Contacts of the helix formed by residues 784 - 790 (chain E) in PDB entry 6BAA
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 VAL 784 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782E ALA 3.8 0.2 + - - -
783E THR* 1.3 70.8 - - - +
785E GLU* 1.3 58.2 + - - +
787E ASN* 3.2 9.7 + - - +
788E ILE* 2.9 28.8 + - - +
799E TYR* 5.5 0.9 - - - +
818E GLY 4.4 4.7 - - - +
819E ASP* 3.1 18.0 + - + +
821E THR* 3.1 14.6 + - - +
823E ILE* 4.8 9.3 - - + +
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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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783E THR* 3.2 4.2 - - - -
784E VAL* 1.3 75.9 - - - +
786E GLU* 1.3 57.0 + - - +
788E ILE* 3.0 8.9 + - - +
789E THR* 2.8 28.1 + - - -
794E PHE* 4.0 20.0 - - + -
799E TYR* 4.5 9.4 - - + +
819E ASP* 3.0 34.0 + - + +
820E GLN* 5.5 0.2 - - - -
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Residues in contact with GLU 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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780E LEU* 5.9 1.7 - - - +
782E ALA* 4.1 18.6 - - + -
783E THR* 3.3 14.1 + - - +
785E GLU* 1.3 76.4 - - - +
787E ASN* 1.3 65.2 + - - +
789E THR* 4.3 7.6 - - - +
790E PHE* 3.1 21.5 + - - -
791E GLU 5.0 0.3 + - - -
794E PHE* 4.7 6.0 - - + -
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Residues in contact with ASN 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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779E LEU* 5.5 7.0 - - + -
780E LEU* 4.9 22.7 - - - +
782E ALA* 5.0 0.8 - - - +
783E THR 2.9 14.6 + - - +
784E VAL* 3.2 14.3 + - - +
786E GLU* 1.3 76.1 - - - +
788E ILE* 1.3 60.2 + - - +
790E PHE* 4.2 6.2 - - - +
823E ILE* 6.0 3.8 - - + -
838E ILE* 4.8 14.7 - - + +
842E ARG* 3.8 16.1 - - - +
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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 VAL 2.9 11.6 + - - +
785E GLU 3.0 8.9 + - - +
787E ASN* 1.3 77.7 - - - +
789E THR* 1.3 66.3 + - - +
790E PHE* 3.6 0.7 + - - +
799E TYR* 4.2 23.8 - - + -
802E VAL* 6.3 2.7 - - + -
838E ILE 5.3 1.8 - - - -
841E ALA* 5.4 10.5 - - + -
842E ARG* 3.7 23.3 - - - +
845E TYR* 3.7 17.4 - - + +
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Residues in contact with THR 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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785E GLU 2.8 18.8 + - - -
786E GLU* 4.3 4.5 - - - -
788E ILE* 1.3 75.4 - - - +
790E PHE* 1.3 67.2 + - - +
791E GLU 4.6 1.8 - - - -
792E SER* 2.5 39.8 + - - -
794E PHE* 3.6 30.3 - - - -
799E TYR* 6.1 0.2 - - - -
842E ARG 5.5 0.5 - - - +
845E TYR* 3.8 12.7 - - - -
846E GLN* 5.7 2.4 + - - +
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Residues in contact with PHE 790 (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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786E GLU 3.1 14.6 + - - -
787E ASN 4.2 9.9 - - - +
788E ILE 4.1 6.5 - - - +
789E THR* 1.3 79.8 - - - +
791E GLU* 1.3 69.0 + - - +
792E SER* 4.4 0.9 - - - -
842E ARG* 4.6 13.2 - - + +
846E GLN* 6.4 1.3 - - + -
1217E PHE* 5.7 9.9 - - + -
1219E TYR* 4.3 16.6 - - + -
1223E PHE* 6.3 1.1 - - - -
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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