Contacts of the strand formed by residues 183 - 187 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106G ALA* 3.7 33.2 - - + +
181G CYS 3.6 1.8 + - - +
182G ALA* 1.3 74.0 - - - +
184G LYS* 1.3 81.5 + - - +
185G MET* 3.7 8.5 - - + -
193G SER* 3.9 12.1 - - - +
194G SER* 2.9 15.9 - - - -
195G GLY 2.8 42.7 + - - +
233G LEU* 3.7 20.6 - - + -
234G GLY* 3.3 39.5 - - - +
247G ALA* 5.0 0.2 - - + -
248G HIS 3.3 4.5 - - - +
249G ILE* 3.9 15.3 - - + -
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Residues in contact with LYS 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182G ALA* 4.2 10.1 - - + +
183G MET* 1.3 83.9 + - - +
185G MET* 1.3 59.2 + - - +
186G THR* 5.3 2.9 - - + -
191G GLU* 3.7 37.9 - - + +
193G SER 3.6 1.3 - - - -
194G SER* 3.4 21.2 + - - -
195G GLY 4.7 4.9 + - - +
196G ARG* 5.9 2.0 - - - +
247G ALA* 3.5 1.0 - - - -
248G HIS* 2.8 43.5 + - + +
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Residues in contact with MET 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G ILE* 3.7 37.5 - - + +
105G GLU* 4.5 4.5 - - - -
106G ALA 4.3 10.5 - - - +
137G LEU* 3.8 24.5 - - - -
183G MET* 4.0 11.4 - - + -
184G LYS* 1.3 74.6 - - - +
186G THR* 1.3 71.9 + - - +
191G GLU* 3.6 2.5 - - - -
192G VAL* 2.9 27.9 + - + +
193G SER* 2.8 27.5 + - - +
235G PRO 4.8 0.7 - - - +
237G VAL* 3.9 19.7 - - + -
245G PHE* 4.3 11.7 - - + -
246G GLU 3.3 15.5 - - - +
247G ALA* 4.1 3.6 - - + -
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Residues in contact with THR 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184G LYS* 5.3 2.2 - - + -
185G MET* 1.3 80.2 - - - +
187G ARG* 1.3 59.1 + - - +
189G ASN* 3.9 7.9 + - - +
190G GLU 3.2 26.0 - - - -
191G GLU* 4.1 9.0 - - + +
192G VAL* 4.1 3.1 - - - -
244G ARG 3.8 0.9 + - - +
245G PHE* 3.2 10.0 - - - -
246G GLU 2.7 38.8 + - - +
248G HIS* 4.9 5.4 - - + -
1264G PO4 2.4 40.1 + - - +
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Residues in contact with ARG 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G THR* 1.3 71.8 - - - +
188G ASN* 1.3 86.1 + - - +
189G ASN 3.1 1.1 - - - -
190G GLU* 2.8 29.4 + - - +
192G VAL* 3.7 26.9 - - + +
237G VAL* 4.0 11.3 - - - +
238G ALA* 3.4 23.0 + - - +
240G ASN* 4.5 8.9 + - - -
243G ASP* 3.3 29.9 + - + -
244G ARG 3.4 4.3 - - - +
245G PHE* 3.4 25.4 - - + -
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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