154B CYS 3.7 15.0 - - - +
155B ASP* 4.5 4.3 - - - +
156B PRO* 5.4 0.2 - - + -
168B ALA* 4.0 16.6 - - - -
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Residues in contact with MET 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.7 0.4 - - + -
78B CYS* 4.1 13.0 - - + -
79B VAL 3.6 2.9 - - - -
80B MET* 3.5 24.0 - - - -
90B GLN* 3.5 45.3 + - + +
91B VAL* 4.3 2.0 - - + -
94B ALA* 4.0 16.8 - - + -
115B CYS* 5.3 0.2 - - - -
118B ILE* 4.6 9.6 - - - -
137B CYS* 1.3 73.9 - - - +
139B ILE* 1.3 65.0 + - - +
140B LEU* 3.8 38.8 + - + -
153B LYS* 3.3 5.2 - - - +
154B CYS* 3.0 47.0 + - - -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B SER* 5.4 2.5 - - - +
40B VAL 5.7 0.2 - - - -
41B ALA* 3.7 33.4 - - + +
50B ILE* 4.0 12.3 - - + +
78B CYS* 3.1 5.2 - - - -
79B VAL* 2.8 50.4 + - + +
137B CYS* 4.8 3.8 - - - -
138B MET* 1.3 78.3 - - - +
140B LEU* 1.3 68.0 + - - +
151B VAL* 4.2 5.4 - - + -
152B TYR 3.3 8.3 - - - +
153B LYS* 3.7 31.0 - - + -
166B THR* 4.4 12.3 - - - -
167B ALA* 4.5 15.5 - - - -
168B ALA* 4.7 5.8 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 4.1 3.4 - - + -
76B ILE* 3.9 16.2 - - + -
77B GLY 3.3 8.5 - - - +
78B CYS* 3.4 26.0 - - + -
111B VAL* 3.4 19.8 - - + +
114B LEU* 4.0 16.2 - - + -
115B CYS* 3.8 42.2 - - + +
138B MET* 3.8 27.1 - - + -
139B ILE* 1.3 73.1 - - - +
141B ILE* 1.3 67.9 + - - +
150B GLN 3.8 0.3 - - - +
151B VAL* 3.4 1.0 - - - +
152B TYR 2.8 34.8 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA* 4.9 0.4 - - + -
48B ALA* 3.9 20.9 - - + +
49B VAL 5.0 1.8 - - - +
50B ILE* 3.5 43.7 - - + -
75B ASN 4.2 0.3 - - - +
76B ILE* 3.7 5.4 - - - +
77B GLY* 2.9 37.9 + - - +
111B VAL* 4.1 5.2 - - - -
139B ILE* 4.6 0.2 - - + -
140B LEU* 1.3 76.6 - - - +
142B GLY* 1.3 59.9 + - - +
150B GLN 3.1 7.0 - - - +
151B VAL* 3.7 24.7 - - + -
219B VAL* 4.2 4.7 - - - -
220B VAL* 3.8 20.5 - - + +
227B PHE* 3.8 20.0 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.8 0.2 - - - +
75B ASN 3.8 13.5 - - - -
111B VAL* 4.0 12.8 - - - +
141B ILE* 1.3 78.7 - - - +
143B ILE* 1.3 65.8 + - - -
144B ASP 3.9 0.2 - - - -
150B GLN* 2.9 36.8 + - - +
220B VAL* 3.9 11.4 - - - +
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 4.6 1.6 - - - -
75B ASN* 4.4 7.7 + - - +
111B VAL* 6.2 0.2 - - - -
142B GLY* 1.3 73.9 - - - -
144B ASP* 1.3 74.7 + - - +
145B GLU 4.1 0.2 + - - -
148B GLY* 3.7 11.0 - - - +
149B PRO* 3.8 25.4 - - + -
220B VAL* 3.6 28.2 - - + +
221B THR 3.3 33.9 - - - +
222B VAL* 4.1 25.6 - - + +
225B PRO* 4.5 14.1 + - + +
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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
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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) + - + + + + + -
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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