Contacts of the helix formed by residues 90 - 100 (chain A) 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 ASN 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A MET 3.4 11.8 - - - +
67A ARG* 4.1 1.4 - - - -
70A SER* 3.7 23.9 - - - +
75A GLU* 2.8 36.5 + - - +
77A PHE* 3.3 14.3 - - - -
88A VAL* 3.2 21.2 + - - +
89A LEU* 1.3 80.0 - - - +
91A GLY* 1.3 64.8 + - - +
94A VAL* 3.1 18.4 + - - +
95A VAL* 4.7 0.2 - - - -
403A ASN* 3.0 28.2 + - - +
406A SER* 3.2 8.2 + - - +
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Residues in contact with GLY 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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75A GLU* 5.5 3.4 - - - -
90A ASN* 1.3 78.5 - - - +
92A TYR* 1.3 67.4 + - - -
93A ASP 3.3 3.2 + - - -
94A VAL 3.7 0.2 + - - -
95A VAL* 3.3 19.2 + - - +
406A SER* 2.8 26.1 + - - -
407A VAL* 3.7 6.2 - - - +
410A ASP* 3.4 14.6 - - - -
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Residues in contact with TYR 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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91A GLY* 1.3 72.2 - - - +
93A ASP* 1.3 66.8 + - - +
95A VAL* 3.9 1.4 - - + +
96A LYS* 3.0 49.1 + - + +
407A VAL* 3.6 33.1 - - + +
410A ASP* 2.9 16.0 + - + +
413A TYR* 3.8 36.3 - + + -
436A GLU* 2.7 63.9 + - + +
437A ALA* 3.7 11.4 - - + -
439A VAL* 4.2 11.4 - - + -
443A LEU* 4.4 12.0 - - + +
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Residues in contact with ASP 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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75A GLU* 4.2 10.3 - - - +
91A GLY 3.3 1.4 - - - -
92A TYR* 1.3 82.1 - - - +
94A VAL* 1.3 58.2 + - - +
96A LYS* 3.8 6.0 - - - +
97A GLU* 2.9 33.5 + - - +
101A HIS* 5.9 0.2 - - - -
390A ARG* 3.8 19.7 + - - +
410A ASP* 4.5 1.4 + - - -
412A LYS* 2.6 34.3 + - - +
413A TYR* 2.4 28.2 + - - -
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Residues in contact with VAL 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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75A GLU* 3.7 22.0 + - + +
76A ILE* 4.7 7.4 - - + -
89A LEU* 3.9 15.3 - - + -
90A ASN 3.1 42.8 + - - +
91A GLY 3.7 0.8 + - - -
92A TYR 3.5 0.2 - - - -
93A ASP* 1.3 74.4 - - - +
95A VAL* 1.3 69.5 + - - +
97A GLU* 3.5 6.5 - - + +
98A CYS* 3.0 29.0 + - - -
389A VAL* 5.8 3.6 - - + -
390A ARG* 3.3 42.2 - - - +
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Residues in contact with VAL 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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89A LEU* 3.8 36.1 - - + +
91A GLY 3.3 18.9 + - - +
92A TYR* 3.9 4.0 - - + +
93A ASP 3.3 0.2 - - - -
94A VAL* 1.3 77.9 - - - +
96A LYS* 1.3 58.2 + - - +
98A CYS* 3.9 0.5 - - - +
99A LEU* 2.9 49.4 + - + +
402A THR* 4.6 9.0 - - - -
403A ASN 4.7 2.7 - - - +
404A LEU* 4.6 12.6 - - + -
407A VAL* 4.0 20.6 - - + -
439A VAL* 5.5 1.8 - - + -
443A LEU* 4.6 13.0 - - + -
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Residues in contact with LYS 96 (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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92A TYR* 3.0 48.2 + - + +
93A ASP* 3.8 6.7 - - - +
95A VAL* 1.3 73.1 - - - +
97A GLU* 1.3 60.1 + - - +
98A CYS 3.1 1.8 - - - -
100A VAL* 2.8 47.5 + - + +
101A HIS* 3.2 36.3 + - - +
436A GLU* 3.6 16.2 + - - +
443A LEU* 4.3 15.5 - - + +
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Residues in contact with GLU 97 (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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93A ASP* 2.9 20.8 + - - +
94A VAL* 3.5 8.5 - - - +
96A LYS* 1.3 77.6 - - - +
98A CYS* 1.3 58.1 + - - +
101A HIS* 3.2 47.6 - - + +
102A GLN* 3.4 14.6 + - - +
389A VAL* 4.8 11.7 - - + +
390A ARG* 2.8 57.1 + - - +
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Residues in contact with CYS 98 (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 LEU* 3.5 41.5 - - + -
94A VAL* 3.0 13.2 + - - +
97A GLU* 1.3 75.4 - - - +
99A LEU* 1.3 65.3 + - + +
100A VAL 3.2 1.9 + - - -
102A GLN* 3.1 30.8 + - - +
106A PHE* 3.5 40.2 - - + -
389A VAL* 3.7 24.7 - - - -
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Residues in contact with LEU 99 (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 LEU* 5.5 0.7 - - + -
95A VAL* 2.9 28.4 + - + +
98A CYS* 1.3 79.5 - - + +
100A VAL* 1.3 59.5 + - + +
103A SER* 3.5 15.6 - - - +
106A PHE* 3.8 21.3 - - + +
381A HIS* 3.5 37.7 - - + +
400A VAL* 5.9 0.4 - - + -
402A THR* 3.5 28.5 - - + -
404A LEU* 5.6 0.2 - - + -
442A SER* 3.7 23.3 - - - +
443A LEU* 3.7 23.6 - - + +
444A GLY* 3.3 17.8 - - - -
445A ARG 4.5 0.2 + - - -
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Residues in contact with VAL 100 (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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96A LYS* 2.8 28.1 + - + +
99A LEU* 1.3 81.1 - - - +
101A HIS* 1.3 72.1 + - + +
102A GLN 3.3 1.3 - - - -
103A SER* 3.4 16.0 + - - -
443A LEU* 3.8 37.9 - - + -
444A GLY* 4.3 6.3 - - - +
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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