Contacts of the strand formed by residues 2112 - 2119 (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 LEU2112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2111B PHE* 1.3 74.8 - - - +
2113B TYR* 1.3 70.4 + - - +
2260B LYS* 4.1 35.4 - - + +
2261B ALA 3.6 15.9 - - - +
2262B LEU* 3.8 13.3 - - + +
2292B LEU* 3.7 7.0 - - - +
2293B ASP* 3.2 42.0 + - + +
2294B ASP 4.8 1.5 + - - +
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Residues in contact with TYR2113 (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* 6.5 0.2 - - + -
2097B PHE* 5.0 7.4 - + - -
2098B GLU* 2.9 39.4 + - + +
2101B LEU* 2.8 26.5 - - + +
2111B PHE* 3.9 12.8 - - + -
2112B LEU* 1.3 80.9 - - - +
2114B THR* 1.3 61.0 + - - +
2115B VAL* 3.7 14.6 - - + -
2260B LYS* 2.9 9.5 - - - +
2261B ALA 2.7 36.2 + - - +
2263B GLY 3.9 10.3 - - - -
2264B ALA* 4.5 1.3 - - - -
2267B VAL* 3.7 18.8 - - + -
2290B VAL* 3.9 19.1 - - + -
2291B LYS 3.1 11.2 - - - +
2292B LEU* 3.3 39.5 - - + -
2293B ASP* 3.8 4.3 - - - +
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Residues in contact with THR2114 (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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2113B TYR* 1.3 69.9 + - - +
2115B VAL* 1.3 60.6 + - - +
2116B GLU* 3.4 19.2 + - + +
2240B GLN* 4.0 18.2 - - + +
2241B TYR* 3.2 31.7 + - + +
2244B LEU* 4.7 3.8 - - + -
2258B TYR* 4.5 12.8 - - + -
2259B GLU 3.7 7.6 - - - +
2260B LYS* 4.2 1.6 - - - +
2289B VAL 3.8 5.5 - - - +
2291B LYS* 2.8 22.9 + - - +
2293B ASP* 2.6 30.0 + - - +
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Residues in contact with VAL2115 (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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2113B TYR* 4.2 6.3 - - + -
2114B THR* 1.3 71.3 - - - +
2116B GLU* 1.3 62.5 + - - +
2258B TYR* 3.4 4.2 - - - -
2259B GLU* 2.9 31.5 + - - +
2261B ALA* 3.9 15.3 - - + -
2267B VAL* 3.3 38.1 - - + +
2270B VAL* 4.0 20.2 - - + -
2274B PHE* 4.3 4.9 - - - -
2288B VAL* 3.6 31.4 - - + -
2289B VAL 3.3 14.6 - - - +
2290B VAL* 4.7 3.1 - - - +
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Residues in contact with GLU2116 (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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2114B THR* 3.9 13.0 - - + +
2115B VAL* 1.3 75.9 - - - +
2117B HIS* 1.3 67.6 + - - +
2226B TYR* 3.7 15.6 - - - +
2240B GLN* 3.3 22.7 - - - +
2244B LEU* 4.1 7.9 - - - +
2256B HIS* 2.4 37.5 + - + -
2257B GLY 3.4 8.7 - - - +
2258B TYR* 4.1 8.1 - - + -
2274B PHE* 4.4 2.9 - - - -
2288B VAL* 3.1 13.7 - - - +
2289B VAL* 3.1 31.1 + - + +
2291B LYS* 4.4 9.0 - - + +
2700B AMP 3.0 21.3 + - - +
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Residues in contact with HIS2117 (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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2116B GLU* 1.3 77.5 - - - +
2118B LYS* 1.3 61.2 + - - +
2119B VAL* 3.5 1.7 + - + -
2256B HIS* 3.9 11.6 - - + -
2257B GLY* 3.1 33.5 + - - +
2274B PHE* 3.2 56.9 + + + +
2281B LEU* 3.3 43.5 - - + +
2283B PHE* 3.9 8.1 - + + -
2285B ALA* 4.3 16.8 - - + -
2287B GLY 3.9 1.3 - - - -
2288B VAL* 4.5 4.0 - - + -
2289B VAL* 4.6 1.0 - - - +
2316B PHE* 5.3 4.0 - + - -
2700B AMP 2.8 22.7 + - - -
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Residues in contact with LYS2118 (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* 1.3 73.1 - - - +
2119B VAL* 1.3 61.2 + - - +
2120B ASP* 6.1 0.8 - - - +
2285B ALA* 2.9 26.9 - - - +
2286B ASP* 3.0 43.7 + - - +
2287B GLY* 2.6 29.4 + - - +
2288B VAL 5.0 0.9 - - - +
2289B VAL* 4.0 17.5 - - + -
2313B ALA* 4.5 13.0 - - + -
2314B TYR 5.1 0.4 - - - -
2315B LYS* 3.0 40.1 - - - +
2700B AMP 3.2 53.5 + - + +
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Residues in contact with VAL2119 (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 4.3 3.6 - - - +
2118B LYS* 1.3 75.7 + - - +
2120B ASP* 1.3 56.2 + - + +
2121B GLY* 2.6 19.2 + - - -
2174B GLU* 3.0 22.6 - - - +
2176B TYR* 3.8 41.7 - - + -
2224B THR* 4.3 13.9 - - + -
2226B TYR* 5.9 1.3 - - + -
2256B HIS* 3.8 35.2 - - + -
2283B PHE* 4.7 12.1 - - + -
2284B GLU 4.1 5.4 - - - +
2285B ALA* 4.7 0.9 - - - +
2700B AMP 3.2 20.0 + - - +
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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