Contacts of the helix formed by residues 669 - 688 (chain C) in PDB entry 5ZRV
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 669 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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667C VAL 4.0 2.0 + - - -
668C SER* 1.3 77.4 - - - +
670C ASP* 1.3 64.9 + - - +
671C GLU 3.4 2.5 - - - +
672C ASP* 3.7 6.6 - - - +
673C ILE* 3.0 19.1 + - - -
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Residues in contact with ASP 670 (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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574C LEU 5.7 0.7 - - - +
669C SER* 1.3 68.5 - - - +
671C GLU* 1.3 60.8 + - - +
673C ILE* 3.3 1.7 + - - -
674C GLN* 2.9 25.8 + - - -
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Residues in contact with GLU 671 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C SER 3.4 0.2 - - - -
670C ASP* 1.3 74.4 - - - +
672C ASP* 1.3 56.0 + - - +
674C GLN* 3.5 1.5 + - - +
675C PHE* 3.0 26.2 + - - -
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Residues in contact with ASP 672 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C SER* 5.1 5.4 - - - +
669C SER* 3.3 15.6 + - - +
670C ASP 3.2 0.8 - - - -
671C GLU* 1.3 77.2 - - - +
673C ILE* 1.3 56.2 + - - +
675C PHE* 3.4 1.6 + - - -
676C ARG* 2.8 24.9 + - - -
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Residues in contact with ILE 673 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C SER* 5.1 1.4 - - - +
669C SER 3.0 13.7 + - - -
670C ASP 3.3 1.5 + - - -
672C ASP* 1.3 73.5 - - - +
674C GLN* 1.3 64.9 + - - +
676C ARG* 3.7 2.9 - - - +
677C LEU* 3.0 20.6 + - - -
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Residues in contact with GLN 674 (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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574C LEU 6.1 0.9 - - - -
670C ASP 2.9 16.7 + - - -
671C GLU* 3.8 2.0 - - - +
673C ILE* 1.3 76.7 - - - +
675C PHE* 1.3 57.5 + - - +
677C LEU* 3.4 0.9 + - - -
678C VAL* 3.0 25.1 + - - -
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Residues in contact with PHE 675 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671C GLU 3.0 14.6 + - - -
672C ASP 3.7 2.5 - - - -
674C GLN* 1.3 76.6 - - - +
676C ARG* 1.3 57.0 + - - +
678C VAL* 4.4 1.6 - - - +
679C THR* 2.8 28.2 + - - +
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Residues in contact with ARG 676 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672C ASP 2.8 16.4 + - - -
673C ILE* 3.2 4.7 + - - +
674C GLN 3.2 0.6 - - - -
675C PHE* 1.3 75.5 - - - +
677C LEU* 1.3 57.5 + - - +
679C THR* 3.9 0.3 - - - -
680C ARG* 3.0 26.0 + - - -
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Residues in contact with LEU 677 (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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553C PRO 5.8 0.2 - - - +
554C MET* 5.7 4.7 - - - +
673C ILE 3.0 14.5 + - - -
674C GLN 3.9 0.9 - - - -
676C ARG* 1.3 75.9 - - - +
678C VAL* 1.3 57.4 + - - +
680C ARG* 3.5 0.5 + - - -
681C PHE* 3.0 24.8 + - - -
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Residues in contact with VAL 678 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674C GLN 3.0 15.7 + - - -
675C PHE* 4.0 1.3 - - - +
677C LEU* 1.3 78.0 - - - +
679C THR* 1.3 56.1 + - - +
681C PHE* 3.2 2.5 + - - +
682C VAL* 2.8 26.7 + - - -
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Residues in contact with THR 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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675C PHE 2.8 22.7 + - - -
676C ARG 4.0 0.2 - - - -
678C VAL* 1.3 69.4 - - - +
680C ARG* 1.3 60.3 + - - +
682C VAL* 3.8 1.4 - - - +
683C ASN* 2.9 24.3 + - - -
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Residues in contact with ARG 680 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C PRO 5.3 7.4 - - - -
676C ARG 3.0 16.3 + - - -
677C LEU 4.0 0.9 - - - -
679C THR* 1.3 73.7 - - - +
681C PHE* 1.3 59.4 + - - +
683C ASN* 3.1 2.6 + - - +
684C GLU* 3.0 25.6 + - - -
744C PHE* 6.4 2.0 - - - +
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Residues in contact with PHE 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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550C CYS* 5.5 7.5 - - - +
553C PRO 5.3 4.8 + - - -
554C MET* 5.9 4.0 - - - +
677C LEU 3.0 15.6 + - - -
678C VAL* 3.2 4.7 + - - +
680C ARG* 1.3 77.8 - - - +
682C VAL* 1.3 55.7 + - - +
684C GLU* 3.4 1.6 + - - -
685C ALA* 2.9 22.0 + - - -
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Residues in contact with VAL 682 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678C VAL 2.8 14.7 + - - -
679C THR* 3.8 2.0 - - - +
681C PHE* 1.3 74.8 - - - +
683C ASN* 1.3 60.3 + - - +
685C ALA* 3.6 3.9 - - - +
686C VAL* 2.8 25.6 + - - -
717C PRO* 4.8 21.3 - - - +
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Residues in contact with ASN 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 THR 2.9 16.0 + - - -
680C ARG* 3.1 5.1 + - - +
682C VAL* 1.3 77.4 - - - +
684C GLU* 1.3 57.0 + - - +
686C VAL* 3.5 1.8 + - - +
687C MET* 2.9 22.7 + - - -
746C PRO* 6.2 2.9 - - - -
747C CYS* 5.6 7.6 + - - +
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Residues in contact with GLU 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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550C CYS* 6.1 8.1 - - - +
680C ARG 3.0 12.9 + - - -
681C PHE 3.8 2.9 - - - -
683C ASN* 1.3 78.4 - - - +
685C ALA* 1.3 56.4 + - - +
687C MET* 3.0 17.4 + - - +
688C CYS* 3.3 9.0 + - - -
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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 PHE 2.9 16.9 + - - -
682C VAL* 3.3 5.5 + - - +
684C GLU* 1.3 75.4 - - - +
686C VAL* 1.3 56.5 + - - +
688C CYS* 4.2 8.8 + - - +
717C PRO* 5.6 7.9 - - - -
718C PHE* 5.4 6.7 + - - -
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Residues in contact with VAL 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682C VAL 2.8 15.3 + - - -
683C ASN* 3.7 2.0 - - - +
685C ALA* 1.3 74.6 - - - +
687C MET* 1.3 64.8 + - - +
688C CYS 3.1 11.2 - - - +
690C GLN* 4.6 3.6 + - - -
747C CYS* 6.5 1.3 - - - -
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Residues in contact with MET 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 ASN 2.9 15.9 + - - -
684C GLU* 3.0 7.7 + - - +
686C VAL* 1.3 76.5 - - - +
688C CYS* 1.3 60.8 + - - +
690C GLN* 3.3 16.0 + - - +
691C GLU 4.1 3.6 + - - -
747C CYS* 6.2 3.4 - - - +
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Residues in contact with CYS 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 GLU 3.3 10.6 + - - -
685C ALA* 4.2 6.6 - - - +
686C VAL* 3.1 16.7 - - - +
687C MET* 1.3 76.5 - - - +
689C LEU* 1.3 56.1 + - - +
690C GLN 3.1 5.6 + - - -
691C GLU 5.4 0.2 - - - +
693C ILE* 5.4 2.5 - - - +
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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