Contacts of the strand formed by residues 501 - 510 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496E VAL 3.7 0.3 - - - +
497E TYR* 3.5 5.7 - - - -
498E SER 2.9 29.9 + - - +
499E ASP 4.2 3.3 + - - +
500E GLY* 1.3 84.9 - - - +
502E ARG* 1.3 67.2 + - - +
503E ARG* 3.5 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 502 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471E GLN* 3.2 43.3 + - + +
472E GLU* 5.3 0.8 - - - +
474E LEU* 2.8 50.7 + - + -
475E LYS* 4.2 9.7 - - - +
496E VAL 3.4 4.5 - - - +
497E TYR* 3.7 23.0 - - + -
500E GLY 5.5 2.4 + - - -
501E GLN* 1.3 76.0 - - - +
503E ARG* 1.3 62.8 + - - +
504E HIS* 4.0 24.5 - - + +
4F GLU* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 503 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E LEU 3.6 1.9 - - - +
495E SER* 3.3 3.3 - - - -
496E VAL* 2.7 41.7 + - - +
498E SER* 2.9 34.3 + - - -
499E ASP* 3.5 19.5 + - - +
501E GLN* 3.5 33.4 + - + +
502E ARG* 1.3 79.4 - - - +
504E HIS* 1.3 63.9 + - - +
505E PHE* 4.0 12.2 - - + -
542E SER* 5.2 4.8 + - - +
544E VAL* 3.9 23.5 - - + +
4F GLU* 3.6 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 504 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467E ARG* 3.5 41.0 + - + +
470E ALA* 4.7 7.6 - - + -
471E GLN* 5.4 3.4 - - - +
474E LEU* 4.9 2.0 - - + -
483E ARG* 3.1 16.2 + - - -
493E VAL* 3.9 2.2 - - + -
494E LEU 3.5 3.1 - - - -
495E SER* 2.7 34.2 + - - -
502E ARG* 4.0 29.4 + - + +
503E ARG* 1.3 77.3 - - - +
505E PHE* 1.3 62.2 + - - +
2F GLU 4.4 3.6 + - - +
3F PTR 3.4 28.3 - - + -
4F GLU* 2.8 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 505 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493E VAL* 3.3 5.4 - - - +
494E LEU* 2.8 56.1 + - + +
496E VAL* 4.3 2.9 - - + -
503E ARG* 4.0 20.2 - - + -
504E HIS* 1.3 74.1 - - - +
506E ILE* 1.3 63.9 + - - +
507E ILE 3.5 0.2 + - - -
516E PHE* 3.8 18.2 - - + -
538E ILE* 3.8 25.8 - - + -
539E THR* 4.0 11.7 - - + -
542E SER* 3.5 34.1 - - - -
544E VAL* 3.8 22.9 - - + -
4F GLU* 3.6 28.0 - - + -
5F ASN* 3.4 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485E SER* 4.4 0.2 - - - +
488E LYS* 3.9 20.6 - - + -
491E GLU* 3.9 31.4 - - + +
492E TYR 3.6 2.9 - - - +
493E VAL* 4.0 12.6 - - + -
504E HIS 4.1 0.8 + - - -
505E PHE* 1.3 71.9 - - - +
507E ILE* 1.3 72.6 + - - +
508E GLN* 3.4 8.4 + - + +
515E ARG 4.7 0.2 - - - +
516E PHE* 3.7 4.9 - - - -
3F PTR 3.8 35.2 - - + -
5F ASN* 2.8 30.7 + - - +
6F VAL* 3.6 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E VAL* 4.2 15.7 - - + -
491E GLU* 3.9 7.3 - - - +
492E TYR* 2.9 42.4 + - + +
494E LEU* 4.1 13.0 - - + +
506E ILE* 1.3 77.0 - - - +
508E GLN* 1.3 64.2 - - - +
509E TYR* 3.5 4.3 + - - +
514E TYR* 4.0 27.4 - - + -
515E ARG 4.2 0.4 - - - +
516E PHE* 3.8 24.9 - - + -
524E ILE* 4.1 23.3 - - + -
527E LEU* 3.7 24.7 - - + -
528E ILE* 4.7 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491E GLU* 5.2 1.1 - - - -
506E ILE* 3.4 11.6 + - + +
507E ILE* 1.3 73.1 - - - +
509E TYR* 1.3 60.5 + - - +
510E VAL* 3.6 31.8 - - + +
513E MET 3.5 0.5 - - - +
514E TYR* 3.2 6.9 - - - +
515E ARG* 2.6 78.5 + - + +
516E PHE* 4.1 5.5 - - - +
5F ASN* 6.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 509 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C ARG* 4.7 4.3 - - - +
468C ILE* 6.0 3.0 + - + +
1D ASP* 2.6 46.4 + - - -
491E GLU* 4.9 7.9 + - - +
507E ILE 3.5 3.7 + - - +
508E GLN* 1.3 74.7 - - - +
510E VAL* 1.3 65.6 - - - +
512E ASN* 3.6 36.1 + - - +
513E MET 3.3 10.3 - - - -
514E TYR* 3.5 46.2 - + + -
522E SER 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E GLN* 3.6 42.4 - - + +
509E TYR* 1.3 80.5 - - - +
511E ASP* 1.3 79.3 + - - +
512E ASN 3.2 2.2 - - - -
513E MET* 2.9 24.5 + - + +
515E ARG* 3.8 20.0 - - - +
----------------------------------------------------------
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