Contacts of the helix formed by residues 754 - 765 (chain B) in PDB entry 3B7B
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 HIS 754 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B SO4 3.1 18.2 + - - +
749B ALA* 3.0 12.6 + - - +
752B ALA* 3.9 30.0 + - + +
753B GLY* 1.3 73.5 - - - +
755B VAL* 1.3 63.7 + - - +
756B ASP 3.2 2.4 + - - -
757B ILE* 3.6 36.4 - - + +
758B CYS* 3.1 24.2 + - - -
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Residues in contact with VAL 755 (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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4B SO4 3.3 16.6 + - - +
753B GLY 3.0 9.5 + - - +
754B HIS* 1.3 70.8 - - - +
756B ASP* 1.3 58.2 + - - +
758B CYS* 3.3 8.0 + - - +
759B HIS* 2.9 29.6 + - + +
789B GLU* 3.8 18.6 - - + +
790B ALA* 3.7 28.5 - - - +
793B TYR* 3.7 31.4 - - + -
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Residues in contact with ASP 756 (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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4B SO4 3.2 21.0 + - - +
754B HIS 3.2 0.4 - - - -
755B VAL* 1.3 77.2 - - - +
757B ILE* 1.3 68.3 + - + +
759B HIS* 3.0 10.0 + - - +
760B MET* 2.8 37.2 + - - +
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Residues in contact with ILE 757 (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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745B PRO* 6.0 0.4 - - + -
749B ALA* 3.7 20.0 - - + -
754B HIS* 3.4 39.6 + - + +
756B ASP* 1.3 81.0 - - + +
758B CYS* 1.3 53.7 + - - +
760B MET* 3.1 7.9 + - + +
761B LEU* 2.8 54.3 + - + +
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Residues in contact with CYS 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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746B LEU* 4.0 17.4 - - - +
749B ALA* 4.0 4.7 - - - +
750B ALA* 3.8 35.2 - - - -
754B HIS 3.1 17.4 + - - +
755B VAL* 3.3 12.8 - - - +
757B ILE* 1.3 79.5 - - - +
759B HIS* 1.3 62.4 + - - +
761B LEU* 3.2 3.0 + - - +
762B VAL* 2.9 28.1 + - - +
790B ALA* 4.9 6.1 - - - -
793B TYR* 4.0 16.6 - - + -
794B LEU* 4.2 12.1 - - + -
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Residues in contact with HIS 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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755B VAL* 2.9 14.3 + - + +
756B ASP* 3.4 11.8 + - - +
758B CYS* 1.3 76.9 - - - +
760B MET* 1.3 78.5 + - - +
762B VAL* 3.2 2.8 + - - +
763B GLN* 2.8 54.7 + - + +
793B TYR* 2.9 47.8 - + + +
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Residues in contact with MET 760 (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 ASP* 2.8 35.5 + - - +
757B ILE* 3.6 10.5 - - + +
759B HIS* 1.3 87.6 - - - +
761B LEU* 1.3 60.2 + - + +
763B GLN* 3.4 8.3 + - + +
764B ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 761 (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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745B PRO* 3.7 18.4 - - + +
746B LEU* 3.5 38.1 - - + +
749B ALA* 4.6 1.1 - - + -
757B ILE* 2.8 40.7 + - + +
758B CYS* 3.7 3.6 - - - +
760B MET* 1.3 73.0 - - + +
762B VAL* 1.3 65.9 + - - +
763B GLN 3.0 1.8 - - - -
764B ALA* 3.0 15.5 + - + +
765B GLY 3.1 0.3 + - - -
766B ALA* 2.9 37.0 + - + +
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Residues in contact with VAL 762 (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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746B LEU* 4.4 11.7 - - + -
758B CYS 2.9 20.7 + - - +
759B HIS 3.7 0.2 - - - +
761B LEU* 1.3 75.4 - - - +
763B GLN* 1.3 65.6 + - - +
765B GLY* 3.4 10.4 + - - -
766B ALA* 4.3 12.0 + - - +
768B ILE* 3.8 39.5 - - + -
793B TYR* 3.6 26.7 - - + +
794B LEU* 4.8 2.2 - - + -
797B ALA* 4.7 6.3 - - + +
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Residues in contact with GLN 763 (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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759B HIS* 2.8 51.2 + - + +
760B MET* 3.6 11.2 - - - +
762B VAL* 1.3 81.8 + - - +
764B ALA* 1.3 60.0 + - - +
765B GLY* 2.9 8.2 + - - -
793B TYR* 5.7 0.4 - - - -
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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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760B MET 3.0 17.3 + - - +
761B LEU* 3.0 15.0 + - + +
763B GLN* 1.3 75.3 - - - +
765B GLY* 1.3 57.5 + - - +
766B ALA* 3.6 1.8 - - + +
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Residues in contact with GLY 765 (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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761B LEU 3.1 0.8 + - - -
762B VAL 3.4 5.5 + - - -
763B GLN 2.9 7.3 - - - -
764B ALA* 1.3 80.7 - - - +
766B ALA* 1.3 71.1 + - - +
767B ASN* 3.6 1.2 + - - +
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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