Contacts of the helix formed by residues 757 - 774 (chain B) in PDB entry 1B70
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 ARG 757 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754B ARG* 4.4 2.9 - - - +
755B THR 3.5 4.0 + - - +
756B LEU* 1.3 72.1 - - - +
758B ASP* 1.3 91.0 + - - +
759B GLU* 2.8 58.3 + - + +
760B GLU* 2.8 35.9 + - - +
761B VAL* 3.5 6.9 + - - +
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Residues in contact with ASP 758 (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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695B ARG* 4.0 7.9 + - - -
756B LEU 3.5 5.2 + - - +
757B ARG* 1.3 92.7 + - - +
759B GLU* 1.3 63.7 + - - +
760B GLU 3.1 0.2 - - - -
761B VAL* 2.9 29.1 + - - +
762B GLU* 2.8 37.4 + - - +
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Residues in contact with GLU 759 (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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757B ARG* 2.8 35.9 + - + +
758B ASP* 1.3 80.6 - - - +
760B GLU* 1.3 61.7 + - + +
762B GLU* 4.9 2.5 - - - +
763B GLU* 2.8 25.3 + - - +
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Residues in contact with GLU 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B TYR* 4.2 15.1 + - + -
754B ARG* 2.7 37.4 + - - -
756B LEU* 4.8 5.8 - - + -
757B ARG* 2.8 38.2 + - - +
759B GLU* 1.3 82.8 - - + +
761B VAL* 1.3 59.9 + - + +
763B GLU* 3.7 13.5 - - - +
764B ALA* 2.9 32.6 + - - +
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Residues in contact with VAL 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ALA* 4.0 24.2 - - + -
695B ARG* 3.2 24.2 - - + +
749B PHE* 5.7 7.2 - - + -
756B LEU* 4.4 16.2 - - + +
757B ARG 3.8 13.7 - - - +
758B ASP* 2.9 31.0 + - - +
760B GLU* 1.3 72.9 - - + +
762B GLU* 1.3 85.1 + - - +
763B GLU 2.7 14.9 + - - -
764B ALA* 3.0 4.9 + - - +
765B VAL* 2.9 22.6 + - - +
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Residues in contact with GLU 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 3.5 18.5 + - - +
758B ASP* 2.8 32.8 + - - +
759B GLU* 4.9 2.8 - - - +
761B VAL* 1.3 102.5 - - - +
763B GLU* 1.3 55.9 + - - +
765B VAL* 2.7 31.3 - - + +
766B SER* 3.9 5.4 + - - -
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Residues in contact with GLU 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759B GLU 2.8 25.6 + - - +
760B GLU* 3.5 20.6 - - - +
761B VAL 2.7 1.6 + - - -
762B GLU* 1.3 76.7 - - - +
764B ALA* 1.3 71.8 + - - +
765B VAL 3.0 3.1 - - - -
766B SER* 2.6 35.5 + - - +
767B ARG* 3.2 31.6 + - - +
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Residues in contact with ALA 764 (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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717B ALA 4.4 0.5 - - - +
718B ALA 4.0 18.7 - - - +
719B GLY* 5.3 3.4 - - - -
749B PHE* 5.4 6.3 - - + -
760B GLU 2.9 21.7 + - - +
761B VAL* 3.9 2.0 - - - +
763B GLU* 1.3 78.1 + - - +
765B VAL* 1.3 61.6 - - - +
767B ARG* 2.9 32.6 + - + +
768B VAL* 3.4 11.1 + - - +
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Residues in contact with VAL 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ARG* 5.6 13.5 - - + +
697B LEU* 4.7 20.5 - - + +
747B LEU* 6.6 0.2 - - + -
749B PHE* 6.1 4.7 - - + -
761B VAL 2.9 12.1 + - - +
762B GLU* 2.7 42.4 - - + +
764B ALA* 1.3 77.8 - - - +
766B SER* 1.3 64.1 + - - +
768B VAL* 3.3 9.4 + - - +
769B ALA* 3.2 19.8 + - + +
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Residues in contact with SER 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762B GLU 4.2 6.7 - - - -
