Contacts of the strand formed by residues 502 - 513 (chain A) in PDB entry 3QGT
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 LYS 502 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A TYR* 3.6 2.3 - - - +
498A VAL* 3.3 6.9 - - - +
499A PHE* 2.7 52.4 + - - +
500A ASP* 3.2 39.7 + - - +
501A GLY* 1.3 77.3 - - - +
503A LEU* 1.3 60.5 + - - +
504A SER* 4.0 0.6 + - - -
538A LEU* 4.4 1.5 - - - +
539A GLN* 3.3 19.7 - - + +
540A PRO 5.4 1.3 - - - +
541A ALA* 4.1 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ILE* 3.9 14.8 - - + -
496A PHE* 3.9 26.7 - - + -
497A TYR 3.5 6.1 - - - +
498A VAL* 3.5 27.1 - - + +
502A LYS* 1.3 71.7 - - - +
504A SER* 1.3 65.2 + - - +
529A THR* 3.9 17.8 - - + +
532A ILE* 3.8 17.7 - - + -
533A ALA* 3.7 32.1 - - + +
538A LEU* 4.1 13.8 - - + +
539A GLN 2.9 13.5 + - - +
540A PRO* 3.7 3.5 - - - +
541A ALA 2.9 22.7 + - - +
542A GLN 4.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A PHE* 3.4 8.3 - - - -
497A TYR* 2.8 43.9 + - - +
502A LYS 4.0 0.7 + - - -
503A LEU* 1.3 73.7 - - - +
505A CYS* 1.3 61.8 - - - +
541A ALA* 3.3 9.5 - - - +
542A GLN* 3.2 35.7 + - - +
544A ILE* 5.1 1.3 - - - -
354B PHE* 4.0 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A CYS* 3.8 23.8 - - - -
495A GLN 3.4 5.4 - - - -
496A PHE* 3.7 24.2 - - + -
503A LEU 4.4 0.2 + - - -
504A SER* 1.3 76.0 - - - +
506A ILE* 1.3 71.5 + - - +
507A MET 4.6 0.2 - - - -
525A TYR* 5.3 2.0 - - - -
528A PHE* 5.7 1.3 - - - -
529A THR* 3.4 26.0 - - + +
542A GLN 2.8 10.5 + - - +
543A PHE* 3.5 12.4 - - + -
544A ILE* 2.7 33.4 + - - +
354B PHE* 4.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 3.8 1.9 - - + +
494A CYS* 3.2 4.9 - - - -
495A GLN* 2.8 33.0 + - + +
505A CYS* 1.3 75.6 - - - +
507A MET* 1.3 66.8 + - - +
508A TYR 4.6 0.2 - - - +
544A ILE* 3.3 22.2 - - + +
546A VAL* 3.9 26.7 - - + -
354B PHE* 3.3 39.7 - - + -
355B GLY* 3.9 16.2 - - - -
508B TYR* 3.7 25.4 - - + +
546B VAL* 6.1 0.4 - - + -
547B LEU 4.3 1.3 - - - +
548B GLY* 3.7 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A HIS* 3.4 23.3 - - + -
493A LEU 3.3 11.4 - - - +
494A CYS* 4.1 7.6 - - - -
506A ILE* 1.3 78.9 - - - +
508A TYR* 1.3 79.8 + - - +
509A GLN* 3.2 29.8 - - - +
521A ASN* 4.6 2.7 - - + -
525A TYR* 3.7 34.5 - - + -
543A PHE* 3.7 22.4 - - + -
544A ILE 2.9 7.4 + - - +
545A HIS* 3.3 18.2 - - + +
546A VAL* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ILE* 3.0 42.2 + - + +
493A LEU* 3.0 26.9 + - + +
506A ILE* 4.2 0.4 - - - +
507A MET* 1.3 76.7 - - - +
509A GLN* 1.3 57.5 + - - +
510A ARG* 3.9 12.1 - - + -
546A VAL* 3.6 31.4 - - + -
548A GLY* 3.7 16.5 - - - -
473B LEU* 5.3 0.7 - - + -
493B LEU* 4.2 20.6 - - + -
495B GLN* 2.6 34.8 + - - +
506B ILE* 3.6 33.2 - - + +
508B TYR* 4.1 26.5 - + + -
546B VAL* 4.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A CYS* 3.3 15.7 - - - +
491A HIS* 3.4 15.7 - - + -
507A MET* 3.2 12.5 - - - +
508A TYR* 1.3 76.5 - - - +
510A ARG* 1.3 61.6 + - - +
511A SER 3.0 23.4 + - - +
512A CYS* 3.6 21.8 - - - +
518A VAL* 4.4 2.8 - - - +
521A ASN* 3.0 22.2 + - - +
545A HIS* 2.7 35.5 + - - +
546A VAL 2.9 14.5 + - - +
548A GLY* 2.8 28.4 + - - -
611A UMP 3.6 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TRP* 3.6 15.5 - - - -
488A PRO* 3.2 25.7 + - - +
489A PRO 2.7 19.3 + - - -
490A CYS* 3.0 23.8 + - - +
492A ILE* 3.7 23.0 - - + +
508A TYR* 3.9 4.3 + - + -
509A GLN* 1.3 72.1 - - - +
511A SER* 1.3 68.4 + - - +
549A ASN* 2.9 25.1 + - - +
611A UMP 2.8 41.0 + - - -
470B ARG 2.8 34.8 + - - +
471B ARG* 3.6 13.1 - - - +
473B LEU* 4.0 8.1 - - + -
495B GLN* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A CYS* 4.0 9.5 + - - +
509A GLN* 3.0 19.1 + - - +
510A ARG* 1.3 95.6 - - - +
512A CYS* 1.3 61.6 + - - +
549A ASN* 3.5 4.5 - - - -
551A HIS* 3.2 7.8 - - - -
611A UMP 2.7 44.5 + - - +
470B ARG* 3.2 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLN* 3.6 33.0 - - - +
511A SER* 1.3 80.1 - - - +
513A ASP* 1.3 59.9 + - - +
514A LEU* 3.2 5.4 + - + -
518A VAL* 3.8 16.8 - - + -
547A LEU* 3.6 32.8 - - + -
548A GLY 4.1 0.4 - - - -
549A ASN 2.8 18.4 + - - +
550A ALA* 4.1 7.0 - - + -
551A HIS* 2.9 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A CYS* 1.3 68.4 - - - +
514A LEU* 1.3 63.5 + - - +
515A GLY* 3.2 6.4 + - - -
516A LEU* 3.1 33.9 + - - +
517A GLY 3.0 19.8 + - - +
518A VAL* 3.0 10.7 + - - +
551A HIS* 3.8 8.7 - - - +
553A TYR* 3.5 26.4 + - - -
556A HIS* 3.8 10.2 + - - -
611A UMP 3.1 38.8 + - + +
----------------------------------------------------------
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