Contacts of the helix formed by residues 782 - 789 (chain E) in PDB entry 6C3P
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 THR 782 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781E ALA* 1.3 80.5 - - - +
783E VAL* 1.3 68.8 + - - +
784E GLU* 3.3 15.3 - - + +
785E GLU* 2.8 24.5 + - - +
786E ASN* 2.9 16.1 + - - +
818E ASP 3.2 19.1 - - - +
819E GLN* 3.5 23.0 - - + +
820E THR 3.5 4.9 - - - -
821E GLN* 2.2 29.7 + - - -
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Residues in contact with VAL 783 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781E ALA 3.6 0.6 + - - -
782E THR* 1.3 70.7 - - - +
784E GLU* 1.3 63.1 + - - +
786E ASN* 2.6 26.4 - - - +
787E ILE* 3.0 32.0 + - + +
798E TYR* 4.9 0.2 - - - +
807E LEU* 5.0 9.9 - - + -
811E ILE* 5.0 10.3 - - + -
814E LEU* 3.9 21.5 - - + -
817E GLY 3.9 4.3 - - - +
818E ASP* 3.1 20.0 - - - +
820E THR* 3.0 17.3 + - - +
822E ILE* 3.9 20.8 - - + +
837E ILE* 5.2 9.9 - - + -
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Residues in contact with GLU 784 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782E THR* 3.3 11.9 - - + +
783E VAL* 1.3 79.2 - - - +
785E GLU* 1.3 58.5 + - - +
787E ILE* 4.4 1.8 - - - -
788E ILE* 2.8 47.3 + - + +
793E PHE* 5.7 1.6 - - + -
798E TYR* 3.6 15.0 - - + +
818E ASP* 3.1 27.0 + - - +
819E GLN* 5.1 5.2 - - + +
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Residues in contact with GLU 785 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781E ALA* 3.6 13.2 - - + -
782E THR* 2.8 35.2 + - - +
784E GLU* 1.3 80.8 - - - +
786E ASN* 1.3 57.0 + - - +
788E ILE* 3.2 5.8 + - - +
789E PHE* 3.0 25.8 + - - -
790E GLU 4.8 0.5 + - - -
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Residues in contact with ASN 786 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778E LEU* 4.2 0.6 - - - +
779E LEU* 4.1 27.2 - - + +
781E ALA* 4.6 1.1 + - - +
782E THR 2.9 15.0 + - - +
783E VAL* 2.6 15.5 - - - +
785E GLU* 1.3 73.3 - - - +
787E ILE* 1.3 89.0 + - - +
789E PHE* 3.8 13.6 + - - +
822E ILE* 3.1 34.1 - - - +
837E ILE* 3.9 8.6 - - - +
841E ARG* 2.8 50.9 + - - +
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Residues in contact with ILE 787 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783E VAL* 3.0 39.1 + - + +
784E GLU* 3.9 3.6 - - - +
786E ASN* 1.3 89.4 + - - +
788E ILE* 1.3 66.2 + - - +
789E PHE* 4.3 2.4 - - - +
798E TYR* 3.8 31.4 - - + +
801E VAL* 5.4 3.4 - - + -
802E ILE* 5.2 10.3 - - + -
807E LEU* 4.7 15.5 - - + -
811E ILE* 5.9 0.4 - - + -
837E ILE* 4.1 16.2 - - + +
840E ALA* 4.6 21.3 - - + -
841E ARG* 4.4 13.7 - - - +
844E TYR* 3.5 22.3 - - + +
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Residues in contact with ILE 788 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784E GLU* 2.8 31.2 + - + +
785E GLU* 3.7 4.7 - - - +
787E ILE* 1.3 79.1 - - - +
789E PHE* 1.3 67.1 + - - +
790E GLU* 3.5 5.4 - - - +
791E SER* 3.2 50.4 - - - +
793E PHE* 3.6 38.6 - - + -
798E TYR* 4.7 5.2 - - + -
844E TYR* 3.6 17.1 - - + +
845E GLN* 4.9 2.9 - - - +
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Residues in contact with PHE 789 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E TRP* 6.4 1.1 - + - -
779E LEU* 5.3 13.7 - - + -
785E GLU 3.0 14.4 + - - -
786E ASN* 3.9 14.1 - - - +
787E ILE 3.4 2.6 - - - +
788E ILE* 1.3 79.1 - - - +
790E GLU* 1.3 70.7 + - + +
791E SER* 3.5 1.2 + - - -
841E ARG* 5.5 8.7 - - + +
845E GLN* 3.2 23.6 + - - +
1212E THR* 6.1 0.4 - - - -
1213E ILE* 5.2 5.2 - - + -
1216E PHE* 3.2 51.6 - + + -
1218E TYR* 3.3 32.5 - + + -
1222E PHE* 3.7 33.4 - + - -
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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