Contacts of the strand formed by residues 464 - 468 (chain A) in PDB entry 1GPU
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 ILE 464 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 5.8 0.4 - - + -
425A MET* 3.7 3.2 - - - +
436A LYS* 5.8 2.7 - - + +
437A PRO 3.3 9.1 + - - +
438A TYR* 3.0 25.2 - - + +
439A GLY 2.8 26.0 + - - -
462A PRO 4.0 8.5 - - - +
463A VAL* 1.3 79.8 - - - +
465A TRP* 1.3 70.9 + - - +
466A VAL* 4.4 5.2 - - + -
511A TYR* 4.7 8.3 - - + -
514A SER* 3.8 30.5 - - - +
515A LEU* 3.6 33.0 - - + -
522A SER* 3.4 7.0 - - - +
524A ILE* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 3.6 15.0 - - + -
421A MET* 3.5 26.7 - - + -
422A GLY* 3.4 26.1 + - - -
425A MET* 3.6 18.7 - - + +
439A GLY 3.4 5.2 - - - -
441A THR* 3.9 15.5 - - + -
446A VAL* 3.9 27.6 - - + -
449A ALA* 3.5 22.9 - - + -
453A VAL* 3.8 29.9 - - + +
456A SER* 5.1 1.6 + - - -
463A VAL* 4.1 14.9 - - + +
464A ILE* 1.3 73.6 - - - +
466A VAL* 1.3 61.2 + - - +
467A ALA 3.3 3.5 + - - +
496A ILE* 6.0 0.7 - - + -
521A PRO* 6.0 0.9 - - + -
522A SER 2.8 20.9 + - - +
523A ILE* 4.1 21.5 - - + -
524A ILE* 2.8 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER* 3.8 10.1 - - - +
366A LEU* 5.2 0.4 - - + -
387A ASN* 4.5 2.3 - - - +
389A THR* 3.7 24.7 - - + -
438A TYR* 3.8 31.0 - - + -
439A GLY 2.8 11.9 + - - +
440A GLY* 3.1 18.9 - - - -
441A THR* 3.2 7.3 + - - +
464A ILE* 4.4 9.6 - - + -
465A TRP* 1.3 70.8 - - - +
467A ALA* 1.3 57.8 + - - +
468A THR* 3.6 10.5 + - + +
511A TYR* 3.5 17.7 - - + +
524A ILE* 4.1 4.0 - - + -
526A LEU* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A THR 3.3 6.5 - - - +
443A LEU* 3.7 39.2 - - + +
446A VAL* 3.9 13.5 - - + -
465A TRP 3.3 1.9 + - - +
466A VAL* 1.3 69.3 - - - +
468A THR* 1.3 64.1 + - - +
470A ASP* 4.6 0.2 - - - +
523A ILE* 4.2 9.6 - - + -
524A ILE 3.0 15.5 + - - +
525A ALA* 3.3 3.2 - - - -
526A LEU* 2.8 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 3.9 15.9 - - + -
387A ASN* 2.8 54.0 + - + +
441A THR 3.2 4.4 + - - -
442A PHE* 3.4 4.0 - - - -
443A LEU 2.9 19.9 + - - -
466A VAL* 4.4 4.5 - - + -
467A ALA* 1.3 73.1 - - - +
469A HIS* 1.3 95.2 + - - +
526A LEU* 3.3 26.5 - - + -
----------------------------------------------------------
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