Contacts of the helix formed by residues 762 - 772 (chain B) in PDB entry 5XA0
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 ASP 762 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756B SER* 4.1 17.0 - - - +
759B LEU* 2.3 51.0 + - + +
761B VAL* 1.3 74.3 - - - +
763B LEU* 1.3 67.3 + - - +
764B ILE 3.1 0.5 + - - -
765B LEU* 3.6 11.6 + - - +
766B ARG* 4.2 3.1 + - - +
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Residues in contact with LEU 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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762B ASP* 1.3 78.4 - - + +
764B ILE* 1.3 64.1 + - - +
766B ARG* 2.9 11.9 + - - +
767B CYS* 2.9 29.1 + - + -
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Residues in contact with ILE 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 ASP 5.4 0.9 - - - +
761B VAL* 2.9 20.9 + - + +
763B LEU* 1.3 77.0 - - - +
765B LEU* 1.3 65.5 + - - +
767B CYS* 4.7 4.3 - - - +
768B MET* 3.0 25.5 + - - +
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Residues in contact with LEU 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 VAL* 4.1 22.5 + - + +
762B ASP 3.6 6.3 + - - +
763B LEU 3.2 0.4 - - - -
764B ILE* 1.3 81.6 - - - +
766B ARG* 1.3 65.0 + - - +
768B MET* 3.6 3.0 - - - +
769B SER* 3.1 21.7 + - - -
782B CYS* 5.2 1.2 - - - +
785B MET* 5.2 14.4 - - + -
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Residues in contact with ARG 766 (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 ASP 4.2 2.0 + - - +
763B LEU* 2.9 17.6 + - - +
765B LEU* 1.3 77.5 - - - +
767B CYS* 1.3 63.5 + - - +
769B SER* 3.4 5.3 + - - -
770B ASP* 3.1 24.9 + - - +
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Residues in contact with CYS 767 (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 LEU* 2.9 22.8 + - + +
764B ILE* 4.5 3.1 - - - +
766B ARG* 1.3 75.1 - - - +
768B MET* 1.3 56.7 + - - +
770B ASP* 4.5 4.3 - - - +
771B GLU* 2.8 35.9 + - + +
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Residues in contact with MET 768 (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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764B ILE 3.0 21.9 + - - +
765B LEU* 3.6 3.8 - - - +
767B CYS* 1.3 74.8 - - - +
769B SER* 1.3 70.3 + - - +
770B ASP 3.1 1.4 + - - -
771B GLU* 3.7 8.6 + - - +
772B ASN 4.9 1.2 + - - -
773B LEU 5.4 0.3 + - - -
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Residues in contact with SER 769 (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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765B LEU 3.1 8.2 + - - -
766B ARG* 3.7 8.5 - - - -
768B MET* 1.3 79.7 - - - +
770B ASP* 1.3 60.2 + - - +
773B LEU* 3.0 27.1 + - - +
778B ARG 5.4 0.4 - - - -
779B ALA* 4.6 8.6 - - - +
782B CYS* 2.7 41.2 - - - +
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Residues in contact with ASP 770 (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 ARG 3.1 15.9 + - - +
767B CYS* 4.3 3.4 - - - +
768B MET 3.1 1.2 - - - -
769B SER* 1.3 78.8 - - - +
771B GLU* 1.3 66.5 + - - +
772B ASN 3.2 12.4 + - - +
773B LEU* 3.9 7.6 - - - +
978B LEU* 4.5 22.8 - - + +
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Residues in contact with GLU 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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767B CYS* 2.8 22.6 + - + +
768B MET* 3.7 5.3 + - - +
769B SER 3.6 1.4 - - - -
770B ASP* 1.3 73.7 - - - +
772B ASN* 1.3 58.8 + - - +
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Residues in contact with ASN 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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768B MET 4.9 1.2 + - - -
769B SER 4.7 0.2 + - - -
770B ASP 3.5 4.9 - - - +
771B GLU* 1.3 79.0 - - - +
773B LEU* 1.3 66.8 + - - +
774B PRO* 2.9 19.7 - - + +
775B TYR* 5.5 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