Contacts of the strand formed by residues 2170 - 2176 (chain B) in PDB entry 5WBY
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 ARG2170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2019B VAL* 2.8 22.8 + - + +
2020B ALA* 2.7 26.3 + - - +
2022B LEU* 3.6 16.2 - - - +
2025B GLU* 2.8 39.5 + - - -
2118B LEU* 5.0 1.4 - - - +
2121B LEU* 3.7 22.6 - - + +
2160B LEU* 4.3 20.6 - - + -
2161B GLN 3.4 6.1 - - - +
2162B VAL* 3.8 25.7 - - + +
2163B ILE* 5.5 0.2 - - - -
2168B ARG* 3.3 19.4 + - - +
2169B PRO* 1.3 75.2 - - - +
2171B LYS* 1.3 58.7 + - - +
2172B LEU 3.6 0.7 - - - -
2185B LEU* 3.3 9.1 - - - +
2186B LEU* 2.8 48.9 + - + +
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Residues in contact with LYS2171 (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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2159B SER 4.3 0.2 - - - +
2160B LEU* 3.7 18.8 - - - -
2161B GLN* 2.7 47.4 + - + +
2163B ILE* 5.1 6.7 - - + -
2170B ARG* 1.3 70.2 - - - +
2172B LEU* 1.3 62.6 + - - +
2173B THR* 3.7 10.7 + - + +
2183B VAL* 3.8 31.9 - - + -
2184B PHE 3.5 5.4 - - - +
2185B LEU* 4.3 8.3 - - + -
2239B TRP* 3.4 41.6 - - + +
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Residues in contact with LEU2172 (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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2016B LEU* 3.4 34.3 - - + -
2123B LEU* 5.7 1.8 - - + -
2130B LEU* 5.9 1.6 - - + -
2156B ILE* 3.9 24.2 - - + -
2160B LEU* 3.8 30.9 - - + +
2170B ARG* 3.6 3.6 + - - +
2171B LYS* 1.3 74.7 - - - +
2173B THR* 1.3 60.3 + - - +
2174B LEU* 3.9 21.3 - - + -
2182B PHE 4.2 0.4 - - - +
2183B VAL* 3.5 2.4 - - - +
2184B PHE* 2.7 46.1 + - + +
2186B LEU* 4.4 13.2 - - + -
2236B LEU* 3.5 23.1 - - + -
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Residues in contact with THR2173 (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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2156B ILE* 4.4 0.9 - - - +
2157B ALA* 3.1 47.2 + - + +
2159B SER 4.2 9.6 - - - +
2160B LEU* 4.7 1.2 - - + +
2171B LYS* 4.0 12.3 - - + +
2172B LEU* 1.3 79.6 - - - +
2174B LEU* 1.3 67.2 + - - +
2181B GLU* 4.0 19.6 + - - +
2182B PHE 3.6 4.3 - - - -
2183B VAL* 4.1 19.7 - - - +
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Residues in contact with LEU2174 (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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2140B VAL* 4.2 7.6 - - + -
2141B PRO* 3.5 33.4 - - + -
2153B ILE* 4.3 17.5 - - + -
2155B SER 3.9 5.2 - - - +
2156B ILE* 3.8 36.8 - - + -
2172B LEU* 3.9 22.2 - - + -
2173B THR* 1.3 74.2 - - - +
2175B MET* 1.3 63.4 + - - +
2176B GLY 4.1 0.2 - - - -
2181B GLU* 3.4 6.8 - - - +
2182B PHE* 2.7 41.3 + - + +
2184B PHE* 3.7 20.9 - - + -
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Residues in contact with MET2175 (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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2140B VAL* 5.3 0.4 - - - -
2153B ILE* 3.9 3.3 - - - -
2154B GLN* 2.9 46.6 + - - +
2155B SER* 2.8 32.7 + - - +
2156B ILE* 4.8 0.6 - - - +
2157B ALA 5.2 0.8 - - - +
2173B THR 4.3 0.4 + - - -
2174B LEU* 1.3 73.0 - - - +
2176B GLY* 1.3 62.1 + - - +
2179B GLY* 3.4 26.2 - - - +
2180B HIS 4.2 0.7 - - - +
2181B GLU* 3.4 36.6 - - + +
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Residues in contact with GLY2176 (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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2140B VAL* 4.3 2.9 - - - -
2151B ILE* 4.2 6.3 - - - -
2152B ARG 3.5 7.9 - - - -
2154B GLN* 3.6 9.5 - - - +
2174B LEU 4.0 1.2 + - - -
2175B MET* 1.3 80.0 - - - +
2177B SER* 1.3 63.6 + - - -
2178B ASN* 3.2 10.1 - - - -
2179B GLY* 3.2 13.3 + - - -
2180B HIS 3.0 20.9 + - - -
2182B PHE* 4.2 6.8 - - - -
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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