Contacts of the helix formed by residues 76 - 86 (chain A) in PDB entry 2CVP
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LYS 3.0 14.8 + - - -
74A SER 3.3 1.6 + - - -
75A ARG* 1.3 80.5 - - - +
77A VAL* 1.3 65.3 + - - +
78A GLU 3.4 2.9 - - - -
79A ALA* 3.5 10.8 + - - +
80A ALA* 3.1 24.4 + - - +
503A ILE* 4.2 0.8 - - - +
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Residues in contact with VAL 77 (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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72A ALA* 3.2 28.5 + - + +
73A LYS* 5.0 0.4 - - - +
75A ARG* 4.7 1.1 - - + -
76A GLY* 1.3 76.7 - - - +
78A GLU* 1.3 65.8 + - - +
80A ALA* 3.4 2.3 + - - +
81A ARG* 3.0 23.5 + - + +
307A PHE* 5.1 5.8 - - + -
312A LEU* 4.8 10.3 - - + -
318A VAL* 4.6 11.2 - - + -
499A PHE* 4.7 3.3 - - + -
500A VAL* 4.0 35.2 - - + +
503A ILE* 4.1 15.3 - - + -
504A MET* 3.7 27.6 - - + -
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Residues in contact with GLU 78 (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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73A LYS* 4.1 19.4 + - - +
76A GLY 3.4 0.6 - - - -
77A VAL* 1.3 77.3 - - - +
79A ALA* 1.3 63.4 + - - +
81A ARG* 3.3 28.1 + - - +
82A ASP* 3.0 31.3 + - - +
311A PRO* 6.6 0.2 - - - -
312A LEU* 3.6 43.8 - - + +
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Residues in contact with ALA 79 (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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76A GLY* 3.5 12.5 + - - +
77A VAL 3.4 0.2 - - - -
78A GLU* 1.3 74.9 - - - +
80A ALA* 1.3 65.5 + - - +
82A ASP* 3.4 8.3 + - - +
83A ASN* 3.0 34.7 + - - +
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Residues in contact with ALA 80 (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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76A GLY 3.1 18.1 + - - +
77A VAL 3.6 4.0 - - - +
79A ALA* 1.3 76.4 - - - +
81A ARG* 1.3 57.8 + - - +
83A ASN* 3.3 11.3 + - - +
84A MET* 3.0 23.4 + - - +
90A ILE* 4.8 3.9 - - + +
499A PHE* 3.6 8.4 - - + -
503A ILE* 3.7 39.3 - - + -
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Residues in contact with ARG 81 (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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77A VAL* 3.0 19.4 + - + +
78A GLU* 3.5 37.4 + - - +
80A ALA* 1.3 73.9 - - - +
82A ASP* 1.3 89.1 + - - +
84A MET* 3.1 3.5 + - - +
85A PHE* 3.0 37.5 + - + -
307A PHE* 3.0 57.0 + - + -
308A LEU* 3.2 30.0 + - - +
310A THR 4.5 3.8 + - - -
312A LEU* 4.5 6.3 - - - +
315A ASN* 4.3 6.7 - - - +
499A PHE* 3.6 17.4 - - + -
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Residues in contact with ASP 82 (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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78A GLU* 3.0 17.0 + - - +
79A ALA* 3.7 7.7 - - - +
81A ARG* 1.3 103.0 + - - +
83A ASN* 1.3 58.6 + - - +
85A PHE* 3.3 7.1 + - - +
86A SER* 3.0 31.8 + - - -
308A LEU* 3.7 12.5 - - - +
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Residues in contact with ASN 83 (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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79A ALA* 3.0 24.8 + - - +
80A ALA* 3.4 11.5 - - - +
81A ARG 3.2 0.2 - - - -
82A ASP* 1.3 74.8 - - - +
84A MET* 1.3 65.1 + - - +
86A SER* 3.4 6.9 + - - -
87A GLY 3.4 3.5 + - - -
88A SER* 3.0 41.4 + - - +
90A ILE* 3.8 17.3 - - + +
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Residues in contact with MET 84 (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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80A ALA 3.0 13.2 + - - +
81A ARG 3.4 8.3 - - - +
83A ASN* 1.3 74.6 - - - +
85A PHE* 1.3 87.6 + - + +
87A GLY* 3.1 13.2 + - - -
88A SER 5.0 1.8 - - - +
90A ILE* 3.8 20.1 - - + +
98A VAL* 3.3 38.0 - - - +
99A LEU* 3.3 14.0 - - - +
100A HIS* 4.3 11.4 - - - +
101A VAL* 4.5 8.5 - - + -
307A PHE* 4.3 1.6 - - + -
496A HIS* 4.0 23.6 - - + +
499A PHE* 3.9 37.5 - - + -
510A PHE* 4.3 0.4 - - - -
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Residues in contact with PHE 85 (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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81A ARG* 3.0 44.0 + - + +
82A ASP* 3.8 4.7 - - - +
84A MET* 1.3 98.4 - - + +
86A SER* 1.3 59.1 + - - +
87A GLY 3.3 0.2 - - - -
99A LEU* 4.1 0.8 - - - +
101A VAL* 3.8 33.4 - - + -
111A ILE* 3.5 28.6 - - + +
304A ASP* 3.6 41.1 - - + -
305A GLN* 4.7 4.5 - - - -
307A PHE* 4.0 10.5 - + - -
308A LEU* 3.9 33.0 - - + -
496A HIS* 4.5 0.2 - + - -
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Residues in contact with SER 86 (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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82A ASP 3.0 17.8 + - - -
83A ASN* 3.4 9.7 + - - -
84A MET 3.2 0.4 - - - -
85A PHE* 1.3 77.4 - - - +
87A GLY* 1.3 58.0 + - - +
88A SER* 3.6 11.4 + - - -
111A ILE* 4.1 5.8 - - - +
112A LYS* 3.3 17.7 + - - +
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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