Contacts of the helix formed by residues 769 - 778 (chain A) in PDB entry 2XBB
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 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A LYS* 5.0 0.9 - - - +
665A LEU* 3.6 7.4 - - - -
667A LYS* 4.4 9.2 - - - +
768A PHE* 1.3 74.2 - - - +
770A GLU* 1.3 77.9 + - - +
771A ASN* 3.7 22.1 + - - +
772A GLU* 2.8 45.0 + - - +
773A LEU* 2.9 22.5 + - - +
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Residues in contact with GLU 770 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A ARG* 3.8 32.5 + - + +
661A TYR* 3.9 26.6 - - + +
662A LYS* 3.3 33.4 - - + +
665A LEU* 3.5 12.1 - - + +
667A LYS* 3.2 35.4 + - - +
769A ASP* 1.3 79.5 - - - +
771A ASN* 1.3 67.5 + - - +
773A LEU* 3.8 2.0 - - - +
774A GLU* 3.2 22.3 + - - +
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Residues in contact with ASN 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A ARG* 3.9 28.8 + - - +
769A ASP* 3.2 17.9 + - - +
770A GLU* 1.3 80.4 + - - +
772A GLU* 1.3 64.6 + - + +
774A GLU* 3.4 14.6 + - - +
775A LEU* 3.3 20.4 + - - +
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Residues in contact with GLU 772 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ASP* 4.5 1.0 - - - -
522A TYR* 3.8 33.8 + - + +
525A LYS* 3.0 41.0 + - - +
768A PHE* 3.3 19.9 - - + -
769A ASP* 2.8 42.5 + - - +
771A ASN* 1.3 70.7 - - + +
773A LEU* 1.3 60.4 + - - +
775A LEU* 3.1 10.5 + - + +
776A LEU* 2.9 28.3 + - - +
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Residues in contact with LEU 773 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A TYR* 3.8 26.9 - - + +
664A MET* 3.7 28.0 - - + -
665A LEU* 3.8 20.0 - - + -
756A PHE* 5.1 0.2 - - + -
765A ILE* 3.4 33.2 - - + -
768A PHE* 4.1 9.1 - - + +
769A ASP 2.9 18.4 + - - +
770A GLU 3.8 4.9 - - - +
772A GLU* 1.3 77.1 - - - +
774A GLU* 1.3 61.5 + - - +
776A LEU* 3.1 17.8 + - + +
777A MET* 3.1 35.7 + - - +
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Residues in contact with GLU 774 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617A THR* 6.0 0.3 - - - +
655A PHE* 3.0 37.5 - - + +
656A PHE 4.7 1.7 - - - +
658A ARG* 5.9 3.4 - - - +
661A TYR* 3.2 40.8 + - + +
770A GLU 3.2 10.3 + - - +
771A ASN* 3.6 18.5 - - - +
773A LEU* 1.3 77.9 - - - +
775A LEU* 1.3 60.2 + - + +
777A MET* 4.5 0.2 - - - -
778A CYS* 2.9 30.5 + - - +
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Residues in contact with LEU 775 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A TYR* 4.2 32.5 + - + +
651A LEU* 3.7 3.3 - - - +
655A PHE* 6.6 0.2 - - + -
771A ASN 3.3 9.0 + - - +
772A GLU* 3.1 12.2 + - - +
774A GLU* 1.3 80.6 - - + +
776A LEU* 1.3 61.9 + - - +
777A MET 3.4 0.5 + - - -
778A CYS 3.5 6.6 - - - +
832A ARG* 3.2 42.9 + - - +
835A MET* 5.7 5.4 - - + -
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Residues in contact with LEU 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A TYR* 3.7 10.7 + - + +
526A TYR* 3.4 40.2 - - + -
529A PHE* 4.2 9.0 - - + -
646A VAL* 4.0 35.3 - - + +
650A LYS 4.3 3.5 - - - +
651A LEU* 3.5 11.7 - - - +
765A ILE* 4.4 4.5 - - + -
768A PHE* 3.7 31.6 - - + -
772A GLU 2.9 13.3 + - - +
773A LEU* 3.4 22.7 - - + +
775A LEU* 1.3 78.3 - - - +
777A MET* 1.3 58.0 + - - +
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Residues in contact with MET 777 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A ALA* 4.1 25.1 - - + +
645A ALA* 5.0 1.4 - - + +
646A VAL* 3.7 18.8 - - + +
650A LYS 5.0 1.6 - - - -
651A LEU* 3.6 7.0 - - - -
652A LEU* 2.9 37.8 + - + +
656A PHE* 4.0 26.0 - - + -
661A TYR* 4.3 3.6 - - + -
664A MET* 3.8 34.3 - - + +
752A PHE* 4.4 2.5 - - + -
756A PHE* 4.4 9.6 - - + -
773A LEU* 3.1 31.2 + - + +
774A GLU 4.2 0.2 - - - +
776A LEU* 1.3 77.3 - - + +
778A CYS* 1.3 68.2 + - - +
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Residues in contact with CYS 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 3.6 5.4 - - - +
652A LEU* 3.5 8.5 - - - -
654A GLY 3.1 26.5 - - - +
655A PHE* 3.8 18.2 - - + -
656A PHE* 4.2 14.6 - - - -
661A TYR* 3.4 20.9 - - - +
774A GLU 2.9 19.1 + - - +
775A LEU* 3.5 2.9 - - - +
777A MET* 1.3 96.4 - - - +
779A GLY* 1.3 59.4 + - - +
832A ARG* 3.4 19.4 + - - -
835A MET* 4.6 0.9 - - - +
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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