Contacts of the helix formed by residues 627 - 633 (chain C) in PDB entry 4O64
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 627 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624C CYS* 3.4 5.1 - - - -
625C GLY 3.9 0.2 - - - -
626C GLU* 1.3 81.2 - - - +
628C HIS* 1.3 68.1 + - + +
629C PHE* 3.1 5.9 + - - -
630C CYS* 3.1 15.4 + - - -
631C LYS* 3.0 21.8 + - - +
646C CYS* 3.9 1.3 - - - -
647C ILE* 3.5 48.9 - - + -
2002C ZN 2.4 33.9 - - - -
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Residues in contact with HIS 628 (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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627C CYS* 1.3 74.3 - - - +
629C PHE* 1.3 107.1 + + + +
631C LYS* 3.8 7.6 + - - +
632C ASP* 3.4 22.0 + - - +
642C MET* 3.8 12.8 - - + +
647C ILE* 4.5 11.5 - - + +
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Residues in contact with PHE 629 (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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627C CYS* 3.1 5.3 - - - -
628C HIS* 1.3 100.6 - + - +
630C CYS* 1.3 64.7 + - - +
632C ASP* 3.3 13.6 + - - +
633C MET* 3.4 18.0 + - - +
642C MET* 3.7 29.0 - - + +
644C GLN* 3.5 44.4 - - + +
645C SER 3.4 28.9 - - - +
647C ILE* 3.9 19.1 - - + -
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Residues in contact with CYS 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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623C GLU* 3.6 16.2 - - - -
625C GLY* 3.2 35.0 - - - -
627C CYS* 3.1 5.5 + - - +
629C PHE* 1.3 78.1 - - - +
631C LYS* 1.3 57.5 + - - +
633C MET* 3.0 24.7 + - - +
636C PHE* 3.1 24.0 - - + +
646C CYS* 3.5 18.8 - - - -
2002C ZN 2.3 34.5 - - - -
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Residues in contact with LYS 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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617B GLU* 5.5 12.6 - - + +
625C GLY 3.5 25.6 - - - +
626C GLU* 3.9 25.2 + - - +
627C CYS 3.0 19.7 + - - +
628C HIS* 4.1 7.2 - - - +
630C CYS* 1.3 75.0 - - - +
632C ASP* 1.3 56.7 + - - +
633C MET 3.9 0.3 - - - +
636C PHE* 4.5 12.1 - - + +
637C GLY 4.5 0.2 - - - -
638C GLY* 3.2 24.4 + - - -
639C PRO* 4.7 0.3 - - - +
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Residues in contact with ASP 632 (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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628C HIS 3.4 6.6 + - - +
629C PHE 3.3 6.6 + - - +
630C CYS 3.1 0.8 - - - -
631C LYS* 1.3 79.1 - - - +
633C MET* 1.3 57.4 + - - +
638C GLY* 3.3 2.9 - - - -
639C PRO* 3.4 22.8 - - - +
640C GLY* 2.6 35.3 + - - -
641C ARG* 2.7 30.8 + - - +
642C MET* 2.7 54.4 + - + +
643C LYS 4.3 1.7 + - - -
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Residues in contact with MET 633 (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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623C GLU* 3.9 29.8 - - + +
629C PHE 3.4 13.7 - - - +
630C CYS* 3.0 20.8 + - - +
632C ASP* 1.3 77.1 - - - +
634C LYS* 1.3 64.6 + - - +
635C LYS* 3.8 20.2 - - + -
636C PHE* 3.0 17.7 + - + -
637C GLY 3.2 0.2 + - - -
638C GLY 2.9 17.1 + - - -
640C GLY* 4.6 3.1 - - - -
644C GLN 3.4 25.1 - - - +
645C SER* 4.1 2.9 - - - -
646C CYS 3.7 19.7 - - - +
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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
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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