Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 1OVM
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 VAL 96 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER 5.1 1.8 - - - +
59B ALA* 3.9 28.0 - - + +
60B ASP* 3.9 23.3 - - - +
63B ALA* 4.2 1.1 - - + -
69B ALA* 3.5 5.6 - - + +
71B LEU* 4.4 5.8 - - + -
86B ILE* 4.2 18.9 - - + +
89B SER* 3.7 25.1 - - - +
94B VAL* 2.9 15.7 + - + +
95B PRO* 1.3 76.2 - - - +
97B LEU* 1.3 72.5 + - - +
98B HIS 3.7 0.2 + - - -
156B MET* 4.3 1.6 - - - -
162B PRO* 3.1 10.2 - - + +
163B GLY 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.4 7.6 - - + -
15B LEU* 3.4 33.2 - - + -
68B PHE* 4.1 5.8 - - + -
69B ALA 2.8 17.2 + - - +
70B ALA* 3.3 2.6 - - + -
71B LEU* 2.7 34.5 + - - +
95B PRO 4.2 0.6 - - - -
96B VAL* 1.3 71.5 - - - +
98B HIS* 1.3 62.5 + - - +
99B ILE* 3.9 19.7 - - + -
153B LEU* 3.9 12.6 - - + -
156B MET* 3.2 30.9 - - + -
163B GLY 3.7 10.5 - - - +
165B LEU* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.6 20.3 - - + +
73B THR* 2.8 30.4 + - - +
79B GLU* 3.7 35.0 - - + +
82B ALA* 4.3 9.2 - - + -
83B MET* 5.9 2.7 - - + +
86B ILE* 3.9 28.5 - - + +
96B VAL 3.7 0.6 + - - -
97B LEU* 1.3 73.8 - - - +
99B ILE* 1.3 70.8 + - - +
100B VAL* 3.9 2.1 + - + +
130B SER* 4.9 2.2 + - - -
134B THR* 6.0 0.4 - - + -
163B GLY 2.9 16.9 + - - +
164B TYR* 3.6 24.0 - + + -
165B LEU 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.8 32.1 - - + -
15B LEU* 4.4 10.8 - - + -
23B LEU* 4.3 23.1 - - + -
34B PHE* 4.6 10.5 - - + -
70B ALA* 4.7 1.1 - - + -
71B LEU 2.7 12.6 + - - +
72B LEU* 3.3 17.4 - - + +
73B THR 2.9 24.1 + - - -
97B LEU* 3.9 27.8 - - + -
98B HIS* 1.3 78.4 - - - +
100B VAL* 1.3 63.3 + - - +
101B GLY 5.0 0.2 - - - +
165B LEU* 3.5 12.3 - - + +
167B LEU* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 3.4 13.0 - - - +
74B THR 4.0 2.5 - - - -
75B PHE* 3.6 27.6 - - + +
79B GLU* 3.7 15.3 - - + +
98B HIS* 4.6 2.2 - - - +
99B ILE* 1.3 77.4 - - - +
101B GLY* 1.3 74.1 + - - +
102B ALA* 3.5 1.5 + - + -
164B TYR* 3.2 42.0 - - + +
165B LEU 3.0 12.5 + - - +
166B MET* 3.7 6.0 - - + +
167B LEU 2.9 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.6 24.2 - - - +
31B ASN* 4.1 10.5 - - - -
72B LEU* 4.3 4.4 - - - +
73B THR 3.0 13.3 + - - -
74B THR* 4.0 0.2 - - - -
75B PHE* 2.9 27.0 + - - +
99B ILE* 4.2 1.0 - - - -
100B VAL* 1.3 72.2 - - - +
102B ALA* 1.3 58.3 + - - -
167B LEU* 3.6 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.8 8.9 + - - +
75B PHE* 3.8 11.4 - - + -
100B VAL 4.3 0.4 - - - +
101B GLY* 1.3 74.6 - - - +
103B PRO* 1.3 73.8 - - + +
108B GLN* 3.9 10.8 - - - +
166B MET* 3.7 29.6 - - + -
167B LEU 3.1 7.9 + - - -
168B PRO* 4.3 4.0 - - + -
169B ALA* 2.9 30.0 + - - +
----------------------------------------------------------
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