Contacts of the helix formed by residues 71 - 85 (chain B) in PDB entry 3OVS
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 71 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLU 5.0 0.4 - - - -
69B GLU 3.4 5.9 + - - -
70B PHE* 1.3 73.0 - - - +
72B LYS* 1.3 56.5 + - - +
73B GLU* 3.5 21.8 + - - -
74B GLU* 3.1 25.2 + - - +
75B LEU* 2.8 32.6 + - - +
115B TYR* 3.2 4.9 - - - -
124B LYS* 5.0 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 1.3 74.9 - - - +
73B GLU* 1.3 70.4 + - + +
75B LEU* 3.4 21.6 - - + +
76B ARG* 3.6 12.9 + - + +
96B GLU* 4.5 9.6 + - - -
97B HIS* 3.8 11.0 + - - -
98B PRO* 3.7 31.9 - - - +
115B TYR* 3.3 16.8 + - + +
124B LYS* 4.8 12.1 - - + +
125B SER* 4.3 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.5 16.4 + - - -
72B LYS* 1.3 90.4 + - + +
74B GLU* 1.3 65.2 + - + +
75B LEU 3.3 0.2 - - - -
76B ARG* 3.4 29.2 + - - +
77B GLU* 3.6 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.3 36.9 - - + -
71B SER* 3.1 29.1 + - - +
73B GLU* 1.3 74.7 - - + +
75B LEU* 1.3 66.6 + - - +
77B GLU* 3.6 4.5 + - - +
78B ARG* 3.3 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.6 45.2 - - + -
70B PHE* 4.6 6.2 - - + +
71B SER 2.8 17.3 + - - +
72B LYS* 3.4 31.4 - - - +
74B GLU* 1.3 76.7 - - - +
76B ARG* 1.3 59.2 + - + +
79B GLY* 3.0 24.6 + - - -
97B HIS* 4.5 13.7 - - + +
98B PRO* 5.5 0.7 - - + -
113B PRO* 4.2 8.4 - - + +
114B CYS* 3.6 23.8 - - - +
115B TYR* 3.7 31.4 - - + +
125B SER* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.7 13.7 - - + +
73B GLU* 3.4 25.2 + - - +
75B LEU* 1.3 79.3 - - + +
77B GLU* 1.3 99.4 + - - +
79B GLY 3.7 0.4 - - - +
80B LEU* 2.8 49.7 + - - +
94B TYR* 4.3 13.7 + - - -
98B PRO* 3.4 37.5 - - + -
113B PRO* 4.7 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU 3.6 12.3 + - - +
74B GLU* 3.6 5.7 + - - +
75B LEU 3.5 0.6 - - - -
76B ARG* 1.3 115.2 + - - +
78B ARG* 1.3 63.2 + - + +
80B LEU* 3.8 6.3 - - - +
81B GLU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.7 24.9 - - + -
70B PHE* 3.4 41.6 - - + -
74B GLU* 3.3 19.9 + - - +
75B LEU 4.1 0.2 - - - +
76B ARG 3.3 0.2 - - - -
77B GLU* 1.3 77.9 - - + +
79B GLY* 1.3 59.7 + - - +
81B GLU* 3.8 18.2 + - - +
82B ILE* 3.0 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.8 17.9 - - - +
66B PHE* 3.6 12.7 - - - -
75B LEU 3.0 16.1 + - - -
76B ARG 3.7 2.7 - - - -
78B ARG* 1.3 76.9 - - - +
80B LEU* 1.3 58.8 + - - +
83B GLY* 3.1 22.7 + - - -
100B VAL* 4.3 3.3 - - - +
111B VAL* 5.0 1.0 - - - +
113B PRO* 3.9 18.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 2.8 39.5 + - - +
77B GLU* 3.8 6.1 - - - +
79B GLY* 1.3 76.9 - - - +
81B GLU* 1.3 59.2 + - - +
83B GLY 3.3 0.9 + - - -
84B LYS* 2.8 41.8 + - + +
92B ILE* 4.1 35.4 - - + -
94B TYR* 4.9 5.2 - - + +
98B PRO* 4.5 9.4 - - + -
99B TYR* 4.3 19.3 - - - +
100B VAL* 3.9 17.8 - - + +
113B PRO* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 3.0 18.9 + - - +
78B ARG* 3.8 22.4 + - - +
80B LEU* 1.3 76.2 - - - +
82B ILE* 1.3 63.1 + - - +
84B LYS* 3.6 13.4 + - - +
85B ALA* 3.1 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.1 24.7 - - + -
38B LEU* 4.9 13.7 - - + -
40B VAL* 3.8 33.0 - - + -
64B LEU* 3.8 16.6 - - + -
66B PHE* 4.0 22.4 - - + -
78B ARG* 3.0 24.3 + - + +
79B GLY 4.0 3.1 - - - +
81B GLU* 1.3 76.8 - - + +
83B GLY* 1.3 65.7 + - - +
85B ALA* 3.1 15.0 + - - +
86B VAL* 3.2 18.4 - - + +
111B VAL* 5.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLY 3.1 16.1 + - - -
80B LEU 3.7 2.9 - - - -
82B ILE* 1.3 76.8 - - - +
84B LYS* 1.3 59.4 + - - +
86B VAL* 4.6 1.3 - - - -
87B LEU* 3.3 33.4 + - - +
100B VAL* 3.8 17.3 - - - -
111B VAL* 4.1 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 2.8 34.8 + - + +
81B GLU* 3.9 10.7 - - - +
83B GLY* 1.3 73.4 - - - +
85B ALA* 1.3 57.5 + - - +
86B VAL 3.3 3.3 + - - -
87B LEU 3.7 13.7 - - - +
90B TYR* 3.6 59.7 + - + -
92B ILE* 3.9 19.5 - - + -
100B VAL* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 5.3 0.9 - - - +
38B LEU* 3.6 19.6 - - + +
81B GLU* 3.1 17.6 + - + +
82B ILE 3.1 5.3 + - - +
84B LYS* 1.3 75.4 - - - +
86B VAL* 1.3 67.2 + - - +
----------------------------------------------------------
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