Contacts of the helix formed by residues 609 - 613 (chain A) in PDB entry 5N4D
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 LYS 609 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 4.0 2.4 + - - -
21A ASP* 2.9 32.9 + - - -
23A TYR* 3.6 16.4 - - - +
35A ASP* 2.6 26.1 + - - -
38A GLN* 3.7 12.9 - - - +
41A GLU* 3.2 24.7 + - - +
606A ASP* 3.0 20.4 + - - +
608A LEU* 1.3 76.7 - - + +
610A PHE* 1.3 66.7 + - - +
611A HIS* 3.2 7.9 - - - -
612A LYS* 3.0 26.9 + - + +
613A PHE* 3.3 18.5 - - + -
667A MET* 4.5 2.7 - - + -
671A LYS* 3.7 7.9 - - - +
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Residues in contact with PHE 610 (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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604A VAL* 4.2 7.9 - - + -
606A ASP 3.2 13.3 + - - +
607A LEU* 3.2 37.9 - - + -
609A LYS* 1.3 78.2 - - - +
611A HIS* 1.3 67.9 + - + +
612A LYS 3.2 1.6 + - - -
613A PHE* 3.5 11.9 + - - +
616A GLY* 3.3 39.1 - - - -
619A TRP* 3.8 29.2 - + + -
620A ILE* 3.9 10.8 - - + -
623A TYR* 3.9 23.3 - + + -
624A GLY 3.3 26.0 - - - -
626A PRO* 3.9 11.7 - - + -
635A ILE* 5.2 1.3 - - + -
668A HIS* 3.6 23.3 + - + +
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Residues in contact with HIS 611 (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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23A TYR* 5.7 1.6 - + - -
608A LEU 3.2 26.5 + - - -
609A LYS 3.8 1.4 - - - -
610A PHE* 1.3 90.7 - - + +
612A LYS* 1.3 85.3 + - + +
613A PHE 3.3 3.0 + - - +
616A GLY 3.8 9.2 - - - +
617A GLN* 2.9 38.0 + - - +
620A ILE* 3.9 21.5 - - + -
625A ASN* 3.8 15.7 - - - -
626A PRO* 3.4 25.7 - - + +
627A SER* 3.3 21.8 + - - -
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Residues in contact with LYS 612 (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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23A TYR* 6.5 1.6 - - - -
608A LEU 5.7 0.2 - - - -
609A LYS* 3.0 25.6 + - + +
611A HIS* 1.3 107.7 + - + +
613A PHE* 1.3 73.9 + - + +
617A GLN* 5.9 0.7 - - - +
627A SER* 4.5 8.1 + - - -
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Residues in contact with PHE 613 (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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41A GLU* 3.5 48.5 - - + -
609A LYS* 3.3 28.0 - - + -
610A PHE 3.5 6.4 + - - +
611A HIS 3.3 1.6 - - - +
612A LYS* 1.3 92.6 - - + +
614A THR* 1.3 58.9 + - + +
616A GLY* 2.7 32.7 + - - -
617A GLN* 4.3 1.7 + - - +
665A VAL* 3.8 33.9 - - + -
667A MET* 3.7 23.6 - - + -
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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