Contacts of the helix formed by residues 2285 - 2294 (chain B) in PDB entry 2OVP
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 PRO2285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101A PHE* 5.0 0.7 - - + -
1105A LEU* 3.3 33.0 - - + -
1108A ASN* 5.0 4.7 - - - +
2283B LEU 3.5 4.9 - - - +
2284B LEU* 1.3 79.4 - - + +
2286B LYS* 1.3 69.0 + - - +
2287B GLU* 3.1 4.5 - - + +
2288B LEU* 2.7 37.9 + - + +
2289B ALA 2.9 8.5 + - - -
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Residues in contact with LYS2286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2265B VAL* 4.7 9.2 - - + -
2266B LYS* 5.0 25.6 - - + +
2269B MET* 3.4 37.8 - - + +
2284B LEU 3.1 4.6 + - - -
2285B PRO* 1.3 68.7 - - - +
2287B GLU* 1.3 64.7 - - + +
2289B ALA* 3.2 8.3 + - - +
2290B LEU* 3.0 28.7 + - + +
2310B TYR* 3.0 31.5 + - + +
2314B LEU* 4.4 12.4 - - + +
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Residues in contact with GLU2287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2285B PRO* 2.8 7.7 + - + +
2286B LYS* 1.3 78.4 - - + +
2288B LEU* 1.3 54.2 + - + +
2290B LEU* 2.8 14.1 + - + +
2291B TYR* 2.6 34.7 + - - +
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Residues in contact with LEU2288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A ILE* 3.9 17.7 - - + -
1105A LEU* 3.5 14.6 - - + -
1108A ASN* 3.3 51.8 - - + +
1116A LEU* 4.0 22.0 - - + -
1120A CYS* 5.1 0.2 - - - -
2284B LEU* 4.3 2.5 - - + -
2285B PRO* 2.7 40.8 + - + +
2287B GLU* 1.3 72.2 - - + +
2289B ALA* 1.3 66.5 + - - +
2290B LEU 2.9 1.3 - - - -
2291B TYR* 3.0 8.9 + - + +
2292B VAL* 2.8 30.4 + - - +
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Residues in contact with ALA2289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281B ILE* 3.5 24.5 - - + +
2284B LEU* 3.9 15.3 - - + +
2285B PRO 2.9 10.5 + - - +
2286B LYS* 3.4 8.3 - - - +
2288B LEU* 1.3 75.5 - - - +
2290B LEU* 1.3 58.5 + - - +
2292B VAL* 3.2 5.2 - - - +
2293B LEU* 2.9 33.0 + - - +
2314B LEU* 3.2 30.1 - - + -
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Residues in contact with LEU2290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2265B VAL* 4.4 10.8 - - + -
2286B LYS* 3.0 19.9 + - + +
2287B GLU* 2.8 14.4 + - + +
2289B ALA* 1.3 74.8 - - - +
2291B TYR* 1.3 56.1 + - - +
2292B VAL 2.6 15.7 + - - -
2293B LEU* 2.9 6.6 + - + +
2294B SER* 2.7 25.7 + - - -
2314B LEU* 3.5 44.9 - - + +
2317B ASP* 3.5 35.4 - - + +
2320B LEU* 4.7 9.9 - - + +
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Residues in contact with TYR2291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A LYS* 4.7 10.8 + - + +
1116A LEU* 4.0 22.7 - - + -
1117A ASP* 2.3 44.5 + - - -
1120A CYS* 3.8 16.6 - - - -
2287B GLU 2.6 16.5 + - - +
2288B LEU* 3.0 15.9 + - + +
2290B LEU* 1.3 71.9 - - - +
2292B VAL* 1.3 48.8 + - - +
2294B SER* 2.9 8.7 + - - -
2295B PHE* 2.8 52.8 - + - -
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Residues in contact with VAL2292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104A ILE* 4.9 0.4 - - + -
1120A CYS* 3.5 47.1 - - + +
1123A VAL* 3.8 21.8 - - + -
1124A ALA* 3.6 12.1 - - - +
1127A ILE* 4.2 8.3 - - + -
2281B ILE* 4.9 4.3 - - + -
2284B LEU* 3.9 19.3 - - + -
2288B LEU 2.8 20.2 + - - +
2289B ALA* 3.2 9.4 - - - +
2290B LEU 2.6 4.9 + - - -
2291B TYR* 1.3 72.2 - - - +
2293B LEU* 1.3 60.8 + - + +
2294B SER 2.9 4.0 - - - -
2295B PHE* 2.8 30.4 + - - +
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Residues in contact with LEU2293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A ILE* 3.7 15.9 - - + -
2281B ILE* 3.9 20.9 - - + -
2289B ALA 2.9 19.7 + - - +
2290B LEU* 2.9 9.8 + - + +
2292B VAL* 1.3 74.1 - - + +
2294B SER* 1.3 56.9 + - - +
2296B LEU* 2.9 41.3 + - + +
2301B LEU* 3.0 28.5 - - + +
2304B ALA* 4.5 3.6 - - + -
2311B TRP* 4.3 9.0 - - + +
2314B LEU* 3.5 35.0 - - + -
2315B ALA* 3.7 17.5 - - + +
2320B LEU* 4.4 6.3 - - + -
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Residues in contact with SER2294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2290B LEU 2.7 14.4 + - - -
2291B TYR* 2.9 25.3 + - - -
2292B VAL 2.9 0.2 - - - -
2293B LEU* 1.3 79.0 - - - +
2295B PHE* 1.3 65.6 + - - +
2296B LEU 3.0 4.1 + - - -
2320B LEU* 3.5 25.5 - - - +
2323B GLU* 5.5 6.4 - - - +
2324B LYS* 3.2 20.2 + - - -
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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