Contacts of the strand formed by residues 255 - 259 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B LYS* 5.7 0.4 - - - -
90E ASP* 3.6 3.6 - - - +
135E PRO* 3.8 8.3 - - + +
136E ALA 3.7 31.4 - - - +
137E LEU* 3.8 13.4 - - + +
165E VAL* 3.5 32.5 - - + +
166E ILE 3.7 0.7 - - - -
167E GLY* 3.3 30.7 - - - +
246E GLU* 3.2 6.9 - - - +
247E ALA* 2.8 39.9 + - + +
249E ILE* 5.1 1.6 - - + -
254E SER* 1.3 75.5 - - - +
256E ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS* 3.8 24.0 - - - +
90E ASP* 2.8 9.6 + - - +
91E ASN* 2.8 28.8 + - - -
92E GLU 4.2 0.2 + - - -
137E LEU* 4.1 2.9 - - - -
165E VAL* 3.7 7.6 - - - +
244E ARG* 3.9 22.0 - - - +
245E PHE 3.1 11.4 - - - +
246E GLU* 4.3 3.4 - - + -
255E VAL* 1.3 75.3 - - - +
257E ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ASN* 4.8 0.7 - - - +
92E GLU 4.0 7.6 - - - +
94E ILE* 3.9 26.2 - - + -
137E LEU* 3.9 8.9 - - + +
139E VAL* 5.9 0.7 - - + -
165E VAL* 3.9 15.9 - - + -
243E ASP 4.1 0.5 - - - +
244E ARG* 3.4 2.4 - - - +
245E PHE* 2.7 38.3 + - + +
256E ALA* 1.3 75.8 - - - +
258E THR* 1.3 62.4 + - - +
259E PHE* 4.7 8.7 - - + -
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Residues in contact with THR 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E ASN* 4.3 11.4 + - - -
92E GLU 3.3 11.5 + - - -
93E ILE* 3.4 16.5 - - + +
94E ILE* 2.8 27.6 + - - +
242E GLY 4.2 6.3 - - - +
243E ASP 3.4 9.4 - - - +
244E ARG* 3.5 25.3 + - + +
257E ALA* 1.3 77.2 - - - +
259E PHE* 1.3 75.0 + - - +
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Residues in contact with PHE 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ILE* 4.6 1.1 - - - -
94E ILE* 3.3 36.6 - - + +
95E PRO 5.2 0.2 - - - -
96E PHE* 4.5 17.0 - + + -
99E VAL* 6.0 1.8 - - + -
102E PRO* 5.1 2.7 - - + -
104E ILE* 4.7 3.6 - - + -
139E VAL* 3.8 35.0 - - + -
239E VAL* 3.5 37.7 - - + -
240E ASN 4.2 6.5 - - - +
242E GLY* 3.0 28.2 - - - +
243E ASP 2.8 20.0 + - - +
245E PHE* 3.9 20.0 - + - -
257E ALA* 4.7 11.9 - - + -
258E THR* 1.3 83.6 - - - +
260E SER* 1.3 66.6 + - - +
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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