Contacts of the helix formed by residues 782 - 789 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781H ALA* 1.3 80.4 - - - +
783H VAL* 1.3 70.2 + - - +
784H GLU* 3.3 15.5 - - + +
785H GLU* 2.8 24.8 + - - +
786H ASN* 2.9 15.6 + - - +
818H ASP 3.2 19.1 - - - +
819H GLN* 3.5 22.2 - - + +
820H THR 3.5 4.3 - - - -
821H GLN* 2.2 31.2 + - - -
822H ILE* 4.5 0.2 - - - -
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Residues in contact with VAL 783 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781H ALA 3.6 0.8 + - - -
782H THR* 1.3 69.8 - - - +
784H GLU* 1.3 62.7 + - - +
786H ASN* 2.6 26.6 - - - +
787H ILE* 3.0 31.7 + - + +
798H TYR* 4.9 0.2 - - - +
807H LEU* 5.0 10.3 - - + -
811H ILE* 5.0 9.6 - - + -
814H LEU* 3.9 21.5 - - + -
817H GLY 3.9 4.9 - - - +
818H ASP* 3.1 20.6 - - - +
820H THR* 3.0 18.5 + - - +
822H ILE* 3.9 20.2 - - + +
837H ILE* 5.2 9.4 - - + -
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Residues in contact with GLU 784 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782H THR* 3.2 12.1 - - + +
783H VAL* 1.3 78.7 - - - +
785H GLU* 1.3 57.4 + - - +
787H ILE* 3.9 2.6 - - - +
788H ILE* 2.8 47.0 + - + +
793H PHE* 5.7 2.0 - - + -
798H TYR* 3.6 15.0 - - + +
818H ASP* 3.1 27.1 + - - +
819H GLN* 5.1 5.4 - - + +
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Residues in contact with GLU 785 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781H ALA* 3.6 13.2 - - + -
782H THR* 2.8 36.0 + - - +
784H GLU* 1.3 79.8 - - - +
786H ASN* 1.3 58.4 + - - +
788H ILE* 3.7 5.7 - - - +
789H PHE* 3.0 25.5 + - - -
790H GLU 4.8 0.5 + - - -
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Residues in contact with ASN 786 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778H LEU* 4.2 0.8 - - - +
779H LEU* 4.1 28.1 - - + +
781H ALA 5.3 0.7 - - - +
782H THR 2.9 14.7 + - - +
783H VAL* 2.6 16.4 - - - +
785H GLU* 1.3 74.4 - - + +
787H ILE* 1.3 89.8 + - - +
789H PHE* 3.8 14.1 + - - +
822H ILE* 3.1 34.4 - - - +
837H ILE* 3.9 8.2 - - - +
841H ARG* 2.8 51.4 + - - +
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Residues in contact with ILE 787 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783H VAL* 3.0 39.8 + - + +
784H GLU* 3.9 3.1 - - - +
786H ASN* 1.3 87.5 + - - +
788H ILE* 1.3 66.0 + - - +
789H PHE* 4.3 2.6 - - - +
798H TYR* 3.8 31.0 - - + +
801H VAL* 5.4 3.4 - - + -
802H ILE* 5.2 10.1 - - + -
807H LEU* 4.7 15.3 - - + -
811H ILE* 5.9 0.2 - - + -
837H ILE* 4.1 15.7 - - + -
840H ALA* 4.6 21.8 - - + -
841H ARG* 4.4 14.6 - - - +
844H TYR* 3.5 22.0 - - + +
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Residues in contact with ILE 788 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784H GLU* 2.8 31.5 + - + +
785H GLU* 3.7 4.9 - - - +
787H ILE* 1.3 79.9 - - - +
789H PHE* 1.3 67.0 + - - +
790H GLU* 3.5 5.8 - - - +
791H SER* 3.2 50.3 - - - +
793H PHE* 3.6 38.8 - - + -
798H TYR* 4.7 6.1 - - + -
844H TYR* 3.6 16.2 - - + -
845H GLN* 4.9 2.9 - - - +
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Residues in contact with PHE 789 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777H TRP* 6.4 1.3 - + - -
779H LEU* 5.3 14.1 - - + -
785H GLU 3.0 14.2 + - - -
786H ASN* 3.9 14.1 - - - +
787H ILE 3.4 2.8 - - - +
788H ILE* 1.3 79.3 - - - +
790H GLU* 1.3 70.4 + - + +
791H SER* 4.5 1.4 - - - -
841H ARG* 5.5 8.5 - - + +
845H GLN* 3.2 23.7 + - - +
1212H THR* 6.1 0.2 - - - -
1213H ILE* 5.2 5.8 - - + -
1216H PHE* 3.2 50.5 - + + -
1218H TYR* 3.3 31.9 - + + -
1222H PHE* 3.7 33.7 - + - -
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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