Contacts of the strand formed by residues 605 - 610 (chain D) 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 LYS 605 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A HIS* 4.9 16.1 + - + +
688A VAL* 6.3 2.7 - - + -
594C LYS* 5.2 14.8 - - + +
603D ALA 5.2 0.8 + - - -
604D PRO* 1.3 75.7 + - - +
606D LEU* 1.3 62.7 + - - +
620D ASN 3.6 2.1 - - - +
621D LEU* 3.8 2.4 - - - -
622D ILE* 2.8 58.5 + - + +
624D GLN* 3.1 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A VAL* 4.0 17.0 + - - +
604D PRO* 3.7 5.6 + - + -
605D LYS* 1.3 76.8 - - - +
607D GLU* 1.3 61.2 - - - +
608D GLY 4.5 0.2 + - - -
619D VAL* 4.0 15.0 - - + -
620D ASN 3.5 1.1 - - - -
621D LEU* 3.3 32.8 - - + -
622D ILE* 5.3 0.7 - - - -
671D VAL* 4.9 2.0 - - + +
673D VAL* 3.7 28.3 - - + -
685D ALA* 3.6 35.0 - - + +
686D HIS 4.1 3.8 - - - +
687D PHE* 3.9 36.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 5.0 0.2 - - - +
668A GLU* 2.4 40.6 - - - +
688A VAL* 3.3 30.1 - - + +
689A PHE 3.8 12.3 - - - -
690A ARG* 3.5 15.7 + - + +
592C GLU* 4.1 4.5 - - - +
606D LEU* 1.3 76.0 - - - +
608D GLY* 1.3 65.5 + - - +
619D VAL* 3.5 3.7 - - - +
620D ASN* 2.7 67.2 + - + +
622D ILE* 4.1 11.6 - - + +
687D PHE* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A PHE* 5.4 0.4 - - - -
688A VAL 2.9 12.4 + - - -
689A PHE* 3.2 8.5 - - - +
690A ARG 2.9 26.3 + - - +
607D GLU* 1.3 73.4 - - - +
609D GLN* 1.3 60.2 + - - +
617D ILE* 4.7 2.2 - - - -
618D LYS 3.7 4.3 - - - -
619D VAL* 4.9 0.7 - - - -
687D PHE* 3.5 29.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 609 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG* 3.4 42.5 + - + +
691A THR 4.7 6.0 + - - +
692A ALA* 5.4 1.9 - - - +
1697A SO4 4.7 16.2 + - - -
608D GLY* 1.3 73.9 - - - +
610D ARG* 1.3 67.8 + - + +
617D ILE* 3.3 10.0 - - - +
618D LYS* 2.7 68.6 + - + +
620D ASN* 2.7 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A ARG* 3.4 56.2 - - + +
611A GLY 3.3 25.3 + - - +
612A GLU 4.2 2.8 + - - -
613A ASP* 3.5 15.4 + - - +
614A GLY* 3.4 37.0 - - - +
616A SER 5.2 1.8 + - - -
690A ARG 4.6 3.2 + - - +
692A ALA* 4.8 12.8 - - + +
1697A SO4 4.7 10.9 + - - +
609D GLN* 1.3 85.5 + - + +
611D GLY* 1.3 68.8 + - - +
616D SER 5.1 0.9 - - - -
617D ILE* 5.0 1.6 - - - +
618D LYS* 4.0 8.8 - - - +
----------------------------------------------------------
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