Contacts of the helix formed by residues 76 - 87 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS 3.0 12.2 + - - -
74B SER 3.3 1.6 + - - -
75B ARG* 1.3 80.2 - - - +
77B VAL* 1.3 59.8 + - - +
78B GLU 3.4 2.2 - - - -
79B ALA* 3.4 11.2 + - - +
80B ALA* 2.9 30.1 + - - +
503B ILE* 4.2 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 3.2 28.3 + - + +
73B LYS 4.2 0.8 + - - -
75B ARG* 5.0 0.4 - - + -
76B GLY* 1.3 76.4 - - - +
78B GLU* 1.3 63.3 + - - +
80B ALA* 3.4 1.3 + - - +
81B ARG* 3.0 25.1 + - + +
307B PHE* 5.2 4.3 - - + -
312B LEU* 4.4 21.3 - - + -
318B VAL* 4.7 2.7 - - + -
499B PHE* 5.1 2.3 - - + -
500B VAL* 3.9 34.8 - - + +
503B ILE* 4.2 17.7 - - + -
504B MET* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 4.9 0.2 + - - -
73B LYS* 4.3 20.9 + - + +
76B GLY 3.4 0.4 - - - -
77B VAL* 1.3 77.1 - - - +
79B ALA* 1.3 61.7 + - - +
81B ARG* 3.4 26.5 + - - +
82B ASP* 3.1 31.3 + - - +
310B THR 5.3 0.7 - - - +
311B PRO* 5.2 3.5 - - - +
312B LEU* 3.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY* 3.4 12.4 + - - +
78B GLU* 1.3 77.3 - - - +
80B ALA* 1.3 65.2 + - - +
82B ASP* 3.4 7.8 + - - +
83B ASN* 3.0 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 2.9 17.9 + - - +
77B VAL 3.9 3.1 - - - +
79B ALA* 1.3 74.7 - - - +
81B ARG* 1.3 62.4 + - - +
83B ASN* 3.2 12.3 + - - +
84B MET 3.0 18.7 + - - -
90B ILE* 4.8 3.8 - - + +
499B PHE* 3.6 9.3 - - + -
503B ILE* 3.7 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.0 19.4 + - + +
78B GLU* 3.5 31.5 + - - +
80B ALA* 1.3 75.8 - - - +
82B ASP* 1.3 82.2 + - - +
84B MET* 3.1 3.3 + - - +
85B PHE* 3.1 35.9 + - + -
307B PHE* 2.8 67.8 + - + -
308B LEU* 3.3 30.9 + - + +
310B THR 4.1 6.5 + - - -
312B LEU* 4.4 12.1 - - - +
315B ASN* 4.0 8.7 - - - +
499B PHE* 3.6 15.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 3.1 12.6 + - - +
79B ALA* 3.7 9.8 - - - +
81B ARG* 1.3 101.4 + - - +
83B ASN* 1.3 58.8 + - - +
85B PHE* 3.4 7.0 + - - +
86B SER* 3.0 32.0 + - - -
308B LEU* 3.8 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA* 3.0 27.0 + - - +
80B ALA* 3.4 12.1 - - - +
82B ASP* 1.3 74.7 - - - +
84B MET* 1.3 65.3 + - - +
86B SER* 3.1 9.9 + - - -
88B SER* 3.0 42.5 + - - +
90B ILE* 3.8 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.0 10.9 + - - +
81B ARG 3.1 7.4 + - - +
83B ASN* 1.3 75.0 - - - +
85B PHE* 1.3 82.9 + - + +
87B GLY* 3.2 12.6 + - - -
88B SER 4.6 1.8 + - - +
90B ILE* 3.7 21.0 - - + +
98B VAL* 3.4 28.9 - - + +
99B LEU* 3.3 12.8 - - - +
100B HIS* 4.0 16.6 - - + +
101B VAL* 4.5 10.1 - - + -
496B HIS* 4.6 4.9 - - - +
499B PHE* 3.7 29.4 - - + -
510B PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.1 27.6 + - + +
82B ASP* 3.8 4.7 - - - +
83B ASN 3.3 0.2 - - - -
84B MET* 1.3 90.8 - - + +
86B SER* 1.3 59.0 + - - +
87B GLY 3.3 0.7 + - - -
99B LEU* 4.2 1.3 - - - +
101B VAL* 3.9 37.7 - - + -
111B ILE* 3.7 26.1 - - + +
304B ASP* 3.5 41.7 - - + -
305B GLN* 4.7 4.9 - - - -
307B PHE* 3.9 25.4 - + - -
308B LEU* 3.8 35.7 - - + -
496B HIS* 4.4 0.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP 3.0 15.0 + - - -
83B ASN* 3.1 15.1 + - - -
84B MET 3.2 0.2 - - - -
85B PHE* 1.3 76.7 - - - +
87B GLY* 1.3 57.3 + - - +
88B SER* 3.2 13.3 + - - -
111B ILE* 4.4 4.0 - - - +
112B LYS* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B MET 3.2 12.8 + - - -
85B PHE 3.3 1.8 + - - -
86B SER* 1.3 79.4 - - - +
88B SER* 1.3 66.5 + - - +
89B LYS* 3.7 4.7 + - - +
97B ALA* 3.6 12.4 - - - +
99B LEU* 4.0 22.4 - - - +
112B LYS 3.8 13.7 - - - +
113B VAL* 4.4 6.4 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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