Contacts of the strand formed by residues 255 - 259 (chain F) 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 VAL 255 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASP* 3.6 3.6 - - - +
135F PRO* 3.8 8.5 - - + +
136F ALA 3.7 29.8 - - - +
137F LEU* 3.7 15.4 - - + +
165F VAL* 3.6 33.0 - - + +
167F GLY* 3.3 30.5 - - - +
245F PHE 4.0 0.2 - - - +
246F GLU* 3.3 6.1 - - - +
247F ALA* 2.9 41.3 + - + +
249F ILE* 4.9 1.8 - - + -
254F SER* 1.3 75.8 - - - +
256F ALA* 1.3 59.3 + - - +
179I LYS* 5.8 0.4 - - - -
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Residues in contact with ALA 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ASP* 2.8 12.6 + - - +
91F ASN* 2.8 27.7 + - - -
92F GLU 4.3 0.2 + - - -
137F LEU* 4.0 2.7 - - - -
165F VAL* 3.5 9.2 - - - +
244F ARG* 3.6 31.4 - - - +
245F PHE 3.2 9.9 - - - +
246F GLU* 3.9 11.9 - - - +
255F VAL* 1.3 76.2 - - - +
257F ALA* 1.3 62.8 + - - +
179I LYS* 4.1 6.3 - - - +
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Residues in contact with ALA 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ASN* 4.8 0.7 - - - +
92F GLU 4.0 8.3 - - - +
94F ILE* 3.8 26.7 - - + -
104F ILE* 6.0 0.4 - - + -
137F LEU* 3.9 8.7 - - + -
139F VAL* 5.9 0.4 - - + -
165F VAL* 3.9 15.3 - - + -
243F ASP 4.1 0.3 - - - +
244F ARG* 3.5 2.8 - - - +
245F PHE* 2.7 36.5 + - + +
256F ALA* 1.3 76.0 - - - +
258F THR* 1.3 62.1 + - - +
259F PHE* 4.7 10.3 - - + -
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Residues in contact with THR 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ASN* 4.2 9.9 + - - -
92F GLU 3.2 13.4 + - - -
93F ILE* 3.3 17.5 - - + +
94F ILE* 2.7 34.0 + - - +
242F GLY 4.4 5.6 - - - +
243F ASP 3.5 10.1 - - - +
244F ARG* 3.7 25.4 + - + -
257F ALA* 1.3 76.2 + - - +
259F PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93F ILE* 4.6 1.3 - - - -
94F ILE* 3.2 36.3 - - + +
95F PRO 5.2 0.2 - - - -
96F PHE* 4.4 18.4 - + + -
99F VAL* 5.9 1.8 - - + -
102F PRO* 5.0 3.8 - - + -
104F ILE* 4.7 3.1 - - + -
139F VAL* 3.9 33.9 - - + -
239F VAL* 3.6 38.4 - - + -
240F ASN 4.3 5.6 - - - +
242F GLY* 3.2 25.1 - - - +
243F ASP 2.9 20.7 + - - +
245F PHE* 3.8 20.4 - + - -
257F ALA* 4.7 11.4 - - + -
258F THR* 1.3 84.2 - - - +
260F SER* 1.3 68.8 + - - +
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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