Contacts of the strand formed by residues 631 - 640 (chain E) in PDB entry 2VKX
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 631 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601E PRO* 4.3 14.4 - - + -
602E SER 5.4 1.1 - - - +
623E LYS* 6.1 0.7 - - + -
624E GLN 5.1 5.6 - - - +
626E ASP* 3.9 26.9 - - + -
630E PRO* 1.3 72.5 - - - +
632E ARG* 1.3 59.6 + - - +
633E HIS 3.8 19.5 - - - +
634E TYR* 3.8 26.0 - - + +
653E SER* 2.9 39.6 - - - +
675E ALA* 4.1 17.5 - - + -
676E GLU 3.5 14.4 - - - +
677E ASN* 4.2 0.2 - - - -
507F GLN* 2.6 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630E PRO 3.6 2.3 + - - +
631E ILE* 1.3 77.3 - - - +
633E HIS* 1.3 99.7 + - + +
650E ARG* 4.5 4.8 - - - +
652E PRO* 4.7 0.3 - - - +
653E SER* 3.9 11.3 + - - -
676E GLU* 2.8 27.5 + - + +
677E ASN* 4.5 2.9 - - - -
678E GLN* 4.3 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 633 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631E ILE* 3.7 7.3 - - - +
632E ARG* 1.3 123.1 + - + +
634E TYR* 1.3 67.3 - - - +
635E LEU* 4.6 8.5 - - + -
650E ARG* 2.7 44.2 + - + +
651E LEU 3.5 18.1 + - - +
652E PRO* 4.7 4.6 - - + +
653E SER 4.9 0.7 - - - +
675E ALA 3.8 0.2 - - - -
676E GLU* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 634 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604E PRO* 4.1 20.0 - - + +
621E LEU* 3.7 26.9 - - + -
623E LYS* 3.4 35.3 + - + +
624E GLN 5.7 0.2 + - - -
631E ILE* 3.8 19.6 - - + +
633E HIS* 1.3 74.4 - - - +
635E LEU* 1.3 62.1 + - - +
636E VAL* 5.0 0.4 - - - -
649E ILE 3.4 3.6 - - - +
650E ARG* 3.5 2.9 - - - -
651E LEU* 2.9 45.8 + - + +
652E PRO 3.6 17.7 - - - -
653E SER* 3.6 26.8 + - - -
655E SER* 4.4 1.8 - - - -
673E VAL* 4.4 14.6 - - + -
674E VAL 3.3 2.7 - - - +
675E ALA* 3.9 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 635 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633E HIS* 4.6 8.5 - - + +
634E TYR* 1.3 77.7 - - - +
636E VAL* 1.3 62.4 + - - +
637E ARG* 5.6 0.2 - - - +
648E GLU* 3.8 28.9 - - - +
649E ILE 3.6 0.4 - - - -
650E ARG* 3.5 35.2 - - + +
672E TYR 3.4 2.1 - - - +
673E VAL* 3.2 3.9 - - - -
674E VAL* 2.6 51.2 + - + +
676E GLU* 4.3 12.6 - - + +
681E LYS* 3.8 37.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 636 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634E TYR 4.9 1.1 - - - +
635E LEU* 1.3 77.2 - - - +
637E ARG* 1.3 66.0 + - - +
638E TYR* 4.7 11.3 - - + -
647E PRO 4.9 0.2 - - - +
648E GLU* 3.5 9.1 - - - +
649E ILE* 2.9 48.2 + - + +
651E LEU* 3.9 28.7 - - + -
658E VAL* 4.3 19.5 - - + -
660E LEU* 5.1 1.8 - - + -
671E VAL* 3.5 26.5 - - + -
672E TYR 3.3 2.9 - - - -
673E VAL* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 637 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636E VAL* 1.3 73.6 - - - +
638E TYR* 1.3 62.7 + - - +
645E TRP* 3.3 55.3 - - + +
646E LYS 5.4 5.6 - - - +
647E PRO 6.2 0.2 - - - -
648E GLU* 3.5 36.6 - - + +
671E VAL* 3.4 1.1 - - - +
672E TYR* 2.7 58.6 + - + +
674E VAL* 5.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 638 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636E VAL* 4.7 8.1 - - + -
637E ARG* 1.3 78.3 - - - +
639E ARG* 1.3 71.6 + - - +
645E TRP* 3.4 8.6 - - - -
646E LYS* 3.1 69.0 + - + +
647E PRO* 5.2 2.2 - - + +
649E ILE* 4.2 16.4 - - + -
660E LEU* 3.8 36.1 - - + +
661E LYS 5.2 2.6 + - - -
663E LEU* 4.0 23.0 - - + +
669E TYR* 4.4 11.7 - + + -
670E GLU 3.2 15.3 - - - +
671E VAL* 3.9 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 639 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638E TYR* 1.3 86.7 - - - +
640E ALA* 1.3 61.0 + - - +
641E LEU* 3.4 11.0 + - - +
642E SER* 3.3 30.2 - - - +
643E SER 3.3 17.8 + - - -
644E GLU* 3.6 16.6 - - - +
645E TRP* 3.5 42.5 - - + +
646E LYS* 4.5 4.9 - - - +
669E TYR* 3.1 11.0 - - - -
670E GLU* 2.7 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 640 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639E ARG* 1.3 79.8 + - - +
641E LEU* 1.3 69.2 + - - +
642E SER 2.9 4.2 + - - -
643E SER* 3.2 25.6 + - - +
664E ASP* 4.7 7.6 - - - +
667E ALA* 5.2 4.5 - - + -
668E GLU 3.3 13.0 - - - +
669E TYR* 3.3 26.4 - - + +
----------------------------------------------------------
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