Contacts of the strand formed by residues 522 - 530 (chain A) in PDB entry 2G5T
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 THR 522 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A ILE* 3.3 7.3 - - - +
519A LEU 3.0 31.1 + - - +
520A ASN* 4.1 4.0 + - - -
521A GLU* 1.3 85.0 + - - +
523A LYS* 1.3 79.0 + - - +
524A PHE* 3.5 28.5 - - + -
589A LYS* 4.8 12.3 + - - +
590A ILE* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLY 5.4 4.1 + - - -
516A PHE* 3.2 52.1 - - + -
517A ILE 3.6 5.4 - - - -
518A ILE* 4.6 8.1 - - + +
521A GLU 5.8 0.4 - - - +
522A THR* 1.3 86.9 - - - +
524A PHE* 1.3 62.8 + - - +
525A TRP* 4.2 22.4 - - - +
586A GLN* 4.2 11.6 + - - -
590A ILE* 4.5 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PHE* 3.2 3.5 - - - +
517A ILE* 2.9 38.0 + - + +
519A LEU* 3.6 37.9 - - + -
520A ASN* 5.3 1.3 - - - -
522A THR* 3.5 35.7 - - + -
523A LYS* 1.3 74.4 - - - +
525A TRP* 1.3 62.1 + - - +
526A TYR* 4.3 0.3 - - - -
578A PHE* 3.5 23.6 - + + -
579A ASP 3.4 16.8 - - - +
580A GLY* 3.8 23.1 - - - -
581A ARG* 3.9 22.2 - - - -
586A GLN* 5.0 2.7 - - - +
590A ILE* 4.1 25.6 - - + -
605A ASP* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS 5.6 0.4 - - - -
424A GLY 3.8 17.3 - - - -
425A MET* 4.0 25.8 - - + -
426A PRO* 3.6 31.5 - - + +
427A GLY 5.8 1.3 - - - -
514A LEU* 3.3 38.1 - - + -
515A ASP* 3.3 24.7 - - - -
516A PHE* 3.9 27.3 - + + +
523A LYS* 4.4 22.1 - - - +
524A PHE* 1.3 76.7 - - - +
526A TYR* 1.3 63.7 + - - +
555A ALA* 4.0 15.0 - - + +
578A PHE* 3.4 4.5 - - - -
579A ASP* 3.1 33.0 + - + +
586A GLN* 4.2 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A LYS* 4.1 12.6 - - + +
514A LEU* 3.5 5.5 - - - +
515A ASP* 2.7 72.3 + - + +
516A PHE* 3.6 20.4 + - - -
517A ILE* 3.8 16.8 - - + +
524A PHE 4.3 1.1 - - - -
525A TRP* 1.3 77.9 - - - +
527A GLN* 1.3 72.0 + - - +
528A MET* 4.0 20.9 - - + -
555A ALA* 3.6 7.2 - - - -
577A SER 3.1 16.4 - - - +
578A PHE* 3.8 12.3 - - + -
613A PHE* 3.7 30.5 - + + -
616A MET* 3.6 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 527 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LYS* 3.1 38.7 + - + +
513A LYS 3.0 11.0 - - - +
514A LEU* 4.6 2.5 - - - -
526A TYR* 1.3 75.8 - - - +
528A MET* 1.3 68.3 + - - +
529A ILE* 4.1 14.3 - - + +
554A LYS 3.0 20.9 + - - +
555A ALA* 4.0 3.8 - - - -
556A ASP* 3.0 28.0 + - - +
560A ARG* 4.6 7.3 - - - +
575A VAL 5.4 1.5 + - - +
576A ALA* 3.2 5.4 - - - +
577A SER* 3.0 44.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 528 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A SER 3.3 0.2 - - - +
512A LYS* 3.1 5.2 - - - -
513A LYS* 2.7 46.3 + - + +
526A TYR* 4.0 23.8 - - + -
527A GLN* 1.3 81.3 - - - +
529A ILE* 1.3 63.8 + - - +
530A LEU* 3.3 22.3 + - + +
542A LEU* 4.6 5.6 - - + -
574A ILE* 3.1 30.5 - - + -
575A VAL 3.8 3.8 - - - -
576A ALA* 3.8 15.7 - - + -
613A PHE* 4.8 11.9 - - - -
616A MET* 4.8 1.8 - - - +
618A PHE* 3.2 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A PRO* 4.0 17.9 - - + -
511A SER 3.4 4.3 - - - +
512A LYS* 4.0 31.6 - - + -
527A GLN* 4.1 12.6 - - - +
528A MET* 1.3 71.9 - - - +
530A LEU* 1.3 61.1 + - - +
564A ALA* 4.3 21.5 - - + +
565A THR* 4.7 2.0 - - - +
568A ALA* 3.8 21.8 - - + +
574A ILE* 3.5 7.4 - - - -
575A VAL* 3.0 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A PRO* 3.0 6.5 - - - +
511A SER* 2.7 50.1 + - - +
512A LYS 5.4 0.2 - - - -
513A LYS* 4.0 31.4 - - + +
528A MET* 3.4 42.2 - - + +
529A ILE* 1.3 72.1 - - - +
531A PRO* 1.3 69.9 - - + +
534A PHE* 3.5 49.1 - - + -
568A ALA* 4.2 0.7 - - - -
574A ILE* 4.0 7.9 - - + -
----------------------------------------------------------
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