Contacts of the strand formed by residues 244 - 249 (chain O) 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 ARG 244 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179L LYS* 3.8 11.5 - - - +
91O ASN* 3.4 30.3 + - - +
186O THR* 3.7 1.7 + - - +
187O ARG* 3.5 2.1 - - - -
188O ASN* 2.9 45.6 + - - +
189O ASN* 4.7 11.4 + - - +
242O GLY 4.8 1.1 - - - +
243O ASP* 1.3 72.9 - - - +
245O PHE* 1.3 64.4 + - - +
246O GLU* 2.8 39.0 + - - +
256O ALA* 3.8 11.2 - - - +
257O ALA 3.5 5.2 - - - +
258O THR* 3.6 24.3 + - + +
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Residues in contact with PHE 245 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ILE* 3.1 45.8 - - + -
137O LEU* 4.4 13.6 - - + +
185O MET* 4.3 13.5 - - + -
186O THR 3.4 12.1 - - - -
187O ARG* 3.6 31.2 - - + -
192O VAL* 4.3 2.0 - - + -
237O VAL* 3.5 12.8 - - + -
238O ALA 3.8 12.6 - - - -
239O VAL* 4.0 9.9 - - + -
243O ASP* 3.5 23.3 - - + -
244O ARG* 1.3 78.2 - - - +
246O GLU* 1.3 61.5 + - - +
256O ALA* 3.1 5.2 - - - +
257O ALA* 2.7 40.0 + - + +
259O PHE* 3.9 15.0 - + + -
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Residues in contact with GLU 246 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179L LYS* 3.4 18.7 + - - -
180L ASN* 5.2 1.7 - - - +
137O LEU* 5.2 0.7 - - - -
184O LYS 3.9 0.7 - - - +
185O MET* 3.3 4.3 - - - +
186O THR* 2.9 47.7 + - - +
244O ARG* 2.8 33.3 + - - +
245O PHE* 1.3 76.1 - - - +
247O ALA* 1.3 63.7 + - - +
248O HIS* 3.6 31.5 + - + +
254O SER* 3.8 13.2 + - - -
255O VAL 3.2 9.2 - - - +
256O ALA* 4.3 2.4 - - + +
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Residues in contact with ALA 247 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O ALA* 3.8 29.6 - - + -
137O LEU* 3.8 17.2 - - + +
183O MET* 4.8 1.6 - - + -
184O LYS 3.3 8.5 - - - +
185O MET* 4.1 6.3 - - + -
246O GLU* 1.3 75.0 - - - +
248O HIS* 1.3 63.6 + - - +
249O ILE* 4.2 1.8 - - + -
254O SER* 3.1 8.0 - - - -
255O VAL* 2.8 37.9 + - + +
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Residues in contact with HIS 248 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O ALA 3.4 1.4 - - - +
183O MET* 3.2 6.8 - - - +
184O LYS* 2.8 43.7 + - + +
186O THR* 5.9 5.2 - - + -
246O GLU* 3.6 30.5 - - + +
247O ALA* 1.3 80.2 - - - +
249O ILE* 1.3 63.9 + - - +
250O GLU 4.0 0.7 - - - +
253O GLY 3.6 4.2 + - - +
254O SER* 3.8 17.1 - - - -
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Residues in contact with ILE 249 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O ALA* 4.7 5.8 - - + -
107O GLU 3.6 27.8 - - - +
108O ILE* 4.5 3.1 - - + -
135O PRO* 3.8 22.0 - - + -
136O ALA 4.5 2.2 - - - +
181O CYS* 3.9 18.2 - - + +
182O ALA 3.4 4.3 - - - +
183O MET* 4.0 8.1 - - + -
233O LEU* 3.7 25.6 - - + -
247O ALA* 5.3 1.3 - - + -
248O HIS* 1.3 77.9 - - - +
250O GLU* 1.3 66.2 + - - +
251O GLY 3.3 0.5 + - - -
252O ILE* 3.0 44.3 + - + -
253O GLY 2.8 22.8 + - - +
255O VAL* 5.0 4.0 - - + -
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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