Contacts of the strand formed by residues 775 - 783 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769B ALA 3.5 9.6 - - - -
774B GLY* 1.3 73.5 - - - -
776B SER* 1.3 63.7 + - - -
897B GLU* 3.7 31.9 + - - +
901B ALA* 3.8 11.0 - - - +
904B ARG* 4.6 12.1 + - - -
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Residues in contact with SER 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768B LEU* 3.6 4.3 - - - +
769B ALA* 2.9 35.9 + - - +
771B THR* 4.1 22.4 + - - +
774B GLY 4.0 0.6 + - - -
775B GLY* 1.3 76.6 + - - -
777B THR* 1.3 65.6 + - - +
778B LEU* 3.9 2.9 - - - -
898B LYS* 5.3 0.2 - - - -
901B ALA* 3.7 12.2 - - - +
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Residues in contact with THR 777 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B MET 5.6 2.5 + - - +
766B MET* 2.8 37.5 - - - +
767B GLY 3.7 5.3 + - - -
768B LEU* 4.1 7.5 - - - +
776B SER* 1.3 77.4 - - - +
778B LEU* 1.3 57.6 + - - +
779B PHE* 4.3 16.6 + - + -
901B ALA* 4.3 6.9 - - - +
905B ALA* 4.2 20.3 - - + +
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Residues in contact with LEU 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766B MET* 4.6 0.4 - - - -
767B GLY* 2.9 37.9 + - - +
768B LEU 4.8 1.1 - - - +
769B ALA* 3.0 34.3 - - + -
776B SER* 5.4 3.4 - - - -
777B THR* 1.3 73.5 - - - +
779B PHE* 1.3 61.6 + - - +
780B VAL* 3.6 26.2 - - + +
844B VAL* 5.1 5.8 - - + -
845B PRO* 4.3 35.4 - - + +
846B GLU 5.7 0.4 - - - +
847B GLY* 5.5 1.1 - - - +
848B ALA* 4.5 14.1 - - + +
856B ALA* 5.2 6.3 - - + -
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Residues in contact with PHE 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B MET* 3.3 37.5 - - + -
757B TYR* 3.6 43.3 - + + -
760B THR* 4.2 15.5 - - + -
764B VAL* 3.7 20.4 - - + -
765B VAL 3.5 1.1 - - - -
766B MET* 3.4 47.6 - - + -
777B THR* 4.6 15.0 - - + -
778B LEU* 1.3 71.4 - - - +
780B VAL* 1.3 63.8 + - - +
781B GLU* 3.6 11.8 + - + +
845B PRO* 3.0 29.0 - - + +
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Residues in contact with VAL 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763B GLY 3.6 1.2 - - - +
764B VAL* 3.3 4.5 - - - -
765B VAL 3.0 28.2 + - - +
778B LEU* 3.6 22.7 - - + -
779B PHE* 1.3 72.1 - - - +
781B GLU* 1.3 61.7 + - - +
842B LEU* 3.7 26.7 - - + -
843B HIS 3.6 6.3 - - - +
844B VAL* 4.3 11.9 - - + -
845B PRO* 4.3 1.6 - - + -
856B ALA* 4.7 7.6 - - + -
859B THR* 3.5 40.8 - - + +
860B ILE* 4.0 15.3 - - + -
863B ALA* 4.3 5.9 - - + +
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Residues in contact with GLU 781 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756B MET* 3.2 25.7 - - - +
757B TYR* 3.1 30.8 + - + -
763B GLY 3.3 4.5 - - - -
764B VAL* 3.9 14.4 - - + +
779B PHE* 3.7 13.9 - - - +
780B VAL* 1.3 76.6 - - - +
782B THR* 1.3 62.9 + - - +
841B HIS* 3.7 1.7 - - + +
842B LEU* 3.5 6.8 - - - +
843B HIS* 2.8 63.0 + - + +
845B PRO* 5.7 0.2 - - - +
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Residues in contact with THR 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B PRO 4.4 1.9 - - - +
763B GLY* 2.7 25.3 + - - +
764B VAL* 5.8 0.5 - - - +
781B GLU* 1.3 73.8 - - - +
783B SER* 1.3 62.3 + - - +
840B ILE* 4.1 3.8 - - + -
841B HIS 3.1 8.5 - - - +
842B LEU* 3.8 23.8 - - + -
863B ALA* 2.8 31.9 + - + +
864B LEU* 3.6 31.2 - - + +
867B LEU* 3.2 29.0 - - - +
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Residues in contact with SER 783 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B GLU* 6.4 0.2 - - - -
782B THR* 1.3 74.3 - - - +
784B LEU* 1.3 65.3 + - - +
840B ILE* 3.4 0.6 - - - -
841B HIS* 2.5 63.9 + - - +
867B LEU* 3.6 11.4 - - - +
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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