Contacts of the strand formed by residues 631 - 640 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLN* 2.9 29.2 + - - +
601B PRO* 4.7 6.7 - - + -
602B SER 6.0 0.2 - - - +
623B LYS* 6.1 1.1 - - + -
624B GLN 4.9 6.7 - - - +
626B ASP* 3.8 27.6 - - + +
629B SER 3.6 0.2 + - - -
630B PRO* 1.3 73.1 - - - +
632B ARG* 1.3 59.9 + - - +
633B HIS 3.5 27.4 - - - +
634B TYR* 3.2 37.9 - - + +
653B SER* 3.3 25.7 - - - -
675B ALA* 4.3 12.3 - - + -
676B GLU 3.6 7.4 - - - +
677B ASN* 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 632 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B PRO 3.4 3.1 + - - +
631B ILE* 1.3 75.8 - - - +
633B HIS* 1.3 115.9 + - + +
650B ARG* 4.8 6.1 - - - +
651B LEU 4.6 0.2 - - - +
652B PRO* 4.6 2.1 - - - +
653B SER* 4.2 9.2 + - - -
676B GLU* 2.7 31.1 + - - +
677B ASN* 4.3 8.2 + - - -
678B GLN* 3.0 48.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 633 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B ILE* 3.5 10.4 - - - +
632B ARG* 1.3 136.7 + - + +
634B TYR* 1.3 63.8 + - - +
635B LEU* 3.9 17.0 - - + -
650B ARG* 3.4 46.1 + - + +
651B LEU 3.3 13.9 + - - +
652B PRO* 5.1 2.4 - - - +
653B SER 4.9 0.4 - - - +
675B ALA* 3.8 0.9 - - - -
676B GLU* 3.1 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 634 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B PRO* 4.0 17.3 - - + +
621B LEU* 3.9 24.7 - - + -
623B LYS* 3.8 26.8 - - + +
624B GLN 5.0 1.0 + - - -
631B ILE* 3.2 29.4 - - + +
633B HIS* 1.3 71.8 - - - +
635B LEU* 1.3 65.0 + - - +
636B VAL* 3.5 1.4 + - - +
649B ILE 3.5 2.6 - - - +
651B LEU* 2.8 51.3 + - + +
652B PRO 4.1 15.0 - - - -
653B SER* 4.0 19.1 - - - -
655B SER* 4.5 4.3 - - - -
673B VAL* 4.4 14.1 - - + -
674B VAL 3.4 4.3 - - - -
675B ALA* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 635 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B HIS* 4.2 12.3 - - + -
634B TYR* 1.3 69.5 - - - +
636B VAL* 1.3 60.4 + - - +
637B ARG* 5.6 0.4 - - - -
648B GLU* 3.6 30.5 - - - +
649B ILE 3.6 2.9 - - - -
650B ARG* 3.5 33.7 - - + +
672B TYR 3.6 1.2 - - - +
673B VAL* 3.3 3.1 - - - -
674B VAL* 2.7 54.1 + - + +
676B GLU* 4.2 19.5 - - + +
681B LYS* 3.7 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 636 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B TYR 4.0 3.1 - - - +
635B LEU* 1.3 77.4 - - - +
637B ARG* 1.3 73.8 + - - +
638B TYR* 4.9 3.1 - - + +
648B GLU* 3.4 0.3 - - - +
649B ILE* 2.9 50.9 + - + +
651B LEU* 3.7 30.3 - - + -
658B VAL* 4.1 21.5 - - + -
660B LEU* 5.5 0.7 - - + -
671B VAL* 3.8 20.9 - - + -
672B TYR 3.2 7.2 - - - +
673B VAL* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 637 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635B LEU 5.6 0.4 - - - -
636B VAL* 1.3 83.5 - - - +
638B TYR* 1.3 61.0 + - - +
645B TRP* 3.7 54.6 - - + +
646B LYS 4.6 10.1 - - - +
647B PRO 5.1 2.0 - - - -
648B GLU* 3.5 39.3 + - + +
671B VAL* 3.4 0.9 - - - -
672B TYR* 2.6 56.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 638 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B VAL* 5.4 1.6 - - + -
637B ARG* 1.3 78.1 - - - +
639B ARG* 1.3 73.0 + - - +
645B TRP* 3.3 4.3 - - - -
646B LYS* 3.0 65.3 + - + +
647B PRO* 4.8 4.8 - - + +
649B ILE* 4.4 16.8 - - + -
660B LEU* 3.8 44.2 - - + -
661B LYS 5.6 1.6 + - - -
663B LEU* 4.2 21.3 - - + +
669B TYR* 4.3 14.1 - + + -
670B GLU 3.2 15.0 - - - +
671B VAL* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 639 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B TYR* 1.3 83.9 - - - +
640B ALA* 1.3 67.2 + - - +
641B LEU* 4.9 3.6 - - - +
642B SER 5.4 5.8 - - - +
643B SER 3.7 22.8 + - - -
644B GLU 3.6 17.3 - - - +
645B TRP* 3.5 52.1 - - + +
646B LYS* 4.3 6.7 - - - +
669B TYR* 3.1 11.3 - - - -
670B GLU* 2.5 57.9 + - + -
672B TYR* 4.9 3.2 + - - -
569F GLU 5.8 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 640 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B ARG* 1.3 82.1 - - - +
641B LEU* 1.3 70.7 + - - +
643B SER* 3.4 25.5 + - - -
644B GLU 5.1 0.2 + - - -
646B LYS* 5.5 4.3 - - - +
664B ASP* 5.6 2.9 - - - +
667B ALA* 5.6 3.4 - - + -
668B GLU 3.3 11.0 - - - +
669B TYR* 3.3 26.1 - - + +
541F GLY* 6.4 0.9 - - - -
----------------------------------------------------------
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