Contacts of the strand formed by residues 2160 - 2164 (chain B) in PDB entry 1WUF
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 ARG2160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2134B GLY* 3.4 10.3 - - - -
2135B VAL* 3.2 33.0 + - - +
2136B SER* 3.9 6.1 + - - -
2158B TYR* 3.3 2.5 + - - +
2159B GLU* 1.3 77.8 - - - +
2161B VAL* 1.3 70.6 + - - +
2162B LYS* 3.6 11.1 - - - +
2184B LEU* 4.2 1.1 - - - +
2185B SER* 3.0 23.3 - - - +
2187B MET* 3.6 18.3 - - - +
2288B TRP* 4.3 1.2 - - - -
2313B PHE* 3.4 24.8 - - + -
2314B PRO* 2.3 66.4 + - + +
2315B GLY 3.4 6.3 + - - -
2316B ASP* 2.5 35.8 + - - -
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Residues in contact with VAL2161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135B VAL* 3.5 17.3 - - + +
2137B ILE* 3.6 21.5 - - + -
2150B VAL* 4.9 9.0 - - + -
2153B TYR* 5.2 4.9 - - + -
2154B VAL* 5.0 4.9 - - + -
2158B TYR 5.1 2.2 - - - +
2160B ARG* 1.3 85.5 - - - +
2162B LYS* 1.3 63.5 + - - +
2163B LEU* 3.5 26.2 - - + -
2184B LEU* 3.8 24.5 - - + -
2185B SER 3.3 6.5 + - - -
2186B LEU* 3.1 18.2 - - + +
2187B MET 3.1 23.2 + - - -
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Residues in contact with LYS2162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135B VAL 2.8 15.4 + - - +
2136B SER* 3.0 30.7 - - - +
2137B ILE* 2.9 27.5 + - - +
2160B ARG* 3.6 3.3 - - - +
2161B VAL* 1.3 74.5 - - - +
2163B LEU* 1.3 64.2 + - - +
2164B LYS 5.1 0.2 - - - +
2187B MET* 3.6 39.5 - - + -
2189B ASP* 3.7 37.1 + - + +
2214B GLU* 4.2 1.6 + - - +
2261B ASN* 4.6 2.8 - - - +
2288B TRP* 3.6 10.7 - - + -
2316B ASP* 2.6 26.7 + - - -
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Residues in contact with LEU2163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137B ILE* 3.9 14.4 - - + -
2146B LEU* 4.4 18.8 - - + -
2150B VAL* 4.6 1.3 - - + -
2161B VAL* 3.5 26.5 - - + -
2162B LYS* 1.3 76.3 - - - +
2164B LYS* 1.3 64.4 + - - +
2165B ILE* 3.5 6.9 + - + -
2173B PHE* 4.7 3.1 - - + +
2174B VAL* 4.5 19.1 - - + +
2177B VAL* 3.9 20.4 - - + -
2186B LEU* 3.6 36.6 - - + -
2187B MET 2.9 12.3 + - - +
2188B ALA* 3.3 6.4 - - + +
2189B ASP 2.8 25.3 + - - -
2210B LEU* 5.9 0.7 - - + -
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Residues in contact with LYS2164 (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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2020B LYS* 5.7 12.1 - - + -
2137B ILE 2.9 21.4 + - - +
2138B GLY* 3.6 24.7 + - - +
2139B LEU* 3.3 42.8 - - + +
2162B LYS* 5.1 0.6 - - - +
2163B LEU* 1.3 73.7 - - - +
2165B ILE* 1.3 72.7 + - - +
2166B ALA* 5.4 0.8 - - - +
2169B LYS 4.3 0.9 - - - +
2173B PHE* 6.1 0.5 - - - +
2189B ASP* 3.7 8.7 - - + +
2191B ASN* 3.4 35.5 - - - +
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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
------------------------------------------------------------
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