Contacts of the helix formed by residues 762 - 774 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355C LYS* 3.8 32.3 - - + -
640D ASN* 4.7 0.2 - - - -
676D THR 3.3 16.4 - - - +
677D THR* 4.6 0.2 - - - -
679D GLU* 4.1 18.3 + - + +
760D PRO* 2.8 22.9 + - + +
761D ALA* 1.3 73.3 - - - +
763D PRO* 1.4 65.2 - - - +
764D GLU* 3.5 9.9 + - - +
765D ALA* 3.0 18.9 + - - +
766D VAL* 2.7 33.6 + - - +
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Residues in contact with PRO 763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C LEU* 5.0 0.2 - - + -
354C SER 3.7 15.7 - - - +
355C LYS* 3.5 33.7 - - + +
434C TYR* 3.8 12.8 - - + +
637D THR 3.3 2.8 - - - +
638D GLY* 3.1 37.5 - - - +
639D GLU* 3.6 11.7 - - + +
640D ASN* 4.1 10.3 - - - +
676D THR 5.2 0.4 - - - +
677D THR* 5.4 2.9 - - + -
762D THR* 1.4 89.1 - - - +
764D GLU* 1.3 56.2 + - - +
766D VAL* 4.3 0.2 - - + -
767D LEU* 3.0 23.2 + - - +
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Residues in contact with GLU 764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C LYS* 6.2 0.2 - - - -
429C ARG 3.9 4.3 - - - +
430C ALA* 3.3 23.0 - - - +
431C SER* 2.7 37.4 + - - -
434C TYR* 3.3 41.8 + - + +
679D GLU* 5.7 0.7 - - - +
762D THR* 3.2 9.3 + - - +
763D PRO* 1.3 77.2 - - - +
765D ALA* 1.3 58.6 + - - +
767D LEU* 3.4 2.4 + - - +
768D ALA* 3.0 29.6 + - + +
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Residues in contact with ALA 765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D LEU* 3.8 8.0 - - + +
758D GLN* 4.4 11.4 + - + +
760D PRO 3.4 24.5 - - - +
761D ALA* 3.8 5.4 - - - -
762D THR* 3.0 15.1 + - - +
764D GLU* 1.3 77.8 - - - +
766D VAL* 1.3 65.7 + - - +
768D ALA* 3.3 8.3 + - - +
769D ALA* 3.0 23.0 + - - +
772D ARG* 5.3 0.2 + - - -
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Residues in contact with VAL 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D ILE* 4.0 35.7 - - + -
638D GLY* 3.5 22.0 - - - +
640D ASN* 3.7 14.1 - - - +
743D LEU* 4.1 18.2 - - + -
747D CYS* 3.7 6.5 - - - -
757D LEU* 4.0 9.4 - - + -
761D ALA* 3.6 18.6 - - + +
762D THR 2.7 23.1 + - - +
763D PRO 4.0 0.2 - - - +
765D ALA* 1.3 70.7 - - - +
767D LEU* 1.3 58.3 + - - +
769D ALA* 3.2 4.6 + - - +
770D VAL* 2.9 27.3 + - + +
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Residues in contact with LEU 767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C TYR* 3.7 26.7 - - + -
437C ASN* 3.7 20.0 - - - +
438C ALA* 5.9 1.1 - - - +
635D ARG 3.4 19.5 - - - +
636D LEU 3.4 30.7 - - - +
637D THR* 3.8 8.1 - - - +
638D GLY* 3.9 4.4 - - - +
763D PRO 3.0 19.3 + - - +
764D GLU 3.7 3.8 - - - +
766D VAL* 1.3 73.6 - - - +
768D ALA* 1.3 66.8 + - - +
770D VAL* 3.0 9.2 + - + +
771D ARG* 3.0 48.6 + - + +
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Residues in contact with ALA 768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764D GLU* 3.0 13.8 + - + +
765D ALA* 3.3 11.6 + - - +
767D LEU* 1.3 76.0 - - - +
769D ALA* 1.3 56.2 + - - +
771D ARG* 3.5 7.4 + - - +
772D ARG* 3.2 50.4 + - - +
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Residues in contact with ALA 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D CYS* 3.7 16.4 - - - -
755D PRO* 3.5 18.7 - - + +
757D LEU* 3.9 22.0 - - + -
765D ALA 3.0 12.9 + - - +
766D VAL 3.7 7.2 - - - +
768D ALA* 1.3 73.0 - - - +
770D VAL* 1.3 65.8 + - - +
772D ARG* 3.3 16.7 + - - +
773D ALA* 3.0 23.0 + - - +
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Residues in contact with VAL 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633D ILE* 3.5 31.6 - - + -
634D ASP 5.3 1.1 - - - +
635D ARG* 4.0 23.6 - - - +
747D CYS* 3.7 8.7 - - - +
750D CYS* 4.0 15.7 - - - -
766D VAL* 2.9 21.1 + - + +
767D LEU* 3.0 13.7 + - + +
769D ALA* 1.3 75.0 - - - +
771D ARG* 1.3 59.0 + - + +
773D ALA* 3.1 7.6 + - - +
774D GLU* 2.8 53.3 + - - +
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Residues in contact with ARG 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ASN* 4.0 25.3 - - - +
767D LEU* 3.0 41.2 + - + +
768D ALA* 3.9 6.1 - - - +
770D VAL* 1.3 72.6 - - + +
772D ARG* 1.3 60.3 - - - +
774D GLU* 3.5 10.9 - - - +
775D GLY 3.0 5.7 + - - -
776D ARG* 2.9 77.2 + - + +
777D ALA* 4.1 32.0 - - - +
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Residues in contact with ARG 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D HIS* 3.3 14.6 - - - +
754D TRP 4.2 5.2 - - - +
755D PRO 2.5 47.5 + - - +
756D ASP* 2.6 29.5 + - - -
757D LEU* 4.5 0.4 - - - +
758D GLN* 5.3 7.5 - - - +
768D ALA* 3.2 39.6 + - - +
769D ALA* 3.4 14.8 - - - +
771D ARG* 1.3 75.0 - - - +
773D ALA* 1.3 65.2 + - - +
775D GLY* 3.0 13.0 + - - -
776D ARG 4.6 3.4 - - - +
777D ALA 5.2 8.0 + - - +
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Residues in contact with ALA 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D CYS 3.4 28.3 - - - +
748D ALA 4.8 0.2 - - - +
750D CYS 4.6 0.2 - - - -
751D GLY* 3.2 31.2 - - - +
752D PRO* 3.4 0.2 - - - +
753D HIS* 3.3 36.4 + - - +
755D PRO* 4.2 5.5 - - + +
769D ALA 3.0 13.9 + - - +
770D VAL 3.5 7.2 - - - +
772D ARG* 1.3 75.2 - - - +
774D GLU* 1.3 58.6 + - - +
775D GLY 3.2 3.8 + - - -
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Residues in contact with GLU 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635D ARG* 2.3 44.0 + - - +
750D CYS* 3.2 25.1 - - + +
751D GLY* 4.4 1.3 - - - -
752D PRO* 5.2 2.2 - - - -
753D HIS* 4.4 1.3 - - - -
770D VAL* 2.8 31.7 + - - +
771D ARG* 3.9 9.8 - - - +
772D ARG 3.2 0.2 - - - -
773D ALA* 1.3 74.8 - - - +
775D GLY* 1.3 56.6 + - - +
776D ARG* 3.0 47.1 + - + +
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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
------------------------------------------------------------
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