Contacts of the helix formed by residues 644 - 653 (chain A) in PDB entry 6O0Z
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 644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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643A PHE* 1.3 78.2 - - - +
645A ASP* 1.3 63.5 + - - +
646A LYS* 3.6 14.3 - - - +
647A VAL* 3.3 28.4 + - - +
648A MET* 3.3 22.7 + - - +
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Residues in contact with ASP 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ASP* 1.3 76.0 - - - +
646A LYS* 1.3 60.8 + - - +
648A MET* 3.3 6.8 + - - +
649A LYS* 2.9 43.0 + - + +
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Residues in contact with LYS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ASP* 3.3 14.5 + - - +
645A ASP* 1.3 75.8 - - - +
647A VAL* 1.3 62.9 + - + +
649A LYS* 3.3 6.3 + - - +
650A GLN* 2.9 29.2 + - - +
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Residues in contact with VAL 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ILE 3.3 23.1 - - - +
601A ILE* 3.7 23.8 - - + +
602A LYS* 5.4 4.9 - - + -
643A PHE* 3.7 22.7 - - + -
644A ASP* 3.3 18.5 + - - +
646A LYS* 1.3 76.0 - - + +
648A MET* 1.3 57.4 + - - +
650A GLN* 3.3 6.3 + - - +
651A LEU* 2.9 37.9 + - + +
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Residues in contact with MET 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636A LEU* 4.2 29.6 - - + +
637A LYS* 6.4 0.2 - - - -
639A TYR 3.8 18.2 - - - +
640A ALA* 4.7 6.5 - - - +
642A LEU* 5.4 1.6 - - + -
643A PHE* 3.9 25.6 - - + +
644A ASP 3.3 22.1 + - - +
645A ASP* 3.3 9.8 + - - +
646A LYS 3.2 0.4 - - - -
647A VAL* 1.3 79.5 - - - +
649A LYS* 1.3 63.4 + - + +
651A LEU* 3.6 19.0 - - + +
652A LYS* 2.9 36.0 + - + +
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Residues in contact with LYS 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ASP* 2.9 28.3 + - + +
646A LYS* 3.3 5.8 + - - +
648A MET* 1.3 80.7 - - + +
650A GLN* 1.3 57.2 + - - +
652A LYS* 3.4 34.6 - - + +
653A ARG* 3.0 51.8 + - + +
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Residues in contact with GLN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A ILE* 4.6 17.2 - - + +
646A LYS 2.9 17.5 + - - +
647A VAL* 3.3 8.7 + - - +
649A LYS* 1.3 79.1 - - - +
651A LEU* 1.3 59.5 + - - +
653A ARG* 3.9 25.9 + - - +
654A ARG* 4.2 8.3 + - - +
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Residues in contact with LEU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A LEU* 5.7 9.9 - - + -
600A ILE* 4.8 16.4 - - + +
601A ILE* 6.0 2.5 - - + -
619A ILE* 4.6 13.2 - - + -
623A LEU* 4.0 17.2 - - + +
636A LEU* 3.7 33.2 - - + -
643A PHE* 5.4 1.1 - - + -
647A VAL* 2.9 36.7 + - + +
648A MET* 3.6 22.0 - - + +
650A GLN* 1.3 75.5 - - - +
652A LYS* 1.3 65.7 + - - +
653A ARG 3.2 0.4 - - - -
654A ARG* 3.2 22.6 + - - +
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Residues in contact with LYS 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A LEU* 5.1 2.8 - - - +
629A ARG* 4.2 20.8 + - + +
632A ILE* 4.3 18.6 - - + +
633A GLU* 4.0 32.5 - - + +
636A LEU* 4.2 18.6 - - + -
648A MET* 2.9 23.5 + - + +
649A LYS* 3.4 39.1 - - + +
651A LEU* 1.3 80.2 - - - +
653A ARG* 1.3 64.5 + - - +
654A ARG 3.3 6.2 + - - +
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Residues in contact with ARG 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASP* 4.3 21.9 + - + -
274A ASP* 5.2 6.3 - - - -
277A ASN* 3.8 34.5 - - - +
649A LYS* 3.0 38.2 + - + +
650A GLN* 3.9 23.8 + - - +
651A LEU 3.2 0.6 - - - -
652A LYS* 1.3 79.6 - - + +
654A ARG* 1.3 62.3 + - - +
655A ARG* 5.1 0.7 - - - +
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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