Contacts of the strand formed by residues 775 - 784 (chain D) in PDB entry 2X36
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 GLY 775 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769D ALA 3.4 7.6 - - - -
771D THR* 4.5 1.3 + - - -
774D GLY* 1.3 74.2 - - - -
776D SER* 1.3 64.3 + - - -
897D GLU* 3.5 32.7 + - - +
900D ILE* 6.4 0.2 - - - +
901D ALA* 3.8 8.2 - - - +
904D ARG* 5.8 2.3 + - - -
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Residues in contact with SER 776 (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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768D LEU* 3.6 2.8 - - - -
769D ALA* 2.7 42.7 + - - +
771D THR* 3.5 24.0 - - - -
775D GLY* 1.3 78.0 - - - -
777D THR* 1.3 71.0 + - - +
778D LEU* 4.1 8.1 - - - +
901D ALA* 3.7 11.0 - - - +
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Residues in contact with THR 777 (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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766D MET* 3.5 29.9 - - + -
767D GLY 3.8 3.4 - - - -
768D LEU* 3.6 18.8 - - - +
776D SER* 1.3 79.7 + - - +
778D LEU* 1.3 68.1 + - - +
779D PHE* 4.6 11.2 - - + -
901D ALA* 4.0 16.9 + - - +
902D ALA* 4.4 1.6 - - - -
905D ALA* 4.2 15.7 - - + +
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Residues in contact with LEU 778 (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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766D MET* 3.5 3.3 - - - +
767D GLY* 2.6 62.4 + - - +
768D LEU 4.9 0.9 - - - +
769D ALA* 3.5 32.5 - - + -
776D SER* 4.1 12.3 - - - +
777D THR* 1.3 76.2 - - - +
779D PHE* 1.3 65.8 + - - +
780D VAL* 3.9 7.4 + - + -
844D VAL* 5.4 3.1 - - + -
845D PRO* 4.1 32.3 - - + +
846D GLU 4.0 20.9 - - - +
847D GLY* 4.6 6.1 - - - -
848D ALA* 4.8 2.7 - - + +
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Residues in contact with PHE 779 (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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760D THR* 6.2 5.2 - - + -
764D VAL* 3.9 25.8 - - + -
765D VAL 3.4 14.1 - - - +
766D MET* 4.2 22.7 - - + -
777D THR* 4.6 14.4 - - + -
778D LEU* 1.3 79.5 - - - +
780D VAL* 1.3 66.3 + - - +
781D GLU* 3.7 14.4 + - + +
843D HIS* 4.5 1.9 + - - +
845D PRO* 3.3 21.1 - - - +
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Residues in contact with VAL 780 (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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763D GLY 3.5 0.7 - - - +
764D VAL* 3.3 4.7 - - - +
765D VAL 2.9 34.5 + - - +
767D GLY* 5.3 1.1 - - - +
778D LEU* 3.9 9.6 + - + +
779D PHE* 1.3 75.3 - - - +
781D GLU* 1.3 58.0 + - - +
842D LEU* 3.3 33.4 - - + -
843D HIS 3.8 7.6 - - - +
844D VAL* 4.0 24.0 - - + -
845D PRO* 4.4 3.4 - - + -
856D ALA* 5.1 4.5 - - + -
859D THR* 4.3 26.2 - - + +
860D ILE* 4.1 15.7 - - + -
863D ALA* 4.3 11.1 - - + +
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Residues in contact with GLU 781 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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763D GLY 2.9 7.9 - - - +
764D VAL* 4.1 23.0 - - + +
779D PHE* 4.0 14.7 - - + +
780D VAL* 1.3 78.8 - - - +
782D THR* 1.3 65.1 + - - +
783D SER* 6.1 1.8 - - - -
841D HIS 4.0 0.2 - - - +
842D LEU* 3.6 4.5 - - - +
843D HIS* 2.9 48.6 + - + +
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Residues in contact with THR 782 (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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762D PRO 4.3 2.8 - - - +
763D GLY* 2.7 30.3 + - - +
764D VAL* 5.5 0.9 - - - +
781D GLU* 1.3 78.2 - - - +
783D SER* 1.3 63.2 + - - +
840D ILE* 3.9 3.6 - - + -
841D HIS 3.1 9.6 - - - +
842D LEU* 3.7 15.3 - - + -
863D ALA* 3.4 25.0 + - + -
864D LEU* 3.6 26.5 - - + +
867D LEU* 3.1 29.2 - - - +
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Residues in contact with SER 783 (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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781D GLU* 6.1 1.8 - - - -
782D THR* 1.3 75.9 - - - +
784D LEU* 1.3 64.4 + - - +
785D ARG* 5.6 0.2 - - - +
840D ILE* 3.5 6.4 - - - +
841D HIS* 3.0 45.8 + - - +
867D LEU* 3.7 13.5 - - - -
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Residues in contact with LEU 784 (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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783D SER* 1.3 78.7 + - - +
785D ARG* 1.3 62.4 + - - +
834D TYR* 3.4 29.2 - - + +
838D SER* 3.8 25.4 - - - +
839D HIS 3.0 28.3 - - - +
840D ILE* 4.5 4.7 - - + -
867D LEU* 4.6 1.8 - - + +
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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