Contacts of the helix formed by residues 717 - 725 (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 TYR 717 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715G VAL 3.5 1.0 + - - -
716G LEU* 1.3 74.7 - - + +
718G ALA* 1.3 57.2 + - - +
720G PHE* 2.9 7.5 + - + +
721G LYS* 2.8 24.1 + - - +
740G SER* 3.5 18.3 - - - +
741G LYS* 3.9 42.0 - - + +
744G SER* 2.9 37.2 + - - -
745G GLU* 5.1 0.2 - - - +
760G PHE* 3.1 38.9 - + - +
761G GLY 3.3 25.1 + - - -
762G HIS 4.6 1.1 - - - -
763G THR* 3.6 21.3 - - - +
764G MLY 3.6 5.8 - - - -
765G VAL* 3.4 24.7 - - + +
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Residues in contact with ALA 718 (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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716G LEU* 3.5 8.2 - - + +
717G TYR* 1.3 71.1 - - - +
719G ASP* 1.4 61.6 - - - +
720G PHE 2.8 5.9 + - - -
721G LYS* 2.8 27.1 + - - +
722G GLN* 3.0 20.2 + - - +
740G SER* 4.3 14.8 + - - +
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Residues in contact with ASP 719 (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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28G GLN* 4.3 15.1 + - - +
84G MLY 1.3 245.6 + - - +
85G TYR* 4.2 2.1 - - - -
88G ILE* 5.5 2.0 - - - +
716G LEU* 3.2 20.1 - - + +
718G ALA* 1.4 75.3 - - - +
720G PHE* 1.4 53.8 + - - -
722G GLN* 4.8 3.7 - - - +
723G ARG* 3.7 19.9 + - - +
724G TYR* 4.9 1.4 - - - -
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Residues in contact with PHE 720 (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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84G MLY 2.2 13.5 - - - -
715G VAL* 3.3 31.0 - - + +
716G LEU 2.8 2.7 + - - +
717G TYR* 3.0 17.0 - + + +
718G ALA 2.8 0.2 - - - -
719G ASP* 1.4 72.7 - - - +
721G LYS* 1.3 67.0 + - - +
723G ARG 4.4 0.2 - - - -
724G TYR* 3.5 46.9 + + + +
736G GLN* 3.4 5.0 + - - -
744G SER* 3.3 26.5 - - - +
747G LEU* 4.8 10.8 - - + -
748G LEU* 3.6 35.2 - - + -
765G VAL* 5.5 3.6 - - + -
767G PHE* 3.5 26.7 - + - -
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Residues in contact with LYS 721 (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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717G TYR 2.8 7.9 + - - +
718G ALA* 2.8 14.2 + - - +
720G PHE* 1.3 72.6 - - - +
722G GLN* 1.3 61.6 - - - +
724G TYR 2.9 3.1 + - - -
725G ARG* 2.7 21.3 + - - +
733G PRO 3.9 0.9 - - - -
736G GLN* 0.8 218.9 + - + +
737G PHE* 2.1 27.3 + - + +
740G SER* 4.0 14.5 - - - +
743G ALA* 3.9 2.0 - - + -
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Residues in contact with GLN 722 (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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28G GLN* 5.4 5.7 + - - +
29G ASN* 3.5 29.5 + - - +
718G ALA 3.0 10.6 + - - +
719G ASP* 5.2 3.6 - - - +
721G LYS* 1.3 81.0 - - - +
723G ARG* 1.3 70.1 + - + +
724G TYR 3.3 0.5 + - - -
725G ARG* 3.9 10.6 + - - +
726G VAL* 4.9 6.4 - - - +
736G GLN* 3.2 0.8 + - - -
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Residues in contact with ARG 723 (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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84G MLY 5.8 8.1 - - + +
719G ASP 3.7 15.5 + - - +
720G PHE 4.1 0.2 + - - -
721G LYS 3.3 1.2 - - - -
722G GLN* 1.3 83.7 - - + +
724G TYR* 1.3 93.8 + - + +
726G VAL* 5.2 6.9 - - - +
727G LEU* 5.1 0.2 - - - +
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Residues in contact with TYR 724 (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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84G MLY 5.8 0.4 - - - -
715G VAL* 5.7 4.9 - - + +
719G ASP 5.0 2.5 - - - -
720G PHE* 3.5 50.3 - + + +
721G LYS 2.9 2.6 + - - -
723G ARG* 1.3 108.1 - - + +
725G ARG* 1.3 69.4 + - - +
726G VAL* 3.0 4.7 - - - -
727G LEU* 2.8 48.8 + - + +
736G GLN* 4.9 0.4 - - - +
747G LEU* 3.7 7.8 - - + +
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Residues in contact with ARG 725 (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 2.7 19.5 + - - +
722G GLN* 3.9 6.9 + - - +
723G ARG 3.9 0.8 - - - -
724G TYR* 1.3 70.0 - - - +
726G VAL* 1.3 55.8 + - + +
727G LEU 2.8 12.1 + - - -
729G ALA* 2.9 21.7 + - - +
732G ILE* 3.3 20.7 - - - +
733G PRO* 2.0 60.4 - - + +
734G GLU* 6.1 0.2 - - - +
736G GLN* 3.4 7.6 - - - +
737G PHE* 2.7 33.6 - - - -
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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