Contacts of the helix formed by residues 803 - 815 (chain U) in PDB entry 6FF7
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 803 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727U SER* 5.3 1.3 - - - -
801U GLN 3.5 2.8 + - - -
802U PHE* 1.3 77.3 - - - +
804U HIS* 1.3 61.1 + - - +
805U THR* 3.1 10.3 - - - -
806U GLN* 3.3 11.4 + - - +
807U ILE* 2.9 26.2 + - - +
1135U ALA* 5.4 12.8 - - - -
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Residues in contact with HIS 804 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726U ALA 3.8 8.7 + - - +
727U SER* 3.2 40.6 - - - +
729U PRO* 5.1 8.5 - - + -
803U THR* 1.3 74.5 - - - +
805U THR* 1.3 57.9 + - - +
807U ILE* 3.5 4.2 - - - +
808U GLU* 3.1 24.8 + - - +
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Residues in contact with THR 805 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803U THR* 3.1 6.4 - - - -
804U HIS* 1.3 77.0 - - - +
806U GLN* 1.3 64.5 + - - +
808U GLU* 3.1 17.4 + - - +
809U ALA* 3.2 11.3 + - - +
1131U VAL* 5.0 4.2 - - - +
1132U ASP 4.5 17.0 - - - -
1133U LEU* 4.8 8.7 - - - -
1134U ASP* 4.9 9.6 - - - -
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Residues in contact with GLN 806 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802U PHE* 4.0 12.6 - - + -
803U THR* 3.3 23.9 + - - +
805U THR* 1.3 78.6 - - - +
807U ILE* 1.3 57.1 + - - +
809U ALA* 3.2 9.8 + - - +
810U ILE* 3.0 27.3 + - - +
832U VAL* 5.2 12.8 - - + +
1133U LEU* 5.8 4.2 - - - +
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Residues in contact with ILE 807 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727U SER* 4.2 19.7 - - - +
802U PHE* 4.6 7.3 - - + +
803U THR 2.9 14.8 + - - +
804U HIS* 3.5 13.5 - - - +
806U GLN* 1.3 74.7 - - - +
808U GLU* 1.3 55.3 + - - +
810U ILE* 3.2 6.9 + - - +
811U ARG* 2.8 37.6 + - - +
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Residues in contact with GLU 808 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804U HIS 3.1 13.0 + - - +
805U THR* 3.1 13.9 + - - +
807U ILE* 1.3 76.2 - - - +
809U ALA* 1.3 56.6 + - - +
811U ARG* 3.7 6.9 - - - +
812U ALA* 3.0 29.8 + - - +
1131U VAL* 5.1 8.1 - - + -
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Residues in contact with ALA 809 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805U THR 3.2 10.5 + - - +
806U GLN* 3.4 12.6 - - - +
807U ILE 3.2 0.2 - - - -
808U GLU* 1.3 75.0 - - - +
810U ILE* 1.3 59.3 + - - +
812U ALA* 3.3 5.7 + - - +
813U GLY* 2.9 26.5 + - - -
819U THR* 5.2 1.7 - - - -
821U VAL* 4.8 14.1 - - + -
832U VAL* 5.0 11.9 - - + -
836U ILE* 5.7 0.5 - - - +
1131U VAL* 4.3 19.0 - - + +
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Residues in contact with ILE 810 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717U THR* 6.1 5.2 - - - -
806U GLN 3.0 13.4 + - - +
807U ILE* 3.2 11.0 + - - +
809U ALA* 1.3 75.6 - - - +
811U ARG* 1.3 63.2 + - - +
813U GLY* 3.3 2.1 + - - -
814U MET* 3.1 23.2 + - - +
832U VAL* 5.3 6.9 - - - +
835U GLN* 5.2 14.8 - - + -
836U ILE* 5.1 17.4 - - - +
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Residues in contact with ARG 811 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807U ILE 2.8 21.7 + - - +
808U GLU* 3.7 7.9 - - - +
810U ILE* 1.3 72.9 - - - +
812U ALA* 1.3 61.9 + - - +
814U MET* 3.3 15.2 + - - +
815U GLN* 3.5 12.3 + - - +
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Residues in contact with ALA 812 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702U TYR* 4.7 11.5 - - + +
808U GLU 3.0 19.6 + - - +
809U ALA* 3.6 6.5 - - - +
811U ARG* 1.3 75.2 - - - +
813U GLY* 1.3 64.1 + - - +
815U GLN* 3.1 25.6 + - - +
816U PRO 5.0 0.2 - - - +
817U GLY 6.0 0.3 - - - -
819U THR* 4.1 20.9 - - - -
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Residues in contact with GLY 813 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809U ALA 2.9 15.7 + - - -
810U ILE 3.3 2.4 + - - -
812U ALA* 1.3 77.2 - - - +
814U MET* 1.3 60.1 + - - +
815U GLN 3.6 4.8 + - - +
819U THR* 4.2 11.8 - - - -
836U ILE* 4.9 17.0 - - - +
840U ILE* 5.7 3.6 - - - +
1090U ARG* 4.6 11.1 - - - +
1092U ILE* 5.1 9.0 - - - -
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Residues in contact with MET 814 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709U ILE* 5.9 2.3 - - - +
712U LEU* 5.5 11.4 - - + -
810U ILE 3.1 12.7 + - - +
811U ARG* 3.6 11.2 - - - +
812U ALA 3.2 0.6 - - - -
813U GLY* 1.3 76.5 - - - +
815U GLN* 1.3 60.3 + - - +
816U PRO 4.2 0.2 - - - -
836U ILE* 5.6 2.9 - - - +
839U ASN* 5.1 15.0 - - + -
840U ILE* 5.9 7.9 - - - +
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Residues in contact with GLN 815 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702U TYR* 3.5 29.2 - - + -
708U GLN* 5.7 3.6 - - + -
709U ILE* 5.5 12.6 - - + +
811U ARG 3.5 9.0 + - - +
812U ALA 3.1 15.2 + - - +
813U GLY* 3.9 5.0 - - - +
814U MET* 1.3 82.5 - - - +
816U PRO* 1.3 65.2 - - - +
817U GLY 3.7 2.9 + - - +
1090U ARG* 4.2 9.6 - - - +
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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