Contacts of the helix formed by residues 88 - 95 (chain A) in PDB entry 1GV3
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 SER 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLN* 2.8 37.1 + - - -
33A LEU 3.2 16.4 - - - -
34A GLY* 4.9 2.0 - - - -
35A THR* 4.1 4.9 - - - -
87A SER* 1.3 78.2 - - - +
89A VAL* 1.3 64.7 + - - +
90A GLU* 3.5 7.8 + - - -
91A ALA* 3.3 19.3 + - - +
92A LEU* 3.1 25.8 + - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 2.9 40.8 + - + +
34A GLY 4.3 1.6 - - - +
35A THR* 3.6 22.4 - - + +
74A LEU* 4.0 15.5 - - + -
88A SER* 1.3 71.0 - - - +
90A GLU* 1.3 63.3 + - - +
92A LEU* 3.2 8.6 + - + +
93A LEU* 3.0 34.5 + - + +
111A GLY* 3.5 31.4 - - - +
114A HIS* 4.1 5.2 - - + -
115A LEU* 4.2 11.0 - - + +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.7 4.7 - - - -
26A ILE* 2.9 48.5 + - + +
27A GLY 3.1 12.0 + - - -
31A ARG 4.5 0.2 - - - +
32A GLN* 3.7 15.8 - - - +
33A LEU* 3.0 38.7 + - - +
88A SER* 3.5 9.8 + - - +
89A VAL* 1.3 76.3 - - - +
91A ALA* 1.3 57.2 + - - +
93A LEU* 3.3 1.9 + - - -
94A ARG* 3.0 48.1 + - - +
115A LEU* 4.5 5.2 - - + -
189A ILE* 3.9 12.6 - - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLN* 5.0 3.3 - - - +
87A SER* 4.2 11.4 - - - -
88A SER* 3.3 27.0 + - - +
90A GLU* 1.3 78.0 - - - +
92A LEU* 1.3 63.8 + - - +
94A ARG* 3.6 10.8 + - - +
95A ASP* 3.6 18.5 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 4.2 20.0 - - + -
74A LEU* 5.2 2.9 - - + -
78A LEU* 4.3 16.2 - - + -
84A LEU* 3.9 28.7 - - + +
87A SER* 3.4 20.9 - - - +
88A SER 3.1 17.3 + - - +
89A VAL* 3.2 9.8 + - + +
91A ALA* 1.3 77.9 - - - +
93A LEU* 1.3 61.0 + - + +
95A ASP 3.4 22.0 - - - +
96A LEU* 3.5 11.4 - - - +
99A VAL* 4.0 13.9 - - + +
107A VAL* 4.2 25.6 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.0 37.0 + - + +
92A LEU* 1.3 75.4 - - + +
94A ARG* 1.3 62.3 + - - +
95A ASP 3.2 0.6 + - - -
96A LEU* 3.9 18.8 + - + +
107A VAL* 3.7 26.7 - - + +
108A ARG* 4.0 18.2 - - - +
111A GLY* 3.9 1.1 - - - -
112A GLY* 3.9 17.9 - - - +
115A LEU* 3.9 23.6 - - + -
187A ASN* 4.6 6.5 - - + -
189A ILE* 3.9 15.0 - - + -
190A MET* 3.4 32.8 - - + +
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 5.3 4.9 - - - +
26A ILE* 3.4 34.7 - - - +
32A GLN* 5.6 2.8 - - - +
90A GLU* 3.0 36.8 + - - +
91A ALA* 3.9 9.9 - - - +
92A LEU 3.2 0.2 - - - -
93A LEU* 1.3 77.8 - - - +
95A ASP* 1.3 60.6 + - + +
96A LEU 4.0 0.4 - - - -
189A ILE* 4.0 37.3 + - + +
190A MET* 5.1 4.6 - - - +
192A GLY* 5.1 8.7 - - - -
193A SER 5.6 0.6 + - - -
194A TYR* 5.7 0.2 - - - -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.6 8.7 + - - +
92A LEU* 3.4 10.6 + - - +
94A ARG* 1.3 81.6 - - + +
96A LEU* 1.3 61.3 + - - +
97A ASN* 3.2 17.9 + - - +
98A SER* 2.9 43.6 + - - +
99A VAL* 4.0 3.1 - - - +
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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
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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