Contacts of the strand formed by residues 258 - 261 (chain Q) in PDB entry 2GLJ
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 MET 258 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251Q ASP* 3.7 1.0 - - - +
252Q TYR* 2.8 47.6 + - + +
256Q ARG 4.2 0.3 - - - +
257Q SER* 1.3 78.8 - - - +
259Q VAL* 1.3 64.5 + - - +
363Q LEU* 3.8 16.6 - - + -
438Q LEU* 4.4 1.6 - - + -
446Q ILE* 3.6 28.7 - - + -
447Q SER 2.9 15.0 - - - +
448Q SER* 4.3 0.2 - - - -
449Q LYS* 3.7 9.5 - - - -
200T ASN* 3.2 26.2 - - - +
202T LEU* 4.6 2.2 - - - -
203T ILE* 3.1 57.9 - - + -
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Residues in contact with VAL 259 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Q ARG* 4.1 9.9 - - + -
33Q ASN* 5.2 5.2 - - - +
34Q PHE* 4.0 23.8 - - + -
37Q ASN* 5.4 2.0 - - - +
249Q ALA* 4.5 5.8 - - + -
250Q ARG 3.4 13.9 - - - +
252Q TYR* 4.1 2.9 - - - +
258Q MET* 1.3 80.5 - - - +
260Q MET* 1.3 62.4 + - - +
264Q GLN* 2.7 26.2 - - - +
446Q ILE* 3.2 2.5 - - - -
447Q SER* 2.8 33.5 + - - +
449Q LYS* 3.7 27.6 - - + -
452Q ILE* 4.2 15.0 - - + -
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Residues in contact with MET 260 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249Q ALA* 3.3 4.9 - - - +
250Q ARG* 2.9 33.8 + - + +
252Q TYR* 3.4 49.8 - - + +
259Q VAL* 1.3 73.2 - - - +
261Q GLY* 1.3 60.7 + - - +
264Q GLN* 3.9 0.7 - - - -
439Q ASN* 5.8 0.9 - - - +
444Q TRP* 3.8 23.2 - - + +
445Q GLU 3.1 7.4 - - - +
446Q ILE* 4.1 14.8 - - + +
142T THR 3.7 20.0 - - - +
144T PRO* 3.8 29.8 - - + -
171T VAL* 4.0 14.1 - - + -
172T PHE 4.4 5.4 - - - +
173T GLY* 4.4 7.0 - - - -
174T VAL 5.7 0.9 - - - +
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Residues in contact with GLY 261 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q ASN* 4.0 4.7 - - - -
249Q ALA* 4.0 13.0 - - - -
260Q MET* 1.3 77.5 - - - +
262Q TYR* 1.3 62.9 + - - -
264Q GLN* 3.0 17.8 + - - +
444Q TRP* 3.6 15.7 - - - -
445Q GLU* 2.9 27.8 + - - +
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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