Contacts of the strand formed by residues 504 - 510 (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 SER 504 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502E SER* 4.5 4.0 + - - -
503E PRO* 1.3 78.7 + - - +
505E ILE* 1.3 63.3 + - - +
506E ASP* 3.2 14.1 + - - +
519E PHE* 3.0 24.9 - - - -
520E ASP* 3.2 20.5 + - - -
588E SER* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 505 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503E PRO 4.1 0.2 + - - -
504E SER* 1.3 71.0 - - - +
506E ASP* 1.3 61.5 + - - +
507E GLN 3.8 7.9 - - - +
508E VAL* 3.6 25.1 - - + -
517E VAL* 4.0 15.5 - - + -
518E GLN 3.7 3.8 - - - -
519E PHE* 4.2 1.1 - - - -
574E VAL* 3.7 26.7 - - + +
575E ARG* 3.9 15.7 - - - -
576E LEU* 4.2 14.4 - - + +
588E SER* 3.9 14.8 + - - +
589E ALA 4.2 3.4 - - - +
591E SER* 3.3 30.1 + - - +
623F LYS* 5.3 2.4 + - - +
654F GLY* 3.6 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 506 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504E SER* 3.6 11.9 - - - +
505E ILE* 1.3 76.9 - - - +
507E GLN* 1.3 66.4 + - + +
518E GLN* 2.6 15.9 + - + +
519E PHE* 3.6 3.8 + - - -
520E ASP* 2.5 45.6 + - - +
623F LYS* 6.0 0.9 - - - -
653F SER* 2.6 41.4 + - - +
654F GLY* 4.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 507 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E ILE* 3.6 1.1 - - - +
506E ASP* 1.3 87.2 + - + +
508E VAL* 1.3 73.1 + - - +
509E GLU* 4.2 2.0 - - + +
516E GLN 4.3 0.4 - - - +
517E VAL* 3.4 3.8 - - - +
518E GLN* 2.8 66.8 + - + +
623F LYS* 6.1 2.2 - - - +
626F ASP* 3.8 14.4 + - - +
630F PRO* 3.6 9.7 - - + +
631F ILE* 2.7 55.5 + - - +
653F SER* 3.4 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 508 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505E ILE* 3.6 21.8 - - + -
507E GLN* 1.3 83.9 + - - +
509E GLU* 1.3 63.0 + - - +
510E PRO* 3.1 12.4 - - + +
515E ALA* 4.9 3.1 - - + -
516E GLN 3.4 6.1 - - - +
517E VAL* 4.6 11.0 - - + -
574E VAL* 4.5 6.1 - - + -
591E SER* 4.1 16.2 - - - -
593E PHE* 3.7 44.0 - - + -
623F LYS* 4.4 24.6 - - + +
624F GLN 4.5 2.9 - - - +
626F ASP* 5.1 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507E GLN* 5.2 1.3 - - + +
508E VAL* 1.3 72.0 - - - +
510E PRO* 1.3 67.2 - - - +
511E TYR* 3.3 43.8 + - + +
515E ALA* 3.4 2.5 - - - -
516E GLN* 2.8 49.3 + - + +
625F ASP* 2.7 28.7 - - - +
626F ASP* 3.3 35.4 + - - +
628F GLY* 4.1 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 510 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508E VAL* 3.1 13.9 - - + +
509E GLU* 1.3 95.0 - - - +
511E TYR* 1.3 56.6 + - - +
514E THR 4.1 2.7 - - - +
515E ALA* 4.4 2.7 - - + -
593E PHE* 3.6 26.9 - - + -
594E LYS 3.4 26.5 - - - +
595E THR* 4.2 3.4 - - - -
596E GLN* 2.6 33.6 + - + +
623F LYS 4.5 1.6 - - - +
624F GLN* 3.9 15.0 - - - +
625F ASP 3.8 13.7 - - - +
----------------------------------------------------------
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