Contacts of the helix formed by residues 725 - 740 (chain C) in PDB entry 4OQB
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 725 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724C SER* 1.3 82.4 - - - +
726C ASP* 1.3 65.6 + - - +
727C SER* 4.0 12.1 - - - -
728C GLN* 3.4 13.4 + - - +
729C ILE* 3.2 21.0 + - - +
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Residues in contact with ASP 726 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A MET* 5.8 7.4 - - + -
724C SER 3.8 2.3 + - - +
725C SER* 1.3 71.9 - - - +
727C SER* 1.3 54.1 + - - +
729C ILE* 3.3 13.9 + - - +
730C LEU* 2.6 44.4 + - + +
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Residues in contact with SER 727 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A VAL* 3.7 33.9 - - - +
316A THR* 5.3 1.4 - - - +
319A THR* 4.4 4.2 + - - +
322A MET* 6.1 4.7 - - - +
725C SER* 3.3 7.3 - - - -
726C ASP* 1.3 76.0 - - - +
728C GLN* 1.3 59.7 + - - +
730C LEU* 3.5 8.0 - - - +
731C ASP* 2.9 31.7 + - - +
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Residues in contact with GLN 728 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715C GLU* 5.0 7.9 + - - +
718C GLN* 5.0 9.3 - - - +
719C ALA* 3.9 17.8 - - + +
724C SER* 3.9 20.8 + - - -
725C SER* 3.4 23.8 + - - +
727C SER* 1.3 79.3 - - - +
729C ILE* 1.3 62.1 + - - +
731C ASP* 3.6 7.6 + - - +
732C LEU* 3.4 33.2 + - - +
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Residues in contact with ILE 729 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716C VAL* 5.4 3.3 - - + +
719C ALA* 4.3 23.1 - - + +
720C VAL* 4.6 19.1 - - + -
724C SER 4.3 10.8 - - - +
725C SER 3.2 15.0 + - - +
726C ASP* 3.6 14.8 - - - +
728C GLN* 1.3 73.8 - - - +
730C LEU* 1.3 65.2 + - - +
732C LEU* 3.3 8.3 + - - +
733C SER* 2.8 34.2 + - - +
751C LEU* 4.8 8.5 - - + -
752C LEU 3.5 26.5 - - - +
753C ASN* 4.6 14.4 - - + +
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Residues in contact with LEU 730 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A THR* 4.9 7.2 - - + -
322A MET* 4.5 17.9 - - + -
561C ASP* 5.3 0.2 - - - +
562C ILE* 3.8 26.2 - - + -
563C VAL* 4.3 23.8 - - + -
726C ASP* 2.6 27.1 + - + +
727C SER* 3.2 9.6 + - - +
729C ILE* 1.3 72.8 - - - +
731C ASP* 1.3 58.3 + - - +
733C SER* 3.7 0.7 - - - -
734C ASN* 2.9 52.2 + - - +
751C LEU* 3.6 28.3 - - + -
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Residues in contact with ASP 731 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 3.5 30.2 + - + +
318A TRP* 3.6 16.1 - - - +
319A THR* 3.4 15.0 - - + +
727C SER 2.9 16.8 + - - +
728C GLN* 3.7 9.7 - - - +
730C LEU* 1.3 76.7 - - - +
732C LEU* 1.3 62.2 + - - +
734C ASN* 3.2 2.6 + - - +
735C ARG* 2.7 56.1 + - - +
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Residues in contact with LEU 732 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712C ILE* 3.2 23.9 - - + +
715C GLU* 3.5 64.8 - - + +
716C VAL* 3.4 24.9 - - + +
719C ALA* 4.3 9.9 - - + -
728C GLN* 3.4 25.8 + - - +
729C ILE* 3.3 7.0 + - - +
731C ASP* 1.3 86.0 - - - +
733C SER* 1.3 57.1 + - - +
735C ARG* 4.1 6.1 - - - +
736C PHE* 2.9 26.9 + - - +
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Residues in contact with SER 733 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C ILE* 3.3 23.6 - - - -
716C VAL* 4.9 0.4 - - - +
729C ILE* 2.8 23.6 + - - +
730C LEU 3.7 3.4 - - - -
732C LEU* 1.3 73.6 - - - +
734C ASN* 1.3 64.3 + - - +
736C PHE* 3.5 1.0 + - - +
737C TYR* 3.0 33.5 + - - -
751C LEU* 4.0 3.2 - - - +
752C LEU* 3.1 43.3 + - - +
