Contacts of the helix formed by residues 964 - 972 (chain A) in PDB entry 6DBV
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 964 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A CYS* 2.8 12.4 - - - -
751A LEU* 3.4 33.6 - - + +
752A CYS* 3.5 11.7 - - + -
766A HIS* 3.8 20.0 + - + +
767A SER 4.6 0.2 - - - -
768A ILE* 3.6 15.2 - - + +
813A LEU* 6.0 0.7 - - + -
959A HIS* 3.0 27.8 - + - -
960A LYS* 2.6 21.3 + - + +
963A ALA* 1.3 75.6 - - + +
965A VAL* 1.3 65.9 + - - +
966A PRO* 3.4 3.3 - - - -
967A GLU* 3.5 11.8 + - - +
968A ILE* 3.1 20.4 + - + +
1101A ZN 2.2 32.1 - - - -
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Residues in contact with VAL 965 (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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813A LEU* 5.7 7.2 - - + +
914A VAL* 4.4 8.7 - - + -
915A TRP* 3.7 22.2 - - + -
928A LEU* 6.0 0.7 - - + -
931A TYR* 3.4 42.8 - - + +
960A LYS 3.1 6.4 + - - +
961A THR* 3.5 21.3 + - - +
964A HIS* 1.3 78.3 - - - +
966A PRO* 1.3 73.1 - - + +
968A ILE* 3.1 11.8 - - + +
969A VAL* 3.0 38.8 + - + +
975A ILE* 6.1 1.3 - - + -
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Residues in contact with PRO 966 (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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928A LEU* 5.2 8.3 - - + +
931A TYR* 3.5 29.6 - - + -
932A SER* 5.2 11.9 - - - +
935A SER* 5.4 3.1 - - - +
961A THR 5.1 0.4 - - - +
962A LEU 5.7 0.9 - - - -
963A ALA* 4.3 7.2 - - - +
964A HIS* 3.5 10.1 - - - +
965A VAL* 1.3 95.8 - - + +
967A GLU* 1.3 61.8 + - - +
969A VAL* 3.8 4.5 - - + +
970A GLU* 2.9 26.6 + - - +
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Residues in contact with GLU 967 (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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766A HIS 5.8 2.7 - - - +
767A SER* 6.4 0.2 - - - -
768A ILE* 3.6 39.2 - - + +
963A ALA 5.6 1.5 + - - +
964A HIS* 3.5 12.0 + - - +
965A VAL 3.0 0.8 + - - -
966A PRO* 1.3 81.1 - - - +
968A ILE* 1.3 64.5 + - + +
970A GLU* 3.1 13.1 + - - +
971A ARG* 3.0 35.9 + - - +
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Residues in contact with ILE 968 (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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751A LEU* 5.7 2.7 - - + -
768A ILE* 4.1 15.9 - - + -
811A PRO 3.8 22.0 - - - +
812A THR* 4.2 9.4 - - - +
813A LEU* 3.7 30.1 - - + -
964A HIS* 3.1 14.8 - - + +
965A VAL* 3.1 22.4 - - + +
967A GLU* 1.3 74.3 - - + +
969A VAL* 1.3 65.5 + - + +
971A ARG* 3.0 8.2 + - - +
972A ASP* 2.9 47.2 + - + +
974A SER 5.3 1.1 + - - -
975A ILE* 3.8 21.1 - - + -
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Residues in contact with VAL 969 (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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914A VAL* 4.6 8.1 - - + -
920A PRO* 3.8 22.7 - - + -
928A LEU* 3.6 38.3 - - + +
965A VAL* 3.0 35.7 + - + +
966A PRO* 3.9 3.4 - - + +
968A ILE* 1.3 78.9 - - + +
970A GLU* 1.3 61.2 + - - +
973A GLY* 3.8 19.8 - - - +
974A SER* 5.4 2.9 - - - +
975A ILE* 4.2 25.1 - - + +
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Residues in contact with GLU 970 (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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928A LEU* 5.5 3.1 - - + +
966A PRO* 2.9 19.1 + - - +
967A GLU* 3.3 12.6 - - - +
969A VAL* 1.3 80.2 - - - +
971A ARG* 1.3 65.1 + - + +
973A GLY* 4.5 2.1 + - - -
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Residues in contact with ARG 971 (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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768A ILE* 5.4 6.1 - - - +
810A GLN* 3.4 20.2 - - - +
811A PRO* 3.9 21.7 + - - +
967A GLU* 3.0 28.2 + - - +
968A ILE* 3.0 17.6 + - - +
970A GLU* 1.3 81.4 - - + +
972A ASP* 1.3 97.3 + - - +
973A GLY 3.1 6.2 + - - -
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Residues in contact with ASP 972 (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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725A ARG* 5.2 12.0 + - - +
810A GLN* 3.5 12.1 + - - -
812A THR* 6.4 1.8 - - - -
968A ILE* 2.9 27.2 + - + +
971A ARG* 1.3 120.6 + - - +
973A GLY* 1.3 49.2 + - - +
974A SER 2.7 25.8 + - - +
978A TRP* 3.9 20.0 + - + +
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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