Contacts of the strand formed by residues 255 - 259 (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 VAL 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A LYS* 5.7 0.4 - - - -
90B ASP* 3.6 3.1 - - - +
135B PRO* 3.8 8.3 - - + +
136B ALA 3.7 30.1 - - - +
137B LEU* 3.8 13.6 - - + +
165B VAL* 3.6 33.2 - - + +
167B GLY* 3.2 31.0 - - - +
246B GLU* 3.2 6.5 - - - +
247B ALA* 2.9 39.9 + - + +
249B ILE* 5.0 2.5 - - + -
254B SER* 1.3 75.5 - - - +
256B ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A LYS* 3.9 22.0 - - - +
90B ASP* 2.8 13.5 + - - +
91B ASN* 2.8 29.1 + - - -
92B GLU 4.3 0.2 + - - -
137B LEU* 4.1 3.8 - - - -
165B VAL* 3.6 7.8 - - - +
244B ARG* 3.9 22.2 - - - +
245B PHE 3.2 11.0 - - - +
246B GLU* 4.3 2.2 - - + -
255B VAL* 1.3 77.3 - - - +
257B ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 257 (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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91B ASN* 4.7 1.1 - - - +
92B GLU 4.0 7.9 - - - +
94B ILE* 3.9 26.2 - - + -
104B ILE* 6.1 0.4 - - + -
137B LEU* 3.9 16.7 - - + +
139B VAL* 5.9 0.7 - - + -
165B VAL* 3.9 8.5 - - + -
243B ASP 4.1 0.3 - - - +
244B ARG* 3.5 2.1 - - - +
245B PHE* 2.8 35.5 + - + +
256B ALA* 1.3 76.3 - - - +
258B THR* 1.3 62.8 + - - +
259B PHE* 4.7 8.9 - - + -
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Residues in contact with THR 258 (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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91B ASN* 4.2 12.3 + - - -
92B GLU 3.2 13.0 + - - -
93B ILE* 3.3 17.6 - - + +
94B ILE* 2.8 28.1 + - - +
242B GLY 4.4 5.6 - - - +
243B ASP 3.5 9.9 - - - +
244B ARG* 3.6 25.0 + - + +
257B ALA* 1.3 76.9 - - - +
259B PHE* 1.3 73.5 + - - +
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Residues in contact with PHE 259 (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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93B ILE* 4.5 1.1 - - - -
94B ILE* 3.3 38.6 - - + -
95B PRO 5.2 0.4 - - - -
96B PHE* 4.5 17.9 - + + -
99B VAL* 6.0 1.6 - - + -
102B PRO* 5.2 3.4 - - + -
104B ILE* 4.7 3.4 - - + -
139B VAL* 3.8 35.2 - - + -
239B VAL* 3.6 36.6 - - + -
240B ASN 4.3 6.1 - - - +
242B GLY* 3.1 25.3 - - - +
243B ASP 2.9 21.1 + - - +
245B PHE* 3.9 19.5 - + - -
257B ALA* 4.7 11.9 - - + -
258B THR* 1.3 83.6 - - - +
260B SER* 1.3 68.0 + - - +
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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