Contacts of the strand formed by residues 2181 - 2187 (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 GLU2181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2173B THR* 4.0 17.4 + - - +
2174B LEU 3.4 9.6 - - - +
2175B MET* 3.4 33.2 - - + +
2179B GLY 3.8 0.4 + - - -
2180B HIS* 1.3 78.8 - - - +
2182B PHE* 1.3 69.6 + - - +
2183B VAL* 4.3 9.4 - - + +
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Residues in contact with PHE2182 (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* 3.7 19.5 - - + -
2143B THR* 3.8 18.6 - - + -
2151B ILE* 3.8 28.0 - - + -
2174B LEU* 2.7 40.4 + - + +
2176B GLY* 4.2 8.7 - - - -
2178B ASN* 3.6 22.4 - - - -
2180B HIS* 3.3 26.7 - + + -
2181B GLU* 1.3 77.5 - - - +
2183B VAL* 1.3 60.6 + - - +
2184B PHE* 3.5 25.3 - + + -
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Residues in contact with VAL2183 (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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2171B LYS* 3.8 29.8 - - + -
2172B LEU 3.5 10.3 - - - +
2173B THR* 4.1 17.3 - - - +
2181B GLU* 5.0 9.6 - - + +
2182B PHE* 1.3 77.8 - - - +
2184B PHE* 1.3 73.5 + - - +
2238B GLY* 4.2 0.5 - - - -
2239B TRP* 3.2 53.3 + - + +
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Residues in contact with PHE2184 (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* 3.8 12.1 - - + -
2141B PRO* 3.4 36.3 - - + -
2143B THR* 5.5 0.2 - - + -
2171B LYS* 3.5 6.1 - - - -
2172B LEU* 2.7 40.8 + - + +
2174B LEU* 3.7 27.1 - - + -
2182B PHE* 3.5 31.0 - + + -
2183B VAL* 1.3 82.7 - - - +
2185B LEU* 1.3 65.7 + - - +
2186B LEU 3.9 0.4 - - - -
2226B ALA* 4.9 7.2 - - + -
2228B ILE* 5.2 1.8 - - + -
2236B LEU* 4.0 29.6 - - + -
2237B ILE 3.2 19.1 - - - +
2238B GLY* 4.0 11.2 - - - -
2239B TRP* 4.0 2.9 - - - +
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Residues in contact with LEU2185 (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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2163B ILE* 5.0 10.5 - - + -
2169B PRO* 4.6 14.8 - - + -
2170B ARG 3.3 10.8 - - - +
2171B LYS* 4.3 9.4 - - + -
2184B PHE* 1.3 76.8 - - - +
2186B LEU* 1.3 64.2 + - - +
2187B LYS* 3.4 26.2 + - + +
2235B GLY 3.7 0.9 - - - +
2236B LEU* 3.7 1.0 - - - -
2237B ILE* 2.7 46.2 + - + +
2239B TRP* 3.5 40.4 - - + +
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Residues in contact with LEU2186 (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* 3.5 45.1 - - + +
2019B VAL* 4.0 16.2 - - + -
2020B ALA* 3.7 25.1 - - + +
2160B LEU* 4.7 6.7 - - + -
2169B PRO* 3.5 2.1 - - - +
2170B ARG* 2.8 47.9 + - + +
2172B LEU* 4.4 7.8 - - + +
2184B PHE 3.9 2.2 + - - -
2185B LEU* 1.3 68.1 - - - +
2187B LYS* 1.3 63.0 + - - +
2230B LEU* 4.0 18.4 - - + -
2235B GLY 3.9 4.9 - - - +
2236B LEU* 3.7 23.3 - - + +
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Residues in contact with LYS2187 (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 ALA* 4.0 4.9 - - - +
2169B PRO* 3.9 19.3 - - + -
2185B LEU* 3.8 30.6 - - - +
2186B LEU* 1.3 73.6 - - - +
2188B GLY* 1.3 58.6 + - - +
2190B GLU* 3.4 43.4 + - + +
2192B LEU* 4.2 8.4 - - + +
2233B ASN 5.1 0.2 - - - -
2234B SER* 3.2 24.4 - - - -
2235B GLY 3.0 19.5 + - - +
2237B ILE* 4.1 32.6 - - + +
2356B ILE* 5.5 9.7 - - - +
2357B ASP* 5.9 6.7 - - - +
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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