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Residues in contact with ASN 734 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TRP* 4.2 14.6 + - + +
319A THR* 3.4 24.2 - - + +
560C VAL* 3.3 24.7 - - - +
561C ASP* 4.4 5.1 + - - -
562C ILE* 2.9 33.9 + - - +
730C LEU* 2.9 38.8 + - - +
731C ASP* 3.4 5.4 - - - +
733C SER* 1.3 77.2 - - - +
735C ARG* 1.3 58.0 + - - +
736C PHE 3.2 0.3 + - - -
738C THR* 2.4 34.6 + - - +
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Residues in contact with ARG 735 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TRP* 3.5 56.2 - - + +
639C TYR* 5.0 8.5 + - - -
708C ALA* 5.5 6.1 - - - +
712C ILE* 3.8 32.2 - - + +
715C GLU* 5.1 7.9 + - - -
731C ASP* 2.7 43.0 + - - +
732C LEU* 3.6 11.3 - - - +
734C ASN* 1.3 72.3 - - - +
736C PHE* 1.3 63.4 + - - +
738C THR* 3.6 6.6 + - - -
739C LEU* 3.1 32.8 + - - +
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Residues in contact with PHE 736 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709C ALA* 3.6 22.4 - - + -
712C ILE* 3.9 14.6 - - + +
713C LEU* 3.4 35.7 - - + -
732C LEU 2.9 17.9 + - - +
733C SER 3.9 3.8 - - - +
734C ASN 3.2 0.2 - - - -
735C ARG* 1.3 77.2 - - - +
737C TYR* 1.3 73.6 + + - +
739C LEU* 3.1 3.5 + - - +
740C ILE* 2.8 50.6 + - + +
742C HIS* 3.6 27.6 - + - -
752C LEU* 4.3 13.2 - - + -
761C LYS* 4.0 17.9 - - + -
764C MET* 4.7 0.2 - - - -
765C LEU* 3.9 13.2 - - + -
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Residues in contact with TYR 737 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C VAL* 3.8 17.9 - - + +
562C ILE* 4.0 9.4 - - + -
567C ASN* 4.6 8.4 - - - +
733C SER* 3.0 28.4 + - - +
736C PHE* 1.3 84.1 - + - +
738C THR* 1.3 64.1 + - - +
740C ILE 2.9 19.3 - - - +
741C PRO* 3.9 5.9 - - - +
742C HIS* 3.7 33.7 + + + -
744C PHE* 3.6 20.9 - + + -
749C PRO* 3.8 24.2 - - + -
750C PRO* 2.7 34.4 + - - +
752C LEU* 3.2 23.6 - - + +
761C LYS* 3.4 13.1 + - - -
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Residues in contact with THR 738 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TRP* 3.7 28.2 - - + -
558C GLY* 3.3 37.1 - - - +
559C LEU* 3.9 9.6 - - - +
560C VAL* 2.9 13.3 + - + +
633C LYS* 5.4 2.2 - - - +
639C TYR* 4.4 8.1 - - + -
641C LEU* 3.1 25.0 - - - +
734C ASN 2.4 32.8 + - - -
735C ARG 3.6 4.8 + - - -
737C TYR* 1.3 79.3 - - - +
739C LEU* 1.3 58.6 + - - +
740C ILE 3.5 1.2 + - - -
741C PRO* 4.5 0.7 - - - +
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Residues in contact with LEU 739 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TRP* 5.4 2.2 - - + -
639C TYR* 3.5 31.0 - - + +
641C LEU* 3.9 4.0 - - - +
701C LEU* 4.3 3.5 - - - +
705C GLN* 3.0 59.3 + - + +
708C ALA* 3.8 13.2 - - + -
709C ALA* 3.4 36.3 - - + +
712C ILE* 3.8 9.6 - - + -
735C ARG* 3.1 23.9 + - - +
736C PHE* 3.6 4.5 - - - +
738C THR* 1.3 81.3 - - - +
740C ILE* 1.3 62.4 + - + +
741C PRO* 3.9 5.9 - - - +
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Residues in contact with ILE 740 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691C ILE* 3.3 33.7 - - + -
696C MET* 6.2 1.3 - - - -
701C LEU* 4.2 18.8 - - + -
705C GLN* 5.7 0.4 - - + -
706C ILE* 5.5 2.7 - - + -
709C ALA* 3.4 32.5 - - + -
736C PHE* 2.8 22.3 + - + +
737C TYR* 2.9 16.8 - - - +
739C LEU* 1.3 77.4 - - + +
741C PRO* 1.3 64.7 - - + +
742C HIS* 2.8 29.7 + - + -
765C LEU* 3.5 28.7 - - + -
768C LEU* 6.3 2.7 - - + -
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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
------------------------------------------------------------
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