Contacts of the helix formed by residues 86 - 96 (chain G) in PDB entry 2OV2
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 86 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G VAL* 5.9 0.2 - - - -
83G SER* 3.0 20.2 + - - +
85G VAL* 1.3 78.9 - - - +
87G PRO* 1.3 66.3 - - - +
88G ALA* 3.1 7.2 + - - +
89G SER* 2.8 48.4 + - - -
90G PHE* 3.3 5.2 + - - +
137G ILE* 5.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU 5.5 0.2 - - - +
85G VAL* 3.7 7.9 - - - +
86G SER* 1.3 87.1 - - - +
88G ALA* 1.3 56.5 + - - +
90G PHE* 3.3 9.9 - - + +
91G GLU* 2.9 31.4 + - - +
129G LEU* 4.0 10.5 - - + -
134G LEU* 4.0 35.7 - - + -
135G ALA 3.6 22.9 - - - +
137G ILE* 4.3 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP* 4.2 2.7 - - - +
86G SER* 3.1 7.0 + - - +
87G PRO* 1.3 76.4 - - - +
89G SER* 1.3 65.6 + - - +
91G GLU* 3.2 9.8 + - - +
92G ASN* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP* 3.2 22.1 + - - +
12G GLY 5.7 0.2 - - - -
14G VAL* 3.7 24.7 - - - -
81G CYS 5.1 0.9 - - - +
82G PHE* 3.4 5.5 - - - +
83G SER 3.1 21.2 + - - -
86G SER* 2.8 30.6 + - - -
88G ALA* 1.3 78.8 - - - +
90G PHE* 1.3 60.5 + - - +
92G ASN* 3.2 11.8 + - - +
93G VAL* 3.3 14.7 + - - +
97G TRP* 4.9 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G PHE* 3.4 49.4 - + + -
86G SER 3.3 7.4 + - - +
87G PRO 3.3 9.2 - - - +
89G SER* 1.3 79.0 + - - +
91G GLU* 1.3 68.1 + - + +
93G VAL* 3.1 21.4 + - + +
94G ARG* 5.8 0.9 - - - -
137G ILE* 3.5 32.5 - - + -
141G GLN* 3.5 27.4 - - + -
142G GLY* 4.1 3.1 - - - -
145G MET* 3.5 54.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PRO 2.9 16.1 + - - +
88G ALA* 3.2 12.8 + - - +
90G PHE* 1.3 78.3 - - + +
92G ASN* 1.3 59.4 + - - +
94G ARG* 3.2 24.4 + - - +
95G ALA* 3.1 25.1 + - + +
145G MET* 4.9 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP* 2.7 39.1 + - - +
88G ALA* 3.0 17.1 + - - +
89G SER 3.4 8.1 - - - +
90G PHE 3.1 0.4 - - - -
91G GLU* 1.3 75.7 - - - +
93G VAL* 1.3 59.7 + - - +
94G ARG 3.1 1.6 - - - -
95G ALA* 3.7 15.4 - - - +
96G LYS* 2.8 34.5 + - + +
97G TRP* 3.0 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G ILE* 4.0 15.9 - - + -
81G CYS 4.7 1.6 - - - +
82G PHE* 4.0 29.8 - - + -
89G SER 3.3 10.7 + - - +
90G PHE* 3.1 15.2 + - + +
92G ASN* 1.3 75.2 - - - +
94G ARG* 1.3 59.2 + - - +
97G TRP* 3.9 9.6 - - + -
98G TYR* 2.9 31.2 + - - +
112G LEU* 4.0 13.5 - - + -
145G MET* 4.1 14.1 - - + -
149G ILE* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 5.8 1.0 - - - -
91G GLU* 3.2 25.8 + - - +
92G ASN 3.1 0.2 - - - -
93G VAL* 1.3 80.7 - - - +
95G ALA* 1.3 59.4 + - - +
98G TYR* 4.6 7.9 - - + +
99G PRO* 3.2 23.6 - - - +
145G MET* 3.5 36.9 - - + +
148G GLU* 2.7 41.6 + - - +
149G ILE* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 3.1 16.2 + - + +
92G ASN* 3.9 14.8 - - - +
94G ARG* 1.3 80.4 - - + +
96G LYS* 1.3 58.3 + - + +
99G PRO* 3.8 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ASP* 5.1 2.2 - - - +
60G GLY 5.0 1.4 + - - -
62G GLU* 3.5 20.4 + - - +
65G ASP* 2.9 36.9 + - - -
68G ARG* 4.3 0.6 - - - +
92G ASN* 2.8 26.6 + - + +
94G ARG 3.5 0.4 - - - -
95G ALA* 1.3 75.2 - - + +
97G TRP* 1.3 97.1 + - + +
99G PRO* 3.5 4.7 - - - +
100G GLU* 3.0 45.5 + - + +
----------------------------------------------------------
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