Contacts of the strand formed by residues 510 - 513 (chain B) in PDB entry 2GQ3
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 GLN 510 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLU 4.0 8.5 + - - -
109B ILE* 3.6 25.2 + - + +
112B THR 5.2 3.6 + - - +
114B GLY 5.4 0.6 + - - -
116B GLN* 3.3 19.2 + - - +
266B ILE* 6.0 0.2 - - - +
267B THR* 3.5 32.1 + - - +
337B PHE* 3.8 6.6 - - - -
454B VAL 2.9 9.7 + - - -
455B PHE* 3.3 25.2 - - + +
456B ILE 3.2 23.0 + - - -
505B PHE* 3.3 8.0 - - - -
509B ALA* 1.4 70.7 - - - +
511B VAL* 1.3 61.1 + - - +
512B GLY 3.7 0.4 - - - -
538B SER* 3.4 11.4 - - - +
539B THR* 3.8 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ILE* 3.9 4.3 - - + -
496B ASN* 3.8 21.5 - - - +
497B VAL* 4.0 29.2 - - + -
500B GLY* 4.5 5.8 - - - -
501B LEU* 4.3 12.3 - - + +
505B PHE* 3.8 33.2 - - + -
509B ALA 3.8 0.9 + - - +
510B GLN* 1.3 70.5 - - - +
512B GLY* 1.3 60.5 + - - +
513B LYS* 5.7 0.7 - - - +
536B GLY 4.3 4.7 - - - +
537B ALA* 3.0 9.1 - - + -
538B SER* 2.8 35.6 + - - -
539B THR 3.5 1.4 + - - -
564B GLN* 4.1 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B PHE* 6.2 0.2 - - - -
456B ILE 2.8 15.3 + - - -
457B ASN* 3.2 21.5 - - - -
458B THR* 3.1 21.7 + - - -
496B ASN* 4.1 6.9 - - - +
510B GLN 3.7 1.2 - - - -
511B VAL* 1.3 75.0 - - - +
513B LYS* 1.3 65.7 + - - +
539B THR* 3.1 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ASN* 3.1 18.6 + - - -
458B THR* 3.6 12.2 + - - +
493B GLU* 2.8 59.7 + - - +
494B ASP* 6.0 0.4 - - - -
496B ASN* 4.8 1.6 + - - -
497B VAL* 3.4 22.1 - - + +
511B VAL* 6.0 0.4 - - + -
512B GLY* 1.3 77.3 + - - +
514B GLY* 1.3 63.3 + - - +
532B GLN* 3.5 35.2 - - + +
535B ALA* 4.0 20.4 - - + -
537B ALA* 3.7 18.2 - - + -
539B THR 3.0 8.5 + - - -
540B ALA* 3.4 3.5 - - + -
541B TRP* 3.3 16.5 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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