Contacts of the strand formed by residues 183 - 187 (chain B) in PDB entry 2WQT
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 MET 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B ALA* 3.8 31.0 - - + +
181B CYS 4.6 1.3 - - - +
182B ALA* 1.3 77.0 - - - +
184B LYS* 1.3 82.0 + - - +
185B MET* 3.7 10.1 - - + -
193B SER* 4.0 7.0 - - - +
194B SER* 3.1 47.7 - - - -
195B GLY 2.8 17.7 + - - +
233B LEU* 3.8 17.3 - - + -
234B GLY* 3.5 32.3 - - - +
247B ALA* 4.8 0.4 - - + -
248B HIS 3.2 11.0 - - - +
249B ILE* 4.0 10.3 - - + -
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Residues in contact with LYS 184 (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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182B ALA* 5.6 4.7 - - + +
183B MET* 1.3 82.2 - - - +
185B MET* 1.3 60.4 + - - +
186B THR* 5.4 4.7 - - + -
191B GLU* 3.5 32.8 + - + +
193B SER 3.7 4.7 - - - -
194B SER* 4.7 3.4 - - - -
246B GLU 4.0 0.5 - - - +
247B ALA* 3.3 1.4 - - - +
248B HIS* 2.8 43.0 + - + +
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Residues in contact with MET 185 (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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104B ILE* 3.9 29.2 - - + +
105B GLU* 4.4 7.0 - - - -
106B ALA* 4.5 8.3 - - + +
137B LEU* 3.9 25.6 - - - -
183B MET* 3.7 10.3 - - + -
184B LYS* 1.3 75.6 - - - +
186B THR* 1.3 72.2 + - - +
191B GLU* 3.5 3.6 - - - -
192B VAL* 2.9 29.0 + - + +
193B SER* 2.9 36.7 + - - +
235B PRO 4.7 0.7 - - - +
237B VAL* 4.0 11.2 - - + -
245B PHE* 4.3 13.5 - - + -
246B GLU 3.3 12.8 - - - +
247B ALA* 4.0 7.0 - - + -
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Residues in contact with THR 186 (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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184B LYS* 5.4 4.7 - - + -
185B MET* 1.3 78.1 - - - +
187B ARG* 1.3 60.0 + - - +
188B ASN 5.2 0.2 + - - -
189B ASN* 3.9 14.5 + - - +
190B GLU* 3.3 18.8 - - - +
191B GLU* 3.9 19.3 - - + +
192B VAL* 4.0 3.1 - - - -
244B ARG 3.8 0.5 + - - +
245B PHE* 3.3 8.3 - - - -
246B GLU* 2.8 50.4 + - - +
248B HIS* 5.9 5.2 - - + -
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Residues in contact with ARG 187 (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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186B THR* 1.3 71.8 - - - +
188B ASN* 1.3 88.5 + - - +
189B ASN 3.0 1.9 + - - -
190B GLU* 2.9 26.4 + - - +
192B VAL* 3.7 28.6 - - + +
237B VAL* 3.9 9.7 - - - +
238B ALA* 3.0 27.9 + - - +
240B ASN* 4.2 10.0 + - - -
243B ASP* 3.2 31.1 + - + -
244B ARG 3.5 3.4 - - - +
245B PHE* 3.5 23.8 - - + -
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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