763B GLU* 2.6 21.1 + - - +
765B VAL* 1.3 80.3 - - - +
767B ARG* 1.3 86.5 + - - +
768B VAL 2.7 5.8 + - - -
769B ALA* 4.2 8.7 - - - -
770B GLU* 2.7 29.6 + - - +
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Residues in contact with ARG 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B ALA* 4.1 17.6 - - - +
763B GLU* 3.2 19.6 - - - +
764B ALA* 2.9 33.4 + - + +
766B SER* 1.3 103.1 + - - +
768B VAL* 1.3 60.9 + - - +
770B GLU* 3.8 38.1 + - - +
771B ALA* 4.0 5.2 + - - +
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Residues in contact with VAL 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 5.7 5.8 - - + -
713B LEU* 6.2 0.4 - - + -
714B VAL* 3.9 35.0 - - + +
717B ALA* 3.1 42.0 - - + +
718B ALA* 3.2 13.5 - - + +
764B ALA 3.8 7.9 - - - +
765B VAL* 3.3 9.8 + - - +
766B SER 2.7 1.2 + - - -
767B ARG* 1.3 75.7 - - - +
769B ALA* 1.3 57.2 + - - +
770B GLU 2.8 2.7 + - - -
771B ALA* 3.0 4.2 + - - +
772B LEU* 2.5 46.1 + - + +
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Residues in contact with ALA 769 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B LEU* 6.2 4.0 - - + +
765B VAL* 3.2 13.6 + - + +
766B SER* 3.1 8.2 + - - +
768B VAL* 1.3 79.4 - - - +
770B GLU* 1.3 65.4 + - - +
772B LEU* 3.0 28.8 - - + +
773B ARG* 3.6 4.0 + - - +
774B ALA 4.5 0.2 + - - -
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Residues in contact with GLU 770 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B SER* 2.7 21.7 + - - +
767B ARG* 3.8 39.0 + - - +
768B VAL 2.8 0.4 + - - -
769B ALA* 1.3 78.6 - - - +
771B ALA* 1.3 77.0 + - + +
772B LEU 2.9 2.1 + - - -
774B ALA* 2.6 33.1 + - + +
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Residues in contact with ALA 771 (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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713B LEU* 3.8 19.5 - - + +
717B ALA* 5.4 4.5 - - + -
767B ARG 4.2 6.7 - - - +
768B VAL 3.0 5.2 + - - +
770B GLU* 1.3 85.0 - - + +
772B LEU* 1.3 68.9 + - - +
774B ALA* 3.6 11.2 - - - -
775B ARG* 3.6 14.6 - - - +
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Residues in contact with LEU 772 (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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697B LEU* 5.3 10.1 - - + -
698B ALA 5.4 2.0 - - - +
699B VAL* 4.0 36.6 - - + -
710B VAL* 6.0 1.1 - - + -
713B LEU* 3.8 21.1 - - + +
714B VAL* 4.5 21.3 - - + +
768B VAL* 2.5 30.0 + - + +
769B ALA* 3.0 27.6 - - + +
770B GLU 2.9 2.2 - - - -
771B ALA* 1.3 80.3 - - - +
773B ARG* 1.3 71.6 + - - +
775B ARG* 3.5 14.6 + - - +
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Residues in contact with ARG 773 (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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699B VAL* 3.0 34.1 - - - +
700B VAL* 2.6 46.0 + - - +
701B VAL* 4.0 14.1 - - + +
740B HIS* 6.1 2.2 - - - -
769B ALA 3.6 4.2 + - - +
772B LEU* 1.3 85.4 - - - +
774B ALA* 1.3 56.9 + - - +
775B ARG* 2.7 23.2 + - - +
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Residues in contact with ALA 774 (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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770B GLU* 2.6 30.8 + - + +
771B ALA* 3.6 8.3 - - - -
772B LEU 3.2 0.6 - - - -
773B ARG* 1.3 76.7 - - - +
775B ARG* 1.3 58.2 + - - +
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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