Contacts of the strand formed by residues 255 - 259 (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 VAL 255 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179Q LYS* 5.8 0.4 - - - -
90T ASP* 3.6 3.4 - - - +
135T PRO* 3.7 8.5 - - + +
136T ALA 3.7 31.6 - - - +
137T LEU* 3.8 13.7 - - + +
165T VAL* 3.6 33.4 - - + +
167T GLY* 3.3 30.1 - - - +
246T GLU* 3.3 5.8 - - - +
247T ALA* 2.9 39.8 + - + +
249T ILE* 4.9 2.2 - - + -
254T SER* 1.3 75.1 - - - +
256T ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 256 (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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179Q LYS* 4.0 14.4 - - - +
90T ASP* 2.8 12.4 + - - +
91T ASN* 2.8 29.7 + - - -
92T GLU 4.3 0.2 + - - -
137T LEU* 4.1 3.1 - - - -
165T VAL* 3.6 8.3 - - - +
244T ARG* 4.0 28.7 - - - +
245T PHE 3.2 11.0 - - - +
246T GLU* 4.4 2.9 - - + -
255T VAL* 1.3 76.2 - - - +
257T ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 257 (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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91T ASN* 4.8 0.7 - - - +
92T GLU 4.0 7.4 - - - +
94T ILE* 3.8 26.5 - - + -
104T ILE* 6.0 0.4 - - + -
137T LEU* 3.9 9.5 - - + +
139T VAL* 5.9 0.2 - - + -
165T VAL* 3.9 15.7 - - + -
243T ASP 4.1 0.5 - - - +
244T ARG* 3.5 2.8 - - - +
245T PHE* 2.8 34.8 + - + +
256T ALA* 1.3 75.8 - - - +
258T THR* 1.3 63.4 + - - +
259T PHE* 4.7 11.7 - - + -
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Residues in contact with THR 258 (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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91T ASN* 4.2 12.8 + - - -
92T GLU 3.2 12.8 + - - -
93T ILE* 3.3 17.4 - - + +
94T ILE* 2.8 28.1 + - - +
242T GLY 4.4 5.8 - - - +
243T ASP 3.5 9.4 - - - +
244T ARG* 3.7 23.6 + - + +
257T ALA* 1.3 76.9 - - - +
259T PHE* 1.3 74.1 + - - +
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Residues in contact with PHE 259 (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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93T ILE* 4.6 1.1 - - - -
94T ILE* 3.3 36.1 - - + +
95T PRO 5.2 0.2 - - - -
96T PHE* 4.5 18.6 - + + -
99T VAL* 6.0 1.3 - - + -
102T PRO* 5.1 3.1 - - + -
104T ILE* 4.7 3.4 - - + -
139T VAL* 3.9 34.3 - - + -
239T VAL* 3.6 37.0 - - + -
240T ASN 4.3 6.3 - - - +
242T GLY* 3.1 28.0 - - - +
243T ASP 2.9 20.5 + - - +
245T PHE* 3.9 20.6 - + - -
257T ALA* 4.7 11.4 - - + -
258T THR* 1.3 84.5 - - - +
260T SER* 1.3 66.5 + - - +
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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