Contacts of the strand formed by residues 255 - 259 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179K LYS* 5.4 0.2 - - - -
90L ASP* 3.6 3.6 - - - +
135L PRO* 3.8 8.3 - - + +
136L ALA 3.7 30.3 - - - +
137L LEU* 3.7 14.4 - - + +
165L VAL* 3.5 34.1 - - + +
167L GLY* 3.3 29.8 - - - +
245L PHE 4.0 0.2 - - - +
246L GLU* 3.3 6.6 - - - +
247L ALA* 2.8 41.9 + - + +
249L ILE* 5.0 1.1 - - + -
254L SER* 1.3 75.4 - - - +
256L ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K LYS* 3.8 24.9 - - - +
90L ASP* 2.8 11.5 + - - +
91L ASN* 2.8 31.0 + - + -
92L GLU 4.3 0.5 + - - -
137L LEU* 4.0 2.9 - - - -
165L VAL* 3.5 8.7 - - - +
244L ARG* 3.9 19.7 - - - +
245L PHE 3.2 11.0 - - - +
246L GLU* 4.1 2.5 - - - -
255L VAL* 1.3 75.6 - - - +
257L ALA* 1.3 62.1 + - - +
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Residues in contact with ALA 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L ASN* 4.8 0.4 - - - +
92L GLU 4.0 7.6 - - - +
94L ILE* 3.8 26.5 - - + -
104L ILE* 6.0 0.9 - - + -
137L LEU* 4.0 9.1 - - + +
139L VAL* 5.8 0.9 - - + -
165L VAL* 3.9 15.9 - - + -
243L ASP 4.1 0.3 - - - +
244L ARG* 3.6 2.0 - - - +
245L PHE* 2.8 36.4 + - + +
256L ALA* 1.3 76.0 - - - +
258L THR* 1.3 63.6 + - - +
259L PHE* 4.7 9.2 - - + -
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Residues in contact with THR 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L ASN* 4.2 6.2 + - - -
92L GLU 3.2 12.7 + - - -
93L ILE* 3.3 17.5 - - + +
94L ILE* 2.7 34.1 + - - +
242L GLY 4.4 5.8 - - - +
243L ASP 3.5 9.9 - - - +
244L ARG* 3.6 30.6 + - + +
257L ALA* 1.3 75.9 - - - +
259L PHE* 1.3 67.5 + - - +
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Residues in contact with PHE 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L ILE* 4.6 1.6 - - - -
94L ILE* 3.3 35.7 - - + -
95L PRO 5.2 0.2 - - - -
96L PHE* 4.4 17.9 - + + -
99L VAL* 5.9 1.8 - - + -
102L PRO* 5.1 3.4 - - + -
104L ILE* 4.7 2.7 - - + -
139L VAL* 3.8 35.4 - - + -
239L VAL* 3.6 37.0 - - + -
240L ASN 4.2 6.1 - - - +
242L GLY* 3.1 27.3 - - - +
243L ASP 2.9 20.9 + - - +
245L PHE* 3.7 20.6 - + - -
257L ALA* 4.7 11.2 - - + -
258L THR* 1.3 83.6 - - - +
260L SER* 1.3 66.7 + - - +
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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