Contacts of the strand formed by residues 2285 - 2291 (chain B) in PDB entry 1V9P
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 ALA2285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2117B HIS* 4.3 20.9 - - + -
2118B LYS 2.9 33.0 - - - +
2278B ARG* 3.4 17.1 - - + +
2281B LEU* 4.6 4.7 - - + +
2283B PHE* 4.1 9.2 + - + -
2284B GLU* 1.3 75.2 - - - +
2286B ASP* 1.3 62.9 + - - +
2287B GLY 3.3 6.1 - - - +
2316B PHE* 3.2 18.6 - - + -
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Residues in contact with ASP2286 (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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2118B LYS* 3.0 26.1 + - - +
2120B ASP* 3.3 12.2 + - - +
2278B ARG* 3.9 11.2 + - - +
2284B GLU* 2.7 30.8 - - - +
2285B ALA* 1.3 73.5 - - - +
2287B GLY* 1.3 56.1 + - - +
2315B LYS* 3.5 20.4 + - - +
2316B PHE* 2.8 32.6 + - + +
2700B AMP 4.8 2.8 + - - -
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Residues in contact with GLY2287 (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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2117B HIS* 3.6 2.1 - - - -
2118B LYS* 2.6 41.1 + - - +
2285B ALA* 4.0 3.6 - - - +
2286B ASP* 1.3 80.7 - - - +
2288B VAL* 1.3 59.0 + - - +
2314B TYR 3.4 11.4 - - - -
2316B PHE* 3.1 25.0 - - - -
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Residues in contact with VAL2288 (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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2115B VAL* 3.6 18.4 - - + -
2116B GLU 3.1 12.6 - - - +
2117B HIS* 4.7 1.1 - - + -
2118B LYS* 4.1 1.7 - - - +
2267B VAL* 5.5 1.3 - - + +
2271B TYR* 3.8 36.3 - - + -
2274B PHE* 3.7 38.6 - - + -
2287B GLY* 1.3 78.1 - - - -
2289B VAL* 1.3 66.6 + - - +
2290B VAL* 5.0 2.2 - - + -
2313B ALA* 3.8 0.9 - - - -
2314B TYR* 2.9 44.0 + - + +
2316B PHE* 4.6 4.5 - - + -
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Residues in contact with VAL2289 (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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2085B LEU* 3.4 35.7 - - + -
2114B THR 3.8 1.0 - - - +
2115B VAL* 3.3 9.7 - - - -
2116B GLU* 3.1 30.1 + - + +
2117B HIS 4.6 0.2 - - - +
2118B LYS* 4.0 26.2 - - + -
2288B VAL* 1.3 79.5 - - - +
2290B VAL* 1.3 64.0 + - - +
2291B LYS* 3.6 27.6 + - + +
2312B LEU 3.3 7.9 - - - +
2313B ALA* 4.6 0.7 - - - -
2700B AMP 4.2 24.0 - - + +
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Residues in contact with VAL2290 (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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2094B VAL* 4.3 21.3 - - + -
2097B PHE* 4.7 10.7 - - + -
2113B TYR* 3.9 38.1 - - + -
2115B VAL* 4.7 4.9 - - + -
2267B VAL* 4.0 19.3 - - + -
2288B VAL* 5.0 2.7 - - + -
2289B VAL* 1.3 70.0 - - - +
2291B LYS* 1.3 61.4 + - - +
2292B LEU 4.3 0.4 + - - -
2311B ALA* 3.1 6.1 - - - +
2312B LEU* 2.6 54.9 + - + +
2314B TYR* 4.3 17.0 - - + -
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Residues in contact with LYS2291 (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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2085B LEU* 5.4 4.5 - - - -
2113B TYR* 3.1 7.0 - - - +
2114B THR 2.8 43.0 + - - +
2116B GLU* 4.4 8.4 + - + +
2226B TYR 4.0 18.2 + - - -
2227B ALA* 4.6 8.1 - - - +
2240B GLN* 4.1 21.3 - - + +
2289B VAL* 3.6 16.2 + - + +
2290B VAL* 1.3 74.8 - - - +
2292B LEU* 1.3 59.7 + - - +
2293B ASP* 2.9 3.8 + - - -
2298B TRP* 4.0 31.3 - - + -
2310B PHE* 4.2 5.2 - - - -
2311B ALA* 3.7 24.7 - - + -
2700B AMP 4.4 21.1 - - - -
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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