Contacts of the helix formed by residues 91 - 100 (chain B) in PDB entry 3C6G
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 GLY 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 5.4 3.8 - - - -
90B ASN* 1.3 78.0 - - - +
92B TYR* 1.3 67.0 + - - -
93B ASP* 3.3 3.0 + - - -
95B VAL* 3.1 19.1 + - - +
406B SER* 3.0 22.1 + - - -
407B VAL* 3.7 5.4 - - - +
410B ASP* 3.4 19.1 - - - -
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Residues in contact with TYR 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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91B GLY* 1.3 72.9 - - - -
93B ASP* 1.3 65.2 + - - +
95B VAL* 3.4 2.7 + - + +
96B LYS* 2.9 52.7 + - + +
407B VAL* 3.6 31.0 - - + +
410B ASP* 3.0 8.3 + - - +
413B TYR* 3.8 38.6 - + + -
436B GLU* 3.5 48.0 + - - +
437B ALA* 4.2 11.0 - - + -
439B VAL* 4.2 7.2 - - + -
443B LEU* 4.1 27.6 - - + +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 4.1 6.9 - - - +
91B GLY 3.3 1.0 - - - -
92B TYR* 1.3 78.7 - - - +
94B VAL* 1.3 58.7 + - - +
96B LYS* 3.4 10.3 + - - +
97B GLU* 2.9 27.9 + - - +
390B ARG* 3.9 22.8 + - - +
410B ASP* 4.7 1.1 + - - -
412B LYS* 3.1 22.1 + - - +
413B TYR* 2.7 34.0 + - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU* 3.1 37.7 + - + +
76B ILE* 4.4 8.5 - - + -
89B LEU* 3.6 30.7 - - + -
90B ASN 4.1 8.7 - - - +
91B GLY 3.8 1.4 + - - -
93B ASP* 1.3 73.6 - - - +
95B VAL* 1.3 66.2 + - - +
97B GLU* 3.3 6.8 + - + +
98B CYS* 3.1 30.0 + - - -
389B VAL* 4.3 12.6 - - + -
390B ARG* 3.4 27.1 - - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 4.1 34.1 - - + +
91B GLY 3.1 19.5 - - - +
92B TYR* 3.4 4.4 + - + +
93B ASP 3.4 0.6 - - - -
94B VAL* 1.3 77.8 - - - +
96B LYS* 1.3 55.8 + - - +
98B CYS* 4.1 0.3 - - - +
99B LEU* 3.0 57.6 + - + +
402B THR* 4.6 9.0 - - - -
403B ASN 4.8 5.8 - - - +
404B LEU* 4.7 8.3 - - + -
407B VAL* 3.5 23.3 - - + -
439B VAL* 5.4 2.0 - - + -
443B LEU* 4.4 11.9 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B TYR* 2.9 58.5 + - + +
93B ASP* 3.6 8.1 - - - +
95B VAL* 1.3 73.9 - - - +
97B GLU* 1.3 59.7 + - - +
100B VAL* 2.8 53.2 + - + +
101B HIS* 3.2 28.8 + - + +
436B GLU* 5.1 4.2 + - - -
443B LEU* 4.2 10.7 - - + +
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Residues in contact with GLU 97 (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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93B ASP 2.9 14.9 + - - +
94B VAL* 3.4 14.6 - - + +
96B LYS* 1.3 77.4 - - - +
98B CYS* 1.3 62.8 + - - +
101B HIS* 3.3 28.3 + - - +
102B GLN* 3.0 56.3 + - - +
389B VAL* 4.9 9.9 - - + -
390B ARG* 5.7 8.1 - - + +
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Residues in contact with CYS 98 (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 LEU* 3.7 28.0 - - + -
94B VAL 3.1 17.4 + - - +
95B VAL 4.2 0.2 - - - +
97B GLU* 1.3 77.5 - - - +
99B LEU* 1.3 62.5 + - + +
102B GLN* 3.1 30.5 - - - +
106B PHE* 3.3 36.7 - - + +
389B VAL* 3.8 38.1 - - - -
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Residues in contact with LEU 99 (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 LEU* 5.2 0.7 - - + -
95B VAL* 3.0 32.4 + - + +
98B CYS* 1.3 82.2 - - + +
100B VAL* 1.3 59.6 + - + +
103B SER* 2.9 22.0 - - - +
106B PHE* 4.1 17.5 - - + +
381B HIS* 3.8 31.6 - - + +
400B VAL* 6.0 0.2 - - + -
402B THR* 3.5 30.5 - - + -
404B LEU* 5.6 0.4 - - + -
442B SER* 3.8 21.8 - - - +
443B LEU* 4.0 22.4 - - + +
444B GLY* 3.3 13.0 - - - -
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Residues in contact with VAL 100 (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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96B LYS* 2.8 32.5 + - + +
99B LEU* 1.3 79.6 - - - +
101B HIS* 1.3 80.1 + - + +
102B GLN 3.4 0.2 - - - -
103B SER* 3.2 19.2 + - - -
443B LEU* 3.9 31.0 - - + -
444B GLY* 4.5 5.6 - - - +
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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