Contacts of the helix formed by residues 760 - 766 (chain D) in PDB entry 1O23
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 GLN 760 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712D ASN 5.0 0.5 - - - +
714D TRP* 5.8 2.8 + - - -
758D ASN* 2.8 20.8 + - - +
759D PRO* 1.3 76.0 - - + +
761D ARG* 1.3 65.3 + - - +
762D PHE 3.3 2.9 - - - -
763D ASP* 3.1 19.6 + - + +
764D ARG* 2.5 55.9 + - + +
804D SER* 5.1 9.4 + - - +
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Residues in contact with ARG 761 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C HIS 3.9 10.7 + - - -
435C THR 4.5 4.9 + - - -
444C VAL* 5.9 2.0 - - - +
814C PG4 3.9 7.5 - - - -
713D TYR* 4.1 6.9 - - + -
716D TRP* 3.7 30.6 - - - -
717D GLY* 3.6 34.5 - - - +
718D GLY* 3.8 9.9 - - - +
757D PRO* 3.9 10.4 - - - +
758D ASN* 2.9 59.9 + - - +
759D PRO* 3.4 2.8 - - - +
760D GLN* 1.3 76.5 - - - +
762D PHE* 1.3 107.6 + - + +
764D ARG* 3.2 3.0 + - - +
765D ILE* 2.9 33.4 + - - +
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Residues in contact with PHE 762 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C HIS* 3.5 31.9 - + + -
435C THR* 5.0 4.7 - - + -
507C LYS* 3.7 32.8 - - + +
508C ALA* 3.6 37.9 - - + -
511C PRO* 3.8 8.5 - - - +
512C MET* 4.2 10.8 - - + -
718D GLY* 6.5 0.7 - - - -
721D ASP* 5.8 2.7 - - - -
759D PRO 5.0 3.3 + - - +
760D GLN 3.3 1.0 - - - -
761D ARG* 1.3 115.2 - - + +
763D ASP* 1.3 61.2 + - - +
765D ILE* 2.9 36.4 - - + +
766D ALA* 3.5 5.2 + - - +
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Residues in contact with ASP 763 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C LYS* 3.3 33.2 - - - +
759D PRO 5.2 1.9 - - - +
760D GLN* 3.1 14.1 + - + +
762D PHE* 1.3 78.3 - - - +
764D ARG* 1.3 62.9 + - + +
766D ALA* 3.2 11.7 + - - +
767D HIS* 2.9 34.2 + - + +
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Residues in contact with ARG 764 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712D ASN* 3.6 46.7 + - - +
713D TYR* 3.2 31.0 + - + +
714D TRP* 5.9 0.6 - - - -
722D ASP* 4.2 1.0 - - - +
758D ASN* 4.5 5.2 - - - +
760D GLN* 2.5 69.9 + - + +
761D ARG 3.6 4.0 - - - +
763D ASP* 1.3 72.8 - - + +
765D ILE* 1.3 64.5 + - - +
766D ALA 3.1 2.0 - - - -
767D HIS* 3.0 17.2 + - - +
768D THR* 3.4 8.3 + - - -
771D THR* 4.7 3.2 + - - +
804D SER* 5.7 1.8 + - - -
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Residues in contact with ILE 765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511C PRO* 3.5 15.4 - - + +
512C MET* 3.3 33.9 - - - -
713D TYR* 3.5 9.9 - - - +
718D GLY* 3.4 31.4 - - - +
721D ASP* 3.9 14.6 - - + +
722D ASP 4.0 3.4 - - - +
725D ASN* 2.7 31.3 + - - +
761D ARG 2.9 14.2 + - - +
762D PHE* 2.9 39.0 - - + +
764D ARG* 1.3 75.5 - - - +
766D ALA* 1.3 60.7 + - - +
768D THR* 3.3 7.5 + - - -
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Residues in contact with ALA 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510C LYS* 6.0 5.6 - - + -
511C PRO* 4.4 18.8 - - + -
729D PHE* 6.2 0.3 - - - -
762D PHE 3.9 8.1 - - - +
763D ASP* 3.2 14.8 + - - +
764D ARG 3.1 0.8 - - - -
765D ILE* 1.3 81.7 - - - +
767D HIS* 1.3 70.9 + - + +
768D THR 3.6 0.2 - - - -
769D LYS* 5.9 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