Contacts of the helix formed by residues 753 - 762 (chain B) in PDB entry 2XER
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 753 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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752B ASP* 1.3 75.2 - - - +
754B GLN* 1.3 58.2 + - - +
756B LEU* 3.3 19.5 + - - +
757B ASN* 3.0 49.4 + - - +
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Residues in contact with GLN 754 (chain B).
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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752B ASP* 3.3 12.6 + - - +
753B ARG* 1.3 78.7 - - - +
755B LYS* 1.3 68.0 + - + +
757B ASN* 3.0 20.8 + - + +
758B LEU* 3.1 22.7 + - + +
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Residues in contact with LYS 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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726B LEU* 3.4 31.5 - - + +
751B VAL* 2.9 26.9 - - + -
752B ASP* 2.9 22.7 + - - +
754B GLN* 1.3 82.4 - - + +
756B LEU* 1.3 60.3 + - - +
758B LEU* 3.1 18.0 + - + +
759B LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 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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744B VAL* 3.9 26.7 - - + +
747B PHE* 3.7 31.4 - - + -
748B SER* 3.8 27.8 - - - +
751B VAL* 3.8 5.1 - - + +
752B ASP 3.0 21.2 + - - +
753B ARG* 3.3 26.0 - - - +
755B LYS* 1.3 76.8 - - - +
757B ASN* 1.3 62.9 + - - +
759B LEU* 3.3 9.4 + - + +
760B GLU* 3.1 33.5 + - + +
765B LEU* 6.4 0.2 - - + -
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Residues in contact with ASN 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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753B ARG* 3.0 41.5 + - - +
754B GLN* 3.0 11.4 + - + +
756B LEU* 1.3 77.4 - - - +
758B LEU* 1.3 60.0 + - + +
760B GLU* 3.0 25.5 + - - +
761B THR* 3.2 27.5 + - - -
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Residues in contact with LEU 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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726B LEU* 4.1 16.6 - - + +
754B GLN* 3.1 20.2 + - + +
755B LYS* 3.1 23.5 + - + +
757B ASN* 1.3 76.9 - - + +
759B LEU* 1.3 54.1 + - - +
761B THR* 3.2 10.7 + - + +
762B LYS* 2.7 39.1 + - + +
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Residues in contact with LEU 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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722B THR* 4.6 10.8 - - + +
725B LEU* 3.6 48.2 - - + +
726B LEU* 4.1 12.6 - - + +
747B PHE* 4.0 41.7 - - + -
751B VAL* 4.8 8.3 - - + -
755B LYS 3.1 19.7 + - - +
756B LEU* 3.3 12.3 + - + +
758B LEU* 1.3 75.2 - - - +
760B GLU* 1.3 55.8 + - - +
762B LYS* 3.5 5.5 - - + +
763B LEU* 2.8 46.5 + - + +
765B LEU* 4.7 2.7 - - + -
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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
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744B VAL* 3.2 29.4 - - + +
756B LEU* 3.1 18.0 + - + +
757B ASN* 3.0 32.2 + - - +
758B LEU 3.3 0.2 - - - -
759B LEU* 1.3 77.7 - - - +
761B THR* 1.3 52.8 + - - +
764B GLN* 2.7 28.8 + - - -
765B LEU* 2.9 37.4 + - + -
766B VAL* 4.6 20.9 + - + +
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Residues in contact with THR 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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730B GLN* 3.9 10.7 + - - +
757B ASN 3.2 14.3 + - - -
758B LEU* 3.5 14.0 - - + +
760B GLU* 1.3 77.7 - - - +
762B LYS* 1.3 65.4 + - - +
764B GLN* 3.3 20.1 + - - +
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Residues in contact with LYS 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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725B LEU 2.8 25.2 + - - +
726B LEU* 2.7 34.4 + - + +
727B ARG 4.0 0.4 + - - -
728B ILE* 2.8 31.3 + - - -
730B GLN* 2.7 53.0 + - - +
733B LEU* 3.5 15.2 - - + +
758B LEU* 2.7 24.3 + - + +
759B LEU* 3.5 8.5 - - + +
761B THR* 1.3 76.3 - - - +
763B LEU* 1.3 65.3 + - + +
764B GLN* 3.7 3.8 + - - +
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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