Contacts of the strand formed by residues 617 - 622 (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 617 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608E GLY* 4.4 6.1 - - - -
609E GLN 3.1 17.3 - - - +
611E GLY* 4.1 3.4 - - - +
616E SER* 1.3 77.4 - - - +
618E LYS* 1.3 69.0 + - - +
619E VAL* 3.9 15.5 + - + -
659E MET* 3.4 7.2 - - - +
660E LEU* 2.9 47.2 + - + -
687E PHE* 3.6 31.9 - - + -
689E PHE* 3.6 46.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 618 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B ARG* 5.8 2.2 - - - +
609E GLN* 3.0 70.4 + - + +
610E ARG 4.3 8.7 - - - +
611E GLY 4.2 1.2 - - - +
617E ILE* 1.3 77.1 - - - +
619E VAL* 1.3 62.1 + - - +
620E ASN* 3.2 23.6 + - - +
657E HIS* 3.9 29.5 + - + -
658E VAL 4.0 1.8 - - - +
659E MET* 3.5 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 619 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606E LEU* 4.1 35.2 - - + -
607E GLU 3.5 10.5 - - - +
608E GLY* 4.8 0.2 - - - -
617E ILE* 3.9 29.8 - - + -
618E LYS* 1.3 72.3 - - - +
620E ASN* 1.3 64.5 + - - +
621E LEU* 4.8 1.5 - - + +
657E HIS* 3.1 3.2 - - - -
658E VAL* 2.9 53.9 + - + +
660E LEU* 4.7 8.7 - - + -
671E VAL* 4.7 8.1 - - + -
673E VAL* 5.3 2.5 - - + -
687E PHE* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 620 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B ARG* 4.2 6.2 + - - -
605E LYS 3.5 3.3 - - - +
606E LEU* 3.6 2.9 - - - -
607E GLU* 2.7 65.5 + - + +
609E GLN* 3.0 22.2 - - - +
618E LYS* 3.2 36.8 + - - +
619E VAL* 1.3 73.2 - - - +
621E LEU* 1.3 64.9 + - - +
622E ILE* 5.5 0.9 - - + -
656E ASP 3.7 6.3 + - - +
657E HIS* 3.4 10.9 + - - +
592F GLU* 5.4 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 621 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604E PRO* 4.1 10.5 - - + -
605E LYS 3.7 0.7 - - - -
606E LEU* 3.6 26.5 - - + -
619E VAL* 4.8 3.4 - - + +
620E ASN* 1.3 74.5 - - - +
622E ILE* 1.3 63.3 + - - +
623E LYS* 3.8 14.5 + - + +
634E TYR* 3.7 42.4 - - + -
636E VAL* 6.2 0.2 - - + -
651E LEU* 5.1 5.8 - - + -
655E SER* 4.0 22.2 - - - +
656E ASP* 3.1 19.6 + - - +
657E HIS* 4.2 11.0 - - - +
658E VAL* 5.4 4.3 - - + -
673E VAL* 3.8 19.3 - - + -
592F GLU* 4.1 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 622 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.7 4.3 - - + -
688B VAL* 4.5 9.6 - - + -
604E PRO* 3.6 2.8 - - - +
605E LYS* 2.8 64.3 + - + +
607E GLU* 4.0 33.4 - - + +
620E ASN* 4.7 1.8 - - + +
621E LEU* 1.3 75.6 - - - +
623E LYS* 1.3 63.9 + - - +
624E GLN* 3.5 3.1 - - - +
571F THR* 4.1 15.9 - - + +
592F GLU* 3.9 24.0 - - - +
593F PHE* 4.0 24.0 - - - +
594F LYS* 4.2 8.7 - - + +
----------------------------------------------------------
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