Contacts of the helix formed by residues 762 - 774 (chain F) in PDB entry 2W3S
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 762 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355E LYS* 4.3 10.5 - - + -
640F ASN* 4.6 0.4 - - - -
676F THR 3.0 18.4 - - - +
677F THR* 4.1 14.8 - - - +
679F GLU* 3.7 25.3 + - + +
760F PRO* 2.9 20.1 + - + +
761F ALA* 1.3 74.0 - - - +
763F PRO* 1.4 77.2 - - - +
764F GLU* 3.7 8.1 + - - +
765F ALA* 2.8 27.4 + - - +
766F VAL* 2.9 11.9 + - - +
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Residues in contact with PRO 763 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E SER 3.5 17.7 - - - +
355E LYS* 3.3 34.5 - - + +
434E TYR* 3.7 17.9 - - + +
637F THR 3.6 1.7 - - - +
638F GLY* 3.3 33.1 - - - +
639F GLU* 3.9 10.5 - - + +
640F ASN* 4.0 11.4 - - - +
677F THR* 5.2 2.9 - - + -
761F ALA 4.8 0.2 - - - +
762F THR* 1.4 87.4 - - - +
764F GLU* 1.3 60.2 + - - +
766F VAL 3.4 0.5 + - - -
767F LEU 3.1 17.7 + - - -
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Residues in contact with GLU 764 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429E ARG 4.6 2.6 - - - +
430E ALA* 3.5 11.3 - - - +
431E SER* 2.9 40.4 + - - -
434E TYR* 3.3 45.7 + - + +
762F THR* 3.1 8.6 + - - +
763F PRO* 1.3 78.9 - - - +
765F ALA* 1.3 64.6 + - - +
767F LEU* 3.1 4.0 + - - +
768F ALA* 2.9 23.5 + - + +
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Residues in contact with ALA 765 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757F LEU* 3.4 13.8 - - + +
758F GLN* 4.5 10.2 + - + +
760F PRO 3.4 26.0 - - - +
761F ALA* 3.6 6.7 - - - -
762F THR* 2.8 20.7 + - - +
764F GLU* 1.3 74.1 - - - +
766F VAL* 1.3 55.0 + - - +
768F ALA* 3.3 9.7 + - - +
769F ALA* 3.0 23.6 + - - +
772F ARG* 5.0 0.2 + - - -
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Residues in contact with VAL 766 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633F ILE* 3.8 37.7 - - + -
638F GLY* 3.5 23.1 - - - +
640F ASN* 3.9 16.6 - - - +
743F LEU* 4.2 13.7 - - + -
747F CYS* 4.2 5.4 - - - -
757F LEU* 3.9 9.0 - - + -
761F ALA* 4.0 21.8 - - + +
762F THR 2.9 15.2 + - - +
763F PRO 3.7 1.3 - - - +
765F ALA* 1.3 73.1 - - - +
767F LEU* 1.3 53.6 + - - +
769F ALA* 3.1 4.4 + - - +
770F VAL* 2.7 34.0 + - + +
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Residues in contact with LEU 767 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E TYR* 4.2 17.3 - - + -
437E ASN* 3.7 21.1 - - + +
438E ALA* 5.8 2.9 - - - +
634F ASP 4.9 0.7 - - - +
635F ARG 3.6 19.3 - - - +
636F LEU 3.1 30.7 - - - +
637F THR* 3.7 20.6 - - - +
638F GLY* 4.1 2.2 - - - +
763F PRO 3.1 7.2 + - - +
764F GLU 3.1 6.5 + - - +
766F VAL* 1.3 72.2 - - - +
768F ALA* 1.3 67.3 + - - +
770F VAL* 4.3 8.1 - - + -
771F ARG* 3.0 51.7 + - + +
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Residues in contact with ALA 768 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764F GLU* 2.9 14.0 + - + +
765F ALA* 3.3 13.7 - - - +
766F VAL 3.2 0.2 - - - -
767F LEU* 1.3 78.4 - - - +
769F ALA* 1.3 58.1 + - - +
771F ARG* 3.5 4.0 + - - +
772F ARG* 3.1 51.9 + - - +
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Residues in contact with ALA 769 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747F CYS* 3.6 22.4 - - - -
755F PRO* 3.3 34.8 - - + +
757F LEU* 3.7 21.1 - - + +
765F ALA 3.0 13.2 + - - +
766F VAL 3.6 2.7 - - - +
768F ALA* 1.3 74.2 - - - +
770F VAL* 1.3 66.0 + - - +
772F ARG* 3.3 4.4 + - - +
773F ALA* 3.1 17.5 + - - +
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Residues in contact with VAL 770 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F ILE* 3.5 32.3 - - + -
634F ASP 5.0 1.3 - - - +
635F ARG* 4.1 22.7 - - - +
747F CYS* 3.8 7.8 - - - -
750F CYS* 4.1 15.7 - - - -
766F VAL* 2.7 26.8 + - + +
767F LEU* 3.9 11.2 - - + +
769F ALA* 1.3 71.4 - - - +
771F ARG* 1.3 60.8 + - + +
773F ALA* 3.0 8.6 + - - +
774F GLU* 2.8 53.6 + - - +
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Residues in contact with ARG 771 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E ASN* 3.3 29.6 + - - +
635F ARG 5.7 0.4 - - - +
767F LEU* 3.0 43.1 + - + +
768F ALA* 3.9 3.4 - - - +
770F VAL* 1.3 77.4 - - + +
772F ARG* 1.3 56.4 - - - +
774F GLU* 3.6 10.0 - - - +
775F GLY 3.0 5.5 + - - -
776F ARG* 2.8 80.2 + - + +
777F ALA* 4.3 14.9 - - - +
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Residues in contact with ARG 772 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753F HIS* 3.4 14.5 - - - +
754F TRP 4.2 6.9 - - - +
755F PRO 2.7 45.6 + - - +
756F ASP* 3.1 30.4 + - - -
757F LEU* 4.6 0.6 - - - +
758F GLN* 5.3 7.8 - - - +
765F ALA 5.0 0.2 + - - -
768F ALA* 3.1 36.7 + - - +
769F ALA* 3.3 17.5 - - - +
770F VAL 3.2 0.2 - - - -
771F ARG* 1.3 75.0 - - - +
773F ALA* 1.3 63.1 + - - +
775F GLY* 3.2 10.3 + - - -
777F ALA 4.4 16.4 - - - +
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Residues in contact with ALA 773 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747F CYS 3.7 22.4 - - - +
748F ALA* 4.7 0.4 - - - -
750F CYS* 4.6 0.4 - - + -
751F GLY* 3.3 17.3 - - - +
753F HIS* 3.2 48.6 + - - +
755F PRO* 4.1 7.8 - - + +
769F ALA 3.1 12.7 + - - +
770F VAL 3.0 8.2 + - - +
772F ARG* 1.3 72.6 - - - +
774F GLU* 1.3 58.6 + - - +
775F GLY 2.9 8.8 + - - -
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Residues in contact with GLU 774 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635F ARG* 2.7 41.6 + - - +
750F CYS* 3.4 21.8 - - + +
751F GLY* 4.0 6.3 - - - -
752F PRO* 5.3 2.1 - - - +
753F HIS* 4.5 2.2 - - - -
770F VAL* 2.8 31.8 + - - +
771F ARG* 3.9 9.1 - - - +
773F ALA* 1.3 71.8 - - - +
775F GLY* 1.3 60.7 + - - +
776F ARG* 2.8 46.8 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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