Contacts of the strand formed by residues 753 - 758 (chain C) in PDB entry 2VF7
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 THR 753 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583C ILE* 4.8 0.2 - - - -
585C ARG* 3.2 36.1 + - + +
587C VAL* 3.2 35.0 - - + -
747C ARG 5.5 3.1 + - - -
748C SER* 5.5 0.9 - - - -
751C GLY 4.0 5.2 + - - -
752C GLY* 1.3 76.8 - - - +
754C VAL* 1.3 62.9 + - - +
755C TYR* 3.6 25.0 + - + +
784C ASN* 3.2 16.7 + - - +
785C THR* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 754 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C LEU* 5.6 3.8 - - + -
522C LEU* 5.8 1.3 - - + -
544C LEU* 5.7 0.4 - - + -
548C LEU* 4.1 26.7 - - + -
583C ILE* 4.4 23.7 - - + +
585C ARG 2.9 20.8 + - - +
586C LEU* 3.4 17.0 - - + +
587C VAL 3.0 23.7 + - - -
752C GLY 4.0 0.8 + - - -
753C THR* 1.3 71.2 - - - +
755C TYR* 1.3 64.5 + - - +
756C VAL* 4.6 7.9 - - + -
785C THR* 3.4 14.1 - - + +
787C ILE* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 755 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585C ARG* 5.3 0.3 + - - -
587C VAL* 3.3 35.2 - - + -
589C VAL* 4.7 7.9 - - + -
741C LEU* 5.4 3.8 - - + -
744C GLU* 3.4 28.8 + - + -
748C SER* 3.2 28.9 - - - -
753C THR* 3.6 33.3 + - + +
754C VAL* 1.3 71.9 - - - +
756C VAL* 1.3 61.0 + - - +
757C LEU* 4.0 13.4 + - + -
779C LEU* 4.0 29.2 - - + -
784C ASN* 3.8 18.2 - - + -
785C THR 2.7 16.0 + - - +
786C VAL* 3.2 9.1 - - + +
787C ILE* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 756 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C VAL* 4.0 24.5 - - + +
541C SER* 4.7 9.0 - - - +
544C LEU* 5.2 7.4 - - + -
545C VAL* 4.1 22.7 - - + -
548C LEU* 6.0 0.7 - - + -
586C LEU* 3.5 28.3 - - + -
587C VAL 3.1 5.6 + - - +
588C ARG* 3.6 6.6 - - + +
589C VAL 3.0 25.6 + - - +
754C VAL* 4.5 9.0 - - + +
755C TYR* 1.3 73.4 - - - +
757C LEU* 1.3 66.6 + - - +
758C ASP* 4.3 0.8 + - + +
787C ILE* 3.2 11.9 - - + +
789C VAL* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 757 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589C VAL* 3.5 30.1 - - + +
737C GLN* 5.0 1.6 - - - +
741C LEU* 5.8 5.4 - - + -
755C TYR* 4.0 24.5 - - + +
756C VAL* 1.3 84.5 - - - +
758C ASP* 1.3 60.6 + - - +
759C GLU 3.8 0.7 + - - -
760C PRO* 4.3 26.5 - - + -
772C LEU* 5.6 1.3 - - + -
776C LEU* 3.8 33.7 - - + -
786C VAL* 3.9 15.3 - - + -
787C ILE 2.9 9.1 + - - +
788C ALA* 3.3 6.5 - - + +
789C VAL* 3.0 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 758 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C SER* 4.9 8.0 + - - -
541C SER* 4.2 16.4 + - - +
589C VAL 3.5 7.7 + - - -
590C ASP* 4.8 15.6 - - + +
591C GLN* 4.5 5.7 - - - +
737C GLN* 3.2 15.9 + - - -
756C VAL* 4.3 1.2 - - + +
757C LEU* 1.3 71.6 - - - +
759C GLU* 1.3 84.9 + - - +
760C PRO 3.4 0.2 - - - -
789C VAL* 3.3 25.0 - - - +
----------------------------------------------------------
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