Contacts of the helix formed by residues 784 - 790 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783H THR* 1.3 71.6 - - - +
785H GLU* 1.3 57.1 + - - +
787H ASN* 3.2 10.7 + - - +
788H ILE* 2.9 28.6 + - - +
799H TYR* 5.5 0.9 - - - +
818H GLY 4.4 4.0 - - - +
819H ASP* 3.1 19.0 + - + +
821H THR* 3.1 13.8 + - - +
823H ILE* 4.8 10.6 - - + +
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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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783H THR* 4.5 4.3 - - - -
784H VAL* 1.3 75.0 - - - +
786H GLU* 1.3 58.8 + - - +
788H ILE* 3.0 9.4 + - - +
789H THR* 2.8 27.5 + - - -
794H PHE* 4.0 21.1 - - + -
799H TYR* 4.5 9.0 - - + +
819H ASP* 3.0 32.8 + - + +
820H GLN* 5.5 0.4 - - - -
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Residues in contact with GLU 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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780H LEU* 5.9 1.1 - - - +
782H ALA* 4.1 17.7 - - + -
783H THR* 3.3 15.5 + - - +
785H GLU* 1.3 76.0 - - - +
787H ASN* 1.3 63.6 + - - +
789H THR* 4.3 7.6 - - - +
790H PHE* 3.1 21.0 + - - -
791H GLU 5.0 0.2 + - - -
794H PHE* 4.7 5.6 - - + -
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Residues in contact with ASN 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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779H LEU* 5.5 7.6 - - + -
780H LEU* 4.9 22.7 - - - +
782H ALA* 5.0 1.2 - - + +
783H THR 2.9 14.7 + - - +
784H VAL* 3.4 13.7 - - - +
786H GLU* 1.3 76.3 - - - +
788H ILE* 1.3 59.6 + - - +
790H PHE* 4.2 5.5 - - - +
823H ILE* 6.0 4.0 - - + -
838H ILE* 4.8 13.7 - - + +
842H ARG* 3.8 16.5 - - - +
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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 VAL 2.9 11.5 + - - +
785H GLU 3.0 9.4 + - - +
787H ASN* 1.3 77.8 - - - +
789H THR* 1.3 65.8 + - - +
790H PHE* 3.6 0.7 + - - +
799H TYR* 4.2 23.8 - - + -
802H VAL* 6.3 2.7 - - + -
838H ILE 5.3 1.8 - - - -
841H ALA* 5.4 10.5 - - + +
842H ARG* 3.7 24.1 - - - +
845H TYR* 3.7 16.5 - - + +
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Residues in contact with THR 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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785H GLU 2.8 17.7 + - - -
786H GLU* 3.7 4.9 + - - -
787H ASN 3.6 0.2 - - - -
788H ILE* 1.3 75.2 - - - +
790H PHE* 1.3 66.5 + - - +
791H GLU 4.6 1.8 - - - -
792H SER* 2.5 39.1 + - - -
794H PHE* 3.6 31.2 - - - -
842H ARG 5.5 0.9 - - - +
845H TYR* 3.8 12.5 - - - -
846H GLN* 5.7 2.4 + - - +
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Residues in contact with PHE 790 (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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786H GLU 3.1 14.0 + - - -
787H ASN* 4.2 9.6 - - - +
788H ILE 4.1 6.3 - - - +
789H THR* 1.3 81.4 - - - +
791H GLU* 1.3 69.4 + - - +
792H SER* 4.4 1.0 - - - -
842H ARG* 4.6 13.0 - - + +
846H GLN* 6.4 2.0 - - + -
1217H PHE* 5.7 9.9 - - + -
1219H TYR* 4.3 16.2 - - + -
1223H PHE* 6.3 0.9 - - - -
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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