Contacts of the strand formed by residues 504 - 510 (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 SER 504 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D SER 5.1 0.7 - - - -
503D PRO* 1.3 76.0 - - - +
505D ILE* 1.3 62.3 + - - +
506D ASP* 3.4 14.7 + - - +
519D PHE* 2.9 6.2 - - - -
520D ASP* 2.8 49.5 + - - -
588D SER* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654C GLY* 3.5 20.1 - - - +
656C ASP* 5.5 1.7 - - - +
503D PRO 4.3 0.2 + - - -
504D SER* 1.3 71.7 + - - +
506D ASP* 1.3 61.4 + - - +
507D GLN 3.8 1.8 - - - +
508D VAL* 3.6 30.5 - - + -
517D VAL* 3.6 20.9 - - + -
518D GLN 3.5 5.6 - - - +
519D PHE* 4.3 0.7 - - - +
574D VAL* 3.8 25.1 - - + +
575D ARG* 4.1 5.8 - - - -
576D LEU* 4.1 19.3 - - + -
588D SER* 3.8 23.0 - - - +
589D ALA 4.3 3.6 - - - +
591D SER* 4.1 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653C SER* 2.9 42.6 + - - +
654C GLY* 4.0 9.0 + - - -
504D SER* 3.6 11.9 + - - -
505D ILE* 1.3 73.9 - - - +
507D GLN* 1.3 67.9 + - + +
518D GLN* 2.8 13.0 + - + +
519D PHE* 4.0 4.9 + - - +
520D ASP* 2.6 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626C ASP* 3.9 12.7 + - - +
630C PRO* 3.8 13.8 - - + +
631C ILE* 2.9 52.1 + - - +
653C SER* 3.2 12.6 + - - -
505D ILE* 3.6 0.4 - - - +
506D ASP* 1.3 87.8 + - + +
508D VAL* 1.3 73.6 + - - +
509D GLU* 5.1 1.8 - - + +
516D GLN 4.0 2.2 - - - +
517D VAL* 3.3 2.8 - - - +
518D GLN* 2.7 67.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 508 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C LYS* 4.4 19.2 - - + +
624C GLN 4.6 2.6 - - - +
626C ASP* 5.3 1.2 - - - +
505D ILE* 3.6 21.3 - - + -
507D GLN* 1.3 85.0 + - - +
509D GLU* 1.3 58.8 + - - +
510D PRO* 3.1 13.2 - - + +
515D ALA* 4.7 8.1 - - + -
516D GLN 3.3 6.1 - - - +
517D VAL* 4.3 11.4 - - + -
574D VAL* 4.5 3.6 - - + -
591D SER* 3.6 19.7 - - - +
593D PHE* 3.5 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624C GLN 4.1 0.2 - - - +
625C ASP* 2.6 26.6 - - - +
626C ASP* 2.8 52.1 + - - +
628C GLY* 4.6 4.6 + - - +
507D GLN* 5.1 2.6 - - + +
508D VAL* 1.3 72.9 - - - +
510D PRO* 1.3 65.4 - - - +
511D TYR* 3.5 40.4 + - + +
515D ALA* 3.6 2.1 - - - -
516D GLN* 2.9 41.8 + - + +
596D GLN* 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 510 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623C LYS 4.3 2.0 - - - +
624C GLN* 4.0 23.3 - - - -
625C ASP* 4.2 2.6 - - - +
508D VAL* 3.1 14.6 - - + +
509D GLU* 1.3 96.1 - - - +
511D TYR* 1.3 62.2 + - - +
514D THR 4.0 4.5 - - - +
515D ALA* 4.3 2.2 - - + -
593D PHE* 3.6 31.9 - - + -
594D LYS 3.5 22.9 - - - +
595D THR* 4.1 6.3 - - + -
596D GLN* 2.9 21.9 + - + +
----------------------------------------------------------
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