Contacts of the helix formed by residues 88 - 95 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 3.1 45.3 + - - -
33B LEU 3.3 16.6 - - - -
34B GLY* 4.9 2.7 - - - -
35B THR* 4.0 2.7 - - - -
86B ASN 4.1 0.6 + - - -
87B SER* 1.3 77.5 - - - +
89B VAL* 1.3 65.9 + - - +
90B GLU* 3.5 3.3 + - - -
91B ALA* 3.1 17.0 + - - +
92B LEU* 3.1 21.5 + - - +
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Residues in contact with VAL 89 (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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33B LEU* 3.0 39.0 + - + +
34B GLY 4.5 0.7 - - - +
35B THR* 3.8 18.3 - - + +
74B LEU* 4.1 8.3 - - + -
88B SER* 1.3 71.6 - - - +
90B GLU* 1.3 64.6 + - - +
92B LEU* 3.2 8.3 + - + +
93B LEU* 3.0 37.6 + - + +
107B VAL* 6.6 0.2 - - + -
111B GLY* 3.6 29.6 - - - +
114B HIS* 4.0 19.3 - - + -
115B LEU* 4.3 11.0 - - + -
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Residues in contact with GLU 90 (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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25B SER 4.5 0.4 - - - -
26B ILE* 2.8 48.9 + - + +
27B GLY 3.1 12.8 + - - -
32B GLN* 3.6 21.1 - - - +
33B LEU* 3.0 37.5 + - - +
88B SER* 3.2 6.4 + - - +
89B VAL* 1.3 77.7 - - - +
91B ALA* 1.3 56.5 + - - +
93B LEU* 3.8 1.2 - - - +
94B ARG* 2.9 52.7 + - - +
115B LEU* 4.6 6.1 - - + -
189B ILE* 4.0 11.6 - - + +
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Residues in contact with ALA 91 (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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32B GLN* 4.7 3.5 - - - +
87B SER* 4.1 11.4 - - - -
88B SER* 3.1 24.9 + - - +
90B GLU* 1.3 79.4 - - - +
92B LEU* 1.3 63.4 + - - +
94B ARG* 3.5 9.0 + - - +
95B ASP* 3.5 20.8 + - - +
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Residues in contact with LEU 92 (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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35B THR* 4.3 20.0 - - + -
74B LEU* 4.9 4.0 - - + -
78B LEU* 4.3 17.5 - - + -
84B LEU* 4.1 27.1 - - + +
87B SER* 3.5 21.1 - - - +
88B SER 3.1 18.1 + - - +
89B VAL* 3.6 9.2 - - + +
91B ALA* 1.3 76.8 - - - +
93B LEU* 1.3 63.0 + - + +
95B ASP 3.3 21.6 - - - +
96B LEU* 3.4 11.1 + - - +
99B VAL* 3.9 13.9 - - + +
107B VAL* 4.0 26.2 - - + -
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Residues in contact with LEU 93 (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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89B VAL* 3.0 36.8 + - + +
90B GLU 4.0 2.9 - - - +
92B LEU* 1.3 73.4 - - + +
94B ARG* 1.3 64.4 + - - +
95B ASP 3.1 3.3 + - - -
96B LEU* 4.1 17.1 + - + +
107B VAL* 3.7 27.1 - - + +
108B ARG* 4.1 17.7 - - - +
111B GLY* 4.0 10.8 - - - +
112B GLY* 4.0 7.0 - - - +
115B LEU* 3.8 23.6 - - + -
187B ASN* 4.7 6.7 - - + -
189B ILE* 4.0 13.0 - - + -
190B MET* 3.4 31.1 - - + +
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Residues in contact with ARG 94 (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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25B SER 4.8 9.3 - - - +
26B ILE* 3.6 32.0 - - - +
32B GLN* 4.6 8.1 - - - +
90B GLU* 2.9 41.8 + - - +
91B ALA* 4.0 7.6 - - - +
92B LEU 3.3 0.4 - - - -
93B LEU* 1.3 76.6 - - - +
95B ASP* 1.3 61.4 + - + +
96B LEU 4.0 0.2 - - - -
189B ILE* 3.9 32.1 + - + +
190B MET* 5.0 5.6 - - - +
192B GLY* 6.1 1.8 - - - -
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Residues in contact with ASP 95 (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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91B ALA 3.5 9.3 + - - +
92B LEU* 3.3 9.3 + - - +
93B LEU 3.1 0.2 - - - -
94B ARG* 1.3 83.0 - - + +
96B LEU* 1.3 62.0 + - - +
97B ASN* 3.2 15.6 + - - +
98B SER* 2.8 42.6 + - - +
99B VAL* 3.9 3.3 - - - +
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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