Contacts of the helix formed by residues 75 - 87 (chain B) in PDB entry 1GQC
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 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B HIS* 4.2 1.9 - - - +
74B GLU* 1.3 82.5 - - - +
76B GLY* 1.3 66.0 + - - +
77B THR 3.5 4.9 + - - -
78B ASP* 3.0 24.9 + - - +
79B ARG* 3.3 10.0 + - - +
201B GLU* 3.2 34.1 + - - -
1243B C5P 3.4 18.3 + - - -
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Residues in contact with GLY 76 (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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8B PRO* 3.8 22.0 - - - +
75B SER* 1.3 72.9 - - - +
77B THR* 1.3 56.6 + - - +
79B ARG* 3.3 4.7 + - - +
80B LEU* 2.9 27.5 + - - +
94B ASN* 4.5 3.4 - - - -
1243B C5P 3.6 33.2 + - - -
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Residues in contact with THR 77 (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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75B SER* 3.1 3.6 + - - -
76B GLY* 1.3 75.4 - - - +
78B ASP* 1.3 58.5 + - - +
80B LEU* 3.1 12.2 + - + +
81B VAL* 3.0 28.5 + - + +
94B ASN* 4.1 10.9 + - - +
176B TYR* 6.1 1.0 - - - -
178B TYR* 4.1 22.5 + - + +
183B LEU* 5.3 2.0 - - + -
186B TYR* 3.6 40.4 - - + +
201B GLU* 3.2 23.4 + - - -
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.1 31.9 - - + +
74B GLU* 3.7 24.0 + - - +
75B SER* 3.0 25.3 + - - +
77B THR* 1.3 78.2 - - - +
79B ARG* 1.3 60.0 + - - +
81B VAL* 3.5 9.7 + - - +
82B GLU 3.4 11.1 + - - -
186B TYR* 4.0 19.2 - - - -
201B GLU* 4.2 4.1 - - - +
204B ARG* 4.8 3.8 + - - -
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Residues in contact with ARG 79 (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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8B PRO* 4.5 4.7 - - + -
10B ARG* 3.8 17.0 - - - +
49B ALA* 3.4 32.3 + - + -
50B THR 5.1 0.2 - - - -
51B ASP* 3.8 15.8 + - - +
69B THR* 2.9 36.2 + - - +
70B ARG 2.9 23.0 + - - -
71B ASN* 5.3 2.2 - - - +
73B HIS* 3.8 25.7 + - + +
75B SER 3.3 6.0 + - - +
76B GLY 3.5 8.7 - - - +
77B THR 3.2 0.2 - - - -
78B ASP* 1.3 75.4 - - - +
80B LEU* 1.3 68.4 + - - +
81B VAL 3.1 0.2 - - - -
82B GLU* 3.0 5.2 + - - +
83B VAL* 3.0 25.3 + - - +
1243B C5P 2.8 45.3 + - - -
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Residues in contact with LEU 80 (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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6B VAL* 3.5 40.4 - - + -
8B PRO* 5.3 1.5 - - + +
76B GLY 2.9 14.7 + - - +
77B THR* 3.3 11.9 - - + +
79B ARG* 1.3 77.8 - - - +
81B VAL* 1.3 55.7 + - - +
83B VAL* 3.1 7.8 + - - +
84B MET* 2.9 26.7 + - - +
92B TYR* 4.5 14.1 - - + -
93B ILE 4.9 0.2 - - - +
94B ASN* 4.0 25.8 - - + +
178B TYR* 3.6 37.0 - - + -
183B LEU* 4.0 20.4 - - + -
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Residues in contact with VAL 81 (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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77B THR* 3.0 15.5 + - + +
78B ASP* 3.6 11.0 - - - +
79B ARG 3.1 0.2 - - - -
80B LEU* 1.3 78.3 - - - +
82B GLU* 1.3 63.1 + - - +
84B MET* 3.2 25.8 + - + +
85B HIS* 3.4 19.2 - - + +
183B LEU* 4.0 28.0 - - + +
186B TYR* 3.9 34.5 - - + -
187B SER* 5.4 10.3 - - - +
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Residues in contact with GLU 82 (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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69B THR* 3.3 20.9 - - + -
70B ARG* 2.8 29.7 + - - +
73B HIS* 2.6 39.3 + - + +
78B ASP 3.4 2.6 + - - -
79B ARG 3.0 9.7 + - - +
81B VAL* 1.3 80.5 - - - +
83B VAL* 1.3 64.2 + - - +
84B MET 3.2 0.5 + - - -
85B HIS* 3.4 18.8 + - + +
86B LYS* 2.9 42.6 + - - +
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Residues in contact with VAL 83 (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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6B VAL* 4.0 31.0 - - + -
47B TRP* 5.3 2.5 - - + -
49B ALA* 3.6 28.9 - - + -
67B ILE* 4.1 15.9 - - + -
69B THR* 4.0 11.7 - - + -
79B ARG 3.0 17.2 + - - +
80B LEU* 3.1 7.8 + - + +
82B GLU* 1.3 75.2 - - - +
84B MET* 1.3 52.4 + - - +
86B LYS* 2.9 10.1 + - - +
87B VAL* 2.7 53.7 + - + -
92B TYR* 5.5 0.9 - - + -
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Residues in contact with MET 84 (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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80B LEU 2.9 13.0 + - - +
81B VAL* 3.3 14.8 - - + +
82B GLU 3.1 0.2 - - - -
83B VAL* 1.3 76.5 - - - +
85B HIS* 1.3 97.3 + - + +
87B VAL 3.2 16.5 + - - +
88B GLU* 5.6 0.3 - - - +
92B TYR* 3.2 39.9 + - + +
180B ARG* 3.6 21.0 + - + +
183B LEU* 3.7 42.6 - - + +
184B GLN* 3.9 20.9 - - - -
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Residues in contact with HIS 85 (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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81B VAL* 3.4 28.8 + - + +
82B GLU* 3.4 10.9 + - + +
83B VAL 3.3 0.6 - - - -
84B MET* 1.3 100.5 - - + +
86B LYS* 1.3 61.8 + - + +
87B VAL 5.3 0.2 - - - -
88B GLU* 5.8 3.0 - - - +
180B ARG* 5.5 4.1 + - - +
184B GLN* 5.6 6.7 - - + -
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Residues in contact with LYS 86 (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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67B ILE* 3.7 28.0 - - + +
68B MET 3.6 16.4 + - - -
69B THR* 4.8 0.4 - - + +
82B GLU* 2.9 41.5 + - - +
83B VAL 2.9 8.1 + - - +
85B HIS* 1.3 84.5 - - + +
87B VAL* 1.3 61.8 + - + +
88B GLU* 4.0 3.3 + - - +
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Residues in contact with VAL 87 (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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4B VAL* 4.2 17.3 - - + -
45B GLU* 3.5 26.5 - - - +
47B TRP* 3.9 28.9 - - + +
67B ILE* 4.6 7.6 - - + -
83B VAL* 2.7 34.9 + - + +
84B MET 3.2 5.1 - - - +
86B LYS* 1.3 80.5 - - + +
88B GLU* 1.3 62.7 + - - +
92B TYR* 2.6 34.2 + - + -
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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