Contacts of the strand formed by residues 501 - 510 (chain A) in PDB entry 6KC4
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 501 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A VAL 3.7 0.2 - - - +
497A TYR* 3.4 10.4 - - - -
498A SER 2.8 35.2 + - - +
499A ASP* 3.8 8.3 - - - +
500A GLY* 1.3 84.2 - - - +
502A ARG* 1.3 68.7 + - - +
503A ARG* 3.8 20.8 + - + +
519I THR* 3.4 30.6 - - - +
520I GLY 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLN* 3.0 50.2 + - + +
472A GLU* 5.2 0.6 - - - +
474A LEU* 3.0 49.0 + - + -
475A LYS* 4.6 4.9 - - - +
496A VAL 3.3 4.9 - - - +
497A TYR* 3.8 18.3 + - + -
500A GLY 5.8 1.0 + - - -
501A GLN* 1.3 79.1 + - - +
503A ARG* 1.3 62.2 + - - +
504A HIS* 3.9 24.9 - - + +
4B GLU* 4.9 1.7 - - - +
522I SER* 5.8 1.8 + - - -
526I GLN* 4.4 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU 3.7 1.4 - - - +
495A SER* 3.4 2.8 - - - -
496A VAL* 2.8 36.6 + - + +
498A SER* 4.1 18.3 + - - -
499A ASP* 5.1 8.9 + - - +
501A GLN* 4.2 26.2 - - + +
502A ARG* 1.3 78.1 - - - +
504A HIS* 1.3 63.0 + - - +
505A PHE* 3.9 11.6 - - + -
541A LYS* 4.8 11.5 + - - +
542A SER* 3.5 40.4 + - - +
544A VAL* 3.8 18.9 - - - +
4B GLU* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 3.4 43.6 + - + +
470A ALA* 4.8 7.6 - - + -
471A GLN* 5.8 0.9 - - - -
474A LEU* 5.0 1.1 - - + -
483A ARG* 3.1 16.3 + - - -
493A VAL* 3.9 2.5 - - + -
494A LEU 3.6 3.6 - - - -
495A SER* 2.8 32.8 + - - -
502A ARG* 3.9 31.2 + - + +
503A ARG* 1.3 75.3 + - - +
505A PHE* 1.3 61.4 + - - +
2B GLU 4.5 3.5 + - - +
3B PTR 3.4 27.1 - - + -
4B GLU* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 3.3 5.5 - - - +
494A LEU* 2.8 54.4 + - + +
496A VAL* 4.5 10.1 - - + -
503A ARG* 3.9 21.3 - - + -
504A HIS* 1.3 74.6 - - - +
506A ILE* 1.3 62.3 - - - +
516A PHE* 3.9 18.4 - - + -
538A ILE* 3.8 25.6 - - + -
539A THR* 3.9 18.6 - - + -
542A SER* 3.5 33.4 - - - -
544A VAL* 4.1 13.9 - - + -
4B GLU* 3.7 26.0 - - + -
5B ASN* 3.4 13.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
485A SER* 4.5 0.4 - - - +
488A LYS* 3.9 21.5 - - + -
491A GLU* 3.9 34.3 - - + +
492A TYR 3.5 11.0 - - - +
493A VAL* 4.1 4.9 - - + -
504A HIS 4.1 0.6 + - - -
505A PHE* 1.3 72.1 - - - +
507A ILE* 1.3 66.0 + - - +
508A GLN* 3.3 19.9 + - - +
516A PHE* 3.8 4.7 - - - -
3B PTR 3.8 35.4 - - + -
5B ASN* 2.7 31.4 + - - -
6B VAL* 3.4 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A VAL* 4.2 13.9 - - + -
491A GLU* 4.1 5.9 - - - +
492A TYR* 2.9 40.2 + - + +
494A LEU* 4.0 20.0 - - + +
506A ILE* 1.3 74.1 - - - +
508A GLN* 1.3 65.1 + - - +
509A TYR* 3.4 4.9 + - - +
514A TYR* 4.0 25.1 - - + -
515A ARG 4.1 2.7 - - - +
516A PHE* 3.7 20.6 - - + -
524A ILE* 4.0 25.8 - - + -
527A LEU* 3.7 26.9 - - + -
528A ILE* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLU* 5.2 0.9 - - - -
506A ILE* 3.7 16.9 - - - +
507A ILE* 1.3 71.4 - - - +
509A TYR* 1.3 58.8 + - - +
510A VAL* 4.0 17.6 - - + +
513A MET 3.4 0.9 - - - +
514A TYR* 3.1 6.6 - - - +
515A ARG* 3.0 51.4 + - + +
516A PHE 4.2 11.4 - - - +
5B ASN* 3.9 10.4 + - - +
6B VAL* 3.0 32.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLU* 4.8 9.2 + - - +
507A ILE 3.4 3.7 + - - +
508A GLN* 1.3 72.9 - - - +
510A VAL* 1.3 65.9 + - - +
511A ASP 5.8 0.2 - - - -
512A ASN* 3.4 41.7 + - - +
513A MET 3.3 10.1 - - - -
514A TYR* 3.5 46.9 - + + -
522A SER 5.4 0.2 - - - -
467E ARG* 4.9 5.7 - - + +
468E ILE* 6.3 1.3 - - + -
1F ASP* 2.5 37.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLN* 4.0 18.4 - - + +
509A TYR* 1.3 84.7 - - - +
511A ASP* 1.3 81.0 + - + +
512A ASN 3.2 1.1 - - - -
513A MET* 2.9 24.2 + - - +
515A ARG* 4.2 20.5 + - + +
----------------------------------------------------------
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