Contacts of the helix formed by residues 629 - 639 (chain C) in PDB entry 5ZI6
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 CYS 629 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608C CYS* 3.4 12.4 - - + +
611C CYS* 4.0 0.4 - - - -
614C ASN* 3.5 30.1 - - + -
615C GLU 3.7 14.6 - - - +
617C ILE* 4.3 3.1 - - + +
618C ALA* 4.0 2.2 - - - -
628C PHE* 1.3 77.6 - - - +
630C MET* 1.3 65.2 + - - +
631C GLU* 3.0 24.7 - - - +
632C CYS* 3.5 13.6 + - - -
633C ALA* 3.1 22.2 + - - +
701C ZN 2.4 34.8 - - - -
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Residues in contact with MET 630 (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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617C ILE* 3.9 23.4 - - + +
618C ALA* 4.0 12.3 - - - -
629C CYS* 1.3 72.8 - - - +
631C GLU* 1.3 67.3 + - + +
633C ALA* 3.9 0.9 - - - +
634C ASN* 3.0 60.7 + - - +
654C ALA* 3.8 26.9 - - + +
655C ILE* 4.2 0.4 - - - -
656C GLN* 4.0 36.1 - - + +
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Residues in contact with GLU 631 (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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613B GLU* 3.4 41.8 - - + +
614C ASN* 3.3 18.3 + - - +
629C CYS* 3.0 24.7 - - - +
630C MET* 1.3 81.5 + - - +
632C CYS* 1.3 58.6 + - - +
634C ASN* 3.4 7.7 + - - +
635C LYS* 3.0 40.6 + - - +
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Residues in contact with CYS 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608C CYS* 3.7 10.8 - - - -
610C ILE* 4.0 24.7 - - + -
611C CYS* 3.8 14.4 - - - -
628C PHE* 4.8 1.8 - - + -
629C CYS* 3.5 6.4 - - - +
630C MET 3.4 0.4 - - - -
631C GLU* 1.3 79.8 - - - +
633C ALA* 1.3 58.1 + - - +
635C LYS* 3.2 14.3 + - - +
636C ILE* 2.9 32.4 + - - +
701C ZN 2.3 36.8 - - - -
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Residues in contact with ALA 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C ALA* 3.9 15.7 - - + -
620C LEU* 4.0 10.7 - - + +
628C PHE* 4.0 6.2 - - + +
629C CYS 3.1 18.8 + - - +
630C MET* 3.9 3.8 - - - +
632C CYS* 1.3 76.6 - - - +
634C ASN* 1.3 62.5 + - - +
636C ILE* 3.0 16.8 + - - +
637C CYS* 3.0 23.7 + - - -
654C ALA* 3.7 23.1 - - + +
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Residues in contact with ASN 634 (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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613B GLU* 6.2 1.8 - - - +
630C MET* 3.0 48.7 + - - +
631C GLU* 3.6 8.2 - - - +
633C ALA* 1.3 76.1 - - - +
635C LYS* 1.3 64.2 + - + +
637C CYS* 2.9 18.1 + - - +
638C GLU* 3.0 28.1 + - - +
654C ALA* 4.5 4.9 - - - +
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Residues in contact with LYS 635 (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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606B HIS* 4.8 6.7 - - - -
613B GLU* 3.4 34.8 + - - -
614B ASN* 2.8 31.4 + - - +
631C GLU* 3.0 25.3 + - - +
632C CYS* 3.2 14.8 + - - +
634C ASN* 1.3 75.2 - - - +
636C ILE* 1.3 63.2 + - - +
638C GLU* 3.4 19.1 + - - +
639C LYS* 3.4 26.4 + - - +
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Residues in contact with ILE 636 (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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610C ILE* 4.8 5.8 - - + -
620C LEU* 4.2 19.7 - - + -
628C PHE* 3.8 25.6 - - + -
632C CYS 2.9 19.3 + - - +
633C ALA* 3.2 13.5 - - - +
635C LYS* 1.3 75.8 - - + +
637C CYS* 1.3 60.2 + - - +
638C GLU 3.4 0.5 + - - -
639C LYS* 3.4 19.1 + - + +
642C PRO* 3.2 15.9 - - - +
643C SER 3.4 28.7 - - - +
645C PRO* 3.7 27.8 - - + -
651C VAL* 4.4 6.5 - - + -
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Residues in contact with CYS 637 (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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620C LEU* 5.2 0.4 - - - -
633C ALA 3.0 7.7 + - - +
634C ASN* 2.9 13.6 + - - +
636C ILE* 1.3 76.9 - - - +
638C GLU* 1.3 60.2 + - + +
639C LYS 3.6 0.5 - - - +
642C PRO* 3.2 26.0 - - - +
651C VAL* 3.9 14.8 - - - -
652C THR 5.2 0.9 - - - -
653C GLN* 3.8 11.2 - - - -
654C ALA* 3.6 41.3 - - - -
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Residues in contact with GLU 638 (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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614B ASN* 3.4 26.7 + - - +
631B GLU* 3.9 33.8 - - + +
635B LYS* 4.2 17.9 + - - +
634C ASN* 3.0 25.7 + - - +
635C LYS* 4.0 12.2 - - - +
636C ILE 3.3 0.6 - - - -
637C CYS* 1.3 76.2 - - + +
639C LYS* 1.3 66.4 + - - +
640C ARG* 3.8 0.9 + - - -
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Residues in contact with LYS 639 (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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635C LYS* 3.4 21.4 + - - +
636C ILE* 3.4 18.2 + - + +
637C CYS 3.3 2.5 - - - +
638C GLU* 1.3 82.3 - - - +
640C ARG* 1.3 68.0 + - - +
641C THR 3.5 4.7 - - - +
642C PRO* 3.2 23.6 - - + +
643C SER 5.7 0.2 - - - +
613G GLU* 4.6 23.6 - - + +
614G ASN* 3.4 35.7 + - - +
631G GLU* 4.9 3.0 + - - +
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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