Contacts of the helix formed by residues 678 - 688 (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 ASP 678 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674C LYS 3.5 20.1 + - - +
675C MET 4.1 7.6 + - - +
676C ILE 3.7 0.6 - - - -
677C PHE* 1.3 73.7 - - - +
679C VAL* 1.3 63.5 + - - +
680C GLU* 3.4 17.5 + - - +
681C SER* 3.1 37.1 + - - +
682C MET* 3.6 12.3 + - - +
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Residues in contact with VAL 679 (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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677C PHE* 3.2 17.2 + - + +
678C ASP* 1.3 71.0 + - - +
680C GLU* 1.3 60.1 + - - +
681C SER 3.2 1.8 - - - -
682C MET* 3.1 16.0 + - + +
683C LYS* 2.8 29.5 + - + +
771C ILE* 4.1 15.7 - - + +
774C ALA* 5.3 7.9 - - + +
775C TYR* 3.3 48.7 - - + +
778C LEU* 4.1 21.8 - - + -
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Residues in contact with GLU 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C ASP* 3.4 10.5 + - - +
679C VAL* 1.3 76.4 - - - +
681C SER* 1.3 58.2 + - - +
683C LYS* 3.4 20.4 + - + +
684C LYS* 3.2 24.9 + - - +
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Residues in contact with SER 681 (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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675C MET 5.6 2.9 - - - -
678C ASP* 3.1 34.5 + - - +
679C VAL 3.2 0.4 - - - -
680C GLU* 1.3 77.9 - - - +
682C MET* 1.3 60.8 + - - +
684C LYS* 3.7 10.4 + - - +
685C ALA* 3.2 20.3 + - - +
866C THR* 6.3 3.6 - - - -
867C THR* 5.0 1.9 - - - +
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Residues in contact with MET 682 (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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675C MET 5.5 0.7 - - - +
676C ILE 3.1 33.0 - - - +
677C PHE* 4.6 3.1 - - - -
678C ASP 3.6 11.9 - - - +
679C VAL* 3.1 22.8 + - + +
681C SER* 1.3 76.5 - - - +
683C LYS* 1.3 65.3 + - - +
685C ALA* 3.3 14.4 - - - +
686C MET 3.4 2.8 + - - -
771C ILE* 3.4 41.8 - - + +
774C ALA* 4.0 26.7 - - + -
866C THR 4.7 1.1 - - - +
867C THR* 3.6 47.1 - - + +
870C ALA* 4.2 0.9 - - + -
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Residues in contact with LYS 683 (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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679C VAL* 2.8 18.5 + - + +
680C GLU* 3.5 23.1 - - + +
681C SER 3.3 0.2 - - - -
682C MET* 1.3 73.8 - - - +
684C LYS* 1.3 67.1 + - - +
686C MET* 2.9 19.8 + - - +
687C VAL* 3.3 13.9 + - - +
693C LEU* 4.2 10.6 - - + +
697C PRO* 3.9 26.3 - - + +
771C ILE* 5.2 3.6 - - + -
775C TYR* 3.2 26.3 + - + +
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Residues in contact with LYS 684 (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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680C GLU 3.2 10.7 + - - +
681C SER* 3.7 12.1 + - - +
683C LYS* 1.3 77.9 - - - +
685C ALA* 1.3 64.0 + - - +
687C VAL* 3.0 29.1 + - + +
688C GLU* 4.0 7.7 + - - +
911C SER* 5.9 0.2 + - - -
914C ASP* 4.9 17.4 + - - +
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Residues in contact with ALA 685 (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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681C SER 3.2 11.5 + - - +
682C MET* 3.3 15.5 - - - +
683C LYS 3.1 0.4 - - - -
684C LYS* 1.3 80.0 - - - +
686C MET* 1.3 62.0 + - + +
688C GLU* 3.3 31.9 - - - +
689C TYR* 3.6 2.9 - - - -
865C ARG* 3.5 25.9 + - - +
867C THR* 4.1 13.5 - - + -
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Residues in contact with MET 686 (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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682C MET 3.4 3.1 + - - +
683C LYS* 2.9 11.2 + - - +
685C ALA* 1.3 81.0 - - + +
687C VAL* 1.3 65.3 + - - +
688C GLU 3.2 2.7 - - - -
689C TYR* 3.1 40.4 + - + +
690C GLU 3.4 7.8 + - - -
691C ILE* 3.7 24.2 + - + -
693C LEU* 4.4 6.7 - - + -
764C MET 4.5 2.0 - - - +
767C ASN* 3.5 27.4 - - + -
768C LEU* 4.0 27.8 - - + -
771C ILE* 3.4 32.8 - - + -
865C ARG* 4.0 5.2 - - - +
867C THR* 5.7 0.9 - - - +
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Residues in contact with VAL 687 (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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683C LYS 3.3 12.1 + - - +
684C LYS* 3.0 24.3 + - + +
686C MET* 1.3 76.0 - - - +
688C GLU* 1.3 61.7 + - - +
690C GLU* 3.2 17.0 + - - +
691C ILE 5.2 0.4 - - - -
693C LEU* 3.5 37.5 - - + -
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Residues in contact with GLU 688 (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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684C LYS* 4.0 6.1 + - - +
685C ALA* 3.3 27.7 - - - +
687C VAL* 1.3 79.7 - - - +
689C TYR* 1.3 72.6 + - + +
690C GLU* 3.4 9.0 + - - +
865C ARG* 3.0 25.3 + - - -
909C HIS* 5.9 0.5 - - - -
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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