Contacts of the helix formed by residues 730 - 739 (chain G) in PDB entry 1O1F
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 SER 730 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728G ASN 2.7 5.1 + - - -
729G ALA* 1.3 72.4 - - - +
731G ALA* 1.3 48.8 + - - -
733G PRO* 3.0 16.0 - - - +
734G GLU* 2.7 36.7 - - - +
109I HIS* 1.7 66.0 - - - +
113I THR* 5.2 1.1 - - - +
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Residues in contact with ALA 731 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728G ASN* 2.6 18.3 + - + +
730G SER* 1.3 74.1 - - - +
732G ILE* 1.3 61.2 + - + +
734G GLU* 4.1 9.5 - - - +
735G GLY* 3.5 15.4 + - - -
746G LYS* 4.4 12.1 - - + +
747G LEU* 4.3 7.9 + - - +
105I ALA* 5.0 2.9 - - + +
106I GLU* 5.9 2.2 - - + -
109I HIS* 2.9 27.8 - - + +
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Residues in contact with ILE 732 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724G TYR 3.7 0.7 - - - +
725G ARG* 3.3 11.0 - - - +
727G LEU* 3.5 15.0 - - + -
728G ASN* 3.1 36.5 + - + +
731G ALA* 1.3 73.9 - - + +
733G PRO* 1.3 70.0 - - - +
735G GLY* 3.4 0.9 + - - -
736G GLN* 3.0 47.9 + - - +
747G LEU* 0.6 137.8 - - + +
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Residues in contact with PRO 733 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725G ARG* 2.0 57.0 - - + +
729G ALA* 1.3 55.0 - - - +
730G SER* 3.0 15.0 - - - +
732G ILE* 1.3 96.5 - - + +
734G GLU* 1.3 53.0 + - + +
736G GLN* 3.3 0.9 + - + -
737G PHE* 1.7 47.5 + - + -
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Residues in contact with GLU 734 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730G SER* 2.7 30.6 - - - +
731G ALA* 4.2 9.6 - - - +
733G PRO* 1.3 81.5 - - + +
735G GLY* 1.3 52.5 + - - +
737G PHE* 4.1 2.9 - - - -
738G MET* 2.3 54.0 + - + +
109I HIS* 4.4 10.0 - - - -
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Residues in contact with GLY 735 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731G ALA 3.5 5.2 + - - -
732G ILE 3.4 4.4 + - - -
733G PRO 3.2 0.6 - - - -
734G GLU* 1.3 80.0 - - - +
736G GLN* 1.3 47.9 - - - +
738G MET* 4.1 2.6 - - - +
739G ASP 3.0 18.0 + - - +
742G LYS* 3.8 1.0 - - - +
743G ALA* 1.9 48.5 + - - +
746G LYS* 3.9 16.2 - - - -
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Residues in contact with GLN 736 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720G PHE* 3.4 8.9 + - - -
721G LYS* 0.8 195.0 + - + +
722G GLN* 3.2 0.7 + - - -
725G ARG* 3.4 15.8 - - - +
732G ILE* 3.0 42.2 + - + +
733G PRO 3.7 2.9 - - - +
735G GLY* 1.3 67.8 - - - +
737G PHE* 1.3 53.4 - - + +
740G SER* 3.4 14.6 - - - -
743G ALA* 2.0 27.6 - - + +
744G SER* 4.2 7.9 - - - +
747G LEU* 3.6 0.8 - - - +
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Residues in contact with PHE 737 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721G LYS* 2.2 16.2 + - + +
725G ARG* 2.7 59.7 - - + -
733G PRO* 1.7 43.0 + - + +
734G GLU* 3.6 4.3 - - - +
736G GLN* 1.3 79.1 - - + +
738G MET* 1.3 70.4 + - + +
739G ASP* 4.4 1.0 - - - -
740G SER 4.8 1.0 + - - -
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Residues in contact with MET 738 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734G GLU* 2.3 42.2 + - + +
735G GLY* 4.1 2.9 - - - +
737G PHE* 1.3 85.9 - - - +
739G ASP* 1.3 60.9 + - - +
742G LYS* 5.7 3.5 - - + +
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Residues in contact with ASP 739 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735G GLY 3.1 5.7 + - - -
736G GLN 3.7 1.1 - - - -
737G PHE 4.4 0.2 - - - -
738G MET* 1.3 81.0 - - - +
740G SER* 1.3 77.3 + - - +
741G LYS* 2.6 23.1 + - - +
742G LYS* 2.7 45.3 + - + +
743G ALA* 2.5 32.4 + - - +
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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