Contacts of the helix formed by residues 737 - 742 (chain D) in PDB entry 1P93
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 PHE 737 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733D LEU 2.5 22.1 + - - +
734D ASN* 4.7 4.0 - - - +
736D CYS* 1.3 74.9 - - - +
738D GLN* 1.3 61.3 + - + +
740D PHE* 2.9 23.0 + + - +
741D LEU* 2.8 50.6 - - + +
757D ILE* 3.2 29.2 - - + -
761D ILE* 3.0 47.3 - - + -
762D PRO* 3.6 27.1 - - + -
765D SER* 5.7 1.6 - - - -
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Residues in contact with GLN 738 (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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734D ASN 2.9 23.7 + - - +
735D TYR* 3.4 19.6 + - - +
736D CYS 3.3 0.2 - - - -
737D PHE* 1.3 77.9 - - + +
739D THR* 1.3 59.5 + - + +
741D LEU* 3.0 29.1 + - + +
742D ASP* 3.4 17.8 + - - +
745D MET* 4.6 2.4 - - - +
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Residues in contact with THR 739 (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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560D MET* 5.6 1.6 - - + -
642D GLN* 5.2 0.2 - - - +
735D TYR* 3.0 33.4 - - + +
736D CYS 3.2 8.3 + - - -
738D GLN* 1.3 74.9 - - + +
740D PHE* 1.3 59.2 + - - +
742D ASP 4.2 7.8 - - - +
745D MET* 4.3 18.7 - - - +
747D ILE* 4.1 28.8 - - + +
749D PHE* 3.4 10.7 - - - -
4999D DEX 2.6 40.6 + - - +
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Residues in contact with PHE 740 (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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736D CYS 3.1 13.5 - - - +
737D PHE* 2.9 19.5 + + - +
739D THR* 1.3 81.5 + - - +
741D LEU* 1.3 77.9 + - + +
747D ILE 5.7 0.6 - - - +
749D PHE* 3.2 33.8 - + + -
754D ALA* 4.9 12.8 - - + -
757D ILE* 3.3 38.8 - - + -
758D THR* 3.8 23.3 - - - -
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Residues in contact with LEU 741 (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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737D PHE* 2.8 49.4 - - + +
738D GLN* 3.0 20.5 + - + +
740D PHE* 1.3 97.8 - - + +
742D ASP* 1.3 71.1 + - - +
743D LYS* 3.0 7.3 + - - +
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Residues in contact with ASP 742 (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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738D GLN 3.4 6.6 + - - +
739D THR 4.2 4.5 - - - +
740D PHE 4.8 0.3 - - - -
741D LEU* 1.3 81.3 - - - +
743D LYS* 1.3 58.3 + - - +
744D THR* 2.9 35.8 + - - +
745D MET* 2.7 62.3 - - + +
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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