Contacts of the strand formed by residues 183 - 187 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106T ALA* 3.8 31.0 - - + +
181T CYS 4.6 1.3 - - - +
182T ALA* 1.3 75.3 - - - +
184T LYS* 1.3 81.9 + - - +
185T MET* 3.7 10.1 - - + -
193T SER* 4.0 6.7 - - - +
194T SER* 3.1 42.6 - - - -
195T GLY 2.8 19.0 + - - +
233T LEU* 3.8 18.4 - - + -
234T GLY* 3.5 37.5 - - - +
247T ALA* 4.8 0.7 - - + -
248T HIS 3.2 11.0 - - - +
249T ILE* 4.0 10.1 - - + -
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Residues in contact with LYS 184 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182T ALA* 5.6 5.2 - - + -
183T MET* 1.3 81.3 - - - +
185T MET* 1.3 59.7 - - - +
186T THR* 5.4 5.2 - - + -
191T GLU* 3.5 32.7 + - + +
193T SER 3.7 4.9 - - - -
194T SER* 4.7 3.6 - - - -
246T GLU 4.0 0.7 - - - +
247T ALA* 3.3 1.9 - - - +
248T HIS* 2.8 43.2 + - + +
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Residues in contact with MET 185 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104T ILE* 3.9 28.7 - - + +
105T GLU* 4.5 6.7 - - - -
106T ALA* 4.4 9.0 - - + +
137T LEU* 3.9 26.0 - - - -
183T MET* 4.0 9.6 - - + -
184T LYS* 1.3 74.8 - - - +
186T THR* 1.3 71.5 + - - +
191T GLU* 3.5 3.5 - - - -
192T VAL* 2.9 30.0 + - + +
193T SER* 2.9 36.6 + - - +
235T PRO 4.7 0.7 - - - +
237T VAL* 4.0 11.7 - - + -
245T PHE* 4.4 12.6 - - + -
246T GLU 3.3 13.0 - - - +
247T ALA* 4.0 7.0 - - + -
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Residues in contact with THR 186 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184T LYS* 5.4 4.7 - - + +
185T MET* 1.3 78.7 - - - +
187T ARG* 1.3 59.4 + - - +
189T ASN* 3.9 14.9 + - - +
190T GLU 3.3 19.1 - - - +
191T GLU* 3.9 18.8 - - + +
192T VAL* 4.0 3.4 - - - -
244T ARG 3.8 0.7 + - - +
245T PHE* 3.3 9.4 - - - -
246T GLU* 2.8 49.0 + - - +
248T HIS* 5.9 5.3 - - + -
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Residues in contact with ARG 187 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186T THR* 1.3 71.2 - - - +
188T ASN* 1.3 84.8 + - - +
189T ASN 3.0 1.2 + - - -
190T GLU* 3.0 26.7 + - - +
192T VAL* 3.7 29.3 - - + +
237T VAL* 4.0 9.7 - - - +
238T ALA* 3.0 27.9 + - - +
240T ASN* 4.2 9.3 + - - -
243T ASP* 3.2 30.5 + - + -
244T ARG 3.5 3.4 - - - -
245T PHE* 3.4 24.2 - - + -
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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