Contacts of the strand formed by residues 255 - 259 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P ASP* 3.6 3.4 - - - +
135P PRO* 3.8 7.9 - - + +
136P ALA 3.7 31.2 - - - +
137P LEU* 3.8 16.0 - - + +
165P VAL* 3.5 32.8 - - + +
166P ILE 3.6 0.7 - - - -
167P GLY* 3.2 31.4 - - - +
246P GLU* 3.2 5.7 - - - +
247P ALA* 2.8 38.6 + - + +
249P ILE* 5.0 1.8 - - + -
254P SER* 1.3 74.8 - - - +
256P ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90P ASP* 2.8 9.9 + - - +
91P ASN* 2.8 30.0 + - - -
92P GLU 4.3 0.3 + - - -
137P LEU* 4.1 3.1 - - - -
165P VAL* 3.6 8.1 - - - +
244P ARG* 3.9 21.8 - - - +
245P PHE 3.1 11.0 - - - +
246P GLU* 4.3 3.1 - - + -
255P VAL* 1.3 76.3 - - - +
257P ALA* 1.3 62.6 + - - +
179S LYS* 3.9 23.8 - - - +
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Residues in contact with ALA 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P ASN* 4.8 0.9 - - - +
92P GLU 4.0 8.1 - - - +
94P ILE* 3.8 26.2 - - + -
104P ILE* 6.1 0.9 - - + -
137P LEU* 4.0 8.5 - - + +
139P VAL* 5.9 0.4 - - + -
165P VAL* 3.9 16.2 - - + -
243P ASP 4.1 0.5 - - - +
244P ARG* 3.5 2.0 - - - +
245P PHE* 2.8 34.7 + - + +
256P ALA* 1.3 76.1 - - - +
258P THR* 1.3 65.0 + - - +
259P PHE* 4.7 9.9 - - + -
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Residues in contact with THR 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P ASN* 4.3 11.4 + - - -
92P GLU 3.2 12.2 + - - -
93P ILE* 3.3 16.7 - - + -
94P ILE* 2.8 26.9 + - - +
242P GLY 4.3 5.8 - - - +
243P ASP 3.5 10.1 - - - +
244P ARG* 3.5 25.8 + - + +
257P ALA* 1.3 77.6 - - - +
259P PHE* 1.3 75.0 + - - +
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Residues in contact with PHE 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P ILE* 4.6 1.3 - - - -
94P ILE* 3.3 41.1 - - + +
95P PRO 5.2 0.2 - - - -
96P PHE* 4.4 17.5 - + + -
99P VAL* 6.0 1.8 - - + -
102P PRO* 5.2 3.4 - - + -
104P ILE* 4.7 3.1 - - + -
139P VAL* 3.8 38.4 - - + -
239P VAL* 3.6 34.5 - - + -
240P ASN 4.3 11.9 - - - +
242P GLY* 3.1 19.6 - - - -
243P ASP 2.9 19.8 + - - +
245P PHE* 4.0 19.7 - + + -
257P ALA* 4.7 8.5 - - + -
258P THR* 1.3 81.8 - - - +
260P SER* 1.3 68.7 + - - +
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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