Contacts of the helix formed by residues 862 - 871 (chain A) in PDB entry 6QVC
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 ALA 862 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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610A VAL* 6.0 2.2 - - + +
847A HIS 4.5 1.1 - - - -
848A LEU* 3.7 19.3 - - + -
860A VAL* 4.1 6.3 + - + -
861A LEU* 1.3 76.7 - - - +
863A LEU* 1.3 66.3 + - - +
864A GLU* 3.6 13.5 - - - +
865A GLU* 3.1 30.0 + - - +
866A LEU* 3.2 24.3 + - - +
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Residues in contact with LEU 863 (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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199A ARG 5.2 7.4 - - - +
200A GLY* 4.3 27.4 - - - +
201A VAL* 4.5 11.4 - - + -
590A LEU* 3.6 27.6 - - + -
841A PHE* 5.4 5.4 - - + -
846A LEU 5.4 2.7 - - - +
847A HIS* 4.0 33.7 + - + +
848A LEU* 4.3 3.9 - - + +
862A ALA* 1.3 72.1 - - - +
864A GLU* 1.3 71.5 + - - +
866A LEU* 3.0 26.3 + - + +
867A GLN* 3.2 20.0 + - - +
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Residues in contact with GLU 864 (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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588A PRO* 6.0 1.1 - - + -
862A ALA* 3.7 10.6 - - - +
863A LEU* 1.3 83.0 + - - +
865A GLU* 1.3 82.5 + - - +
867A GLN* 3.1 21.6 + - - +
868A LYS* 2.9 47.0 + - - +
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Residues in contact with GLU 865 (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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608A ILE* 4.2 33.7 - - + +
610A VAL* 4.7 14.5 - - + +
862A ALA* 3.1 36.3 - - - +
863A LEU 3.2 0.4 - - - -
864A GLU* 1.3 94.2 - - - +
866A LEU* 1.3 59.1 + - - +
868A LYS* 3.7 15.6 + - + +
869A ALA* 2.8 29.8 + - - +
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Residues in contact with LEU 866 (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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590A LEU* 3.8 18.8 - - + -
608A ILE* 5.9 1.1 - - - -
834A LEU* 4.2 14.3 - - + +
837A THR* 4.5 3.6 - - + -
838A HIS* 3.8 38.1 - - + +
841A PHE* 3.6 38.4 - - + -
861A LEU* 3.6 14.0 - - + +
862A ALA 3.2 27.5 + - - +
863A LEU* 3.0 19.4 + - + +
865A GLU* 1.3 77.4 - - - +
867A GLN* 1.3 58.7 + - - +
869A ALA* 3.4 6.3 + - - +
870A ILE* 2.9 32.1 + - - +
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Residues in contact with GLN 867 (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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201A VAL* 3.9 12.3 - - - +
588A PRO* 3.2 29.4 + - + +
589A TYR* 3.3 35.5 - - - +
590A LEU* 3.6 27.4 - - + +
863A LEU* 3.2 8.5 + - - +
864A GLU* 3.1 22.5 + - - +
866A LEU* 1.3 78.4 - - - +
868A LYS* 1.3 58.7 + - + +
870A ILE* 3.3 10.6 + - - +
871A GLU* 3.0 33.3 + - - +
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Residues in contact with LYS 868 (chain A).
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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864A GLU* 2.9 36.9 + - - +
865A GLU* 3.8 15.8 + - + +
866A LEU 3.4 0.2 - - - -
867A GLN* 1.3 73.9 - - + +
869A ALA* 1.3 65.1 + - - +
871A GLU* 3.1 36.8 - - - +
872A GLY 4.8 0.2 + - - -
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Residues in contact with ALA 869 (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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608A ILE* 4.5 20.4 - - + -
834A LEU* 3.6 26.8 - - + +
865A GLU 2.8 18.6 + - - +
866A LEU* 3.6 4.9 - - - +
868A LYS* 1.3 78.7 - - - +
870A ILE* 1.3 58.2 + - - +
871A GLU 3.1 5.6 + - - -
872A GLY* 3.1 18.4 + - - -
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Residues in contact with ILE 870 (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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589A TYR 5.7 0.4 - - - +
590A LEU* 3.8 21.1 - - + -
591A PRO* 4.2 32.5 - - + +
595A TRP* 4.6 20.6 - - + -
834A LEU* 3.8 22.0 - - + +
835A HIS* 4.8 13.9 - - + +
838A HIS* 5.1 9.6 - - + -
866A LEU 2.9 22.5 + - - +
867A GLN* 3.5 9.2 - - - +
869A ALA* 1.3 68.8 - - - +
871A GLU* 1.3 64.3 + - - +
872A GLY 3.1 11.7 + - - +
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Residues in contact with GLU 871 (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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867A GLN 3.0 18.8 + - - +
868A LYS* 3.1 38.9 - - - +
870A ILE* 1.3 75.3 - - - +
872A GLY* 1.3 56.1 + - - +
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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