Contacts of the helix formed by residues 727 - 739 (chain N) in PDB entry 6AH0
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 727 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719N GLU* 6.1 1.3 - - - +
726N GLU* 1.3 74.0 - - - +
728N ALA* 1.3 58.2 - - - +
730N GLU* 3.2 3.2 + - - +
731N ALA* 2.9 25.8 + - - -
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Residues in contact with ALA 728 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716N GLY* 4.9 19.5 - - - -
719N GLU* 5.3 6.3 + - - +
720N GLU* 5.2 7.4 - - - +
726N GLU 3.2 2.8 - - - +
727N LYS* 1.3 76.4 - - - +
729N ARG* 1.3 61.6 + - - +
731N ALA* 3.3 2.0 + - - +
732N TYR* 3.1 18.9 + - - -
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Residues in contact with ARG 729 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726N GLU* 3.4 9.1 + - - +
727N LYS 3.2 0.4 - - - -
728N ALA* 1.3 75.7 - - - +
730N GLU* 1.3 56.5 + - - +
732N TYR* 3.1 2.7 + - - +
733N ASN* 2.9 27.0 + - - -
749N LEU* 6.5 0.7 - - - +
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Residues in contact with GLU 730 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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726N GLU 3.2 9.7 + - - -
727N LYS* 3.2 7.9 + - - +
729N ARG* 1.3 78.4 - - - +
731N ALA* 1.3 61.1 + - - +
733N ASN* 4.1 0.6 - - - +
734N GLN* 3.3 18.2 + - - -
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Residues in contact with ALA 731 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712N TRP 5.9 2.2 - - - -
716N GLY* 6.2 3.6 - - - -
727N LYS 2.9 14.6 + - - -
728N ALA* 3.3 2.9 + - - +
729N ARG 3.3 0.2 - - - -
730N GLU* 1.3 76.1 - - - +
732N TYR* 1.3 58.3 + - - +
734N GLN* 3.6 0.5 + - - -
735N GLY* 2.9 26.9 + - - -
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Residues in contact with TYR 732 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728N ALA 3.1 13.5 + - - -
729N ARG* 3.1 4.0 + - - +
731N ALA* 1.3 77.4 - - - +
733N ASN* 1.3 56.1 + - - +
735N GLY* 3.2 1.6 + - - -
736N LEU* 2.9 28.8 + - - -
749N LEU* 5.8 8.3 - - - +
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Residues in contact with ASN 733 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729N ARG 2.9 15.4 + - - -
730N GLU* 3.5 1.7 + - - +
731N ALA 3.3 0.2 - - - -
732N TYR* 1.3 77.9 - - - +
734N GLN* 1.3 63.2 + - - +
736N LEU* 3.6 5.5 + - - -
737N LYS* 3.6 8.8 + - - -
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Residues in contact with GLN 734 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730N GLU 3.3 13.1 + - - -
731N ALA 4.0 1.8 - - - -
733N ASN* 1.3 76.8 - - - +
735N GLY* 1.3 63.1 + - - +
737N LYS* 3.6 1.4 + - - -
738N LYS* 3.3 17.3 + - - -
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Residues in contact with GLY 735 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712N TRP* 6.1 4.7 - - - -
731N ALA 2.9 17.6 + - - -
732N TYR* 3.2 1.8 + - - -
734N GLN* 1.3 77.4 - - - +
736N LEU* 1.3 57.4 + - - +
738N LYS* 3.2 2.0 + - - -
739N CYS* 2.8 28.8 + - - -
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Residues in contact with LEU 736 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732N TYR 2.9 14.6 + - - -
733N ASN* 3.6 1.5 + - - +
734N GLN 3.3 0.4 - - - -
735N GLY* 1.3 75.7 - - - +
737N LYS* 1.3 54.8 - - - +
739N CYS 4.9 0.9 - - - -
740N PRO* 2.5 39.7 - - - +
745N LEU* 6.4 3.1 - - - +
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Residues in contact with LYS 737 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733N ASN 3.6 8.6 + - - -
734N GLN 3.6 4.8 + - - -
735N GLY 3.3 0.4 - - - -
736N LEU* 1.3 77.2 - - - +
738N LYS* 1.3 62.7 + - - +
740N PRO* 3.7 4.4 - - - +
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Residues in contact with LYS 738 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734N GLN 3.3 10.3 + - - -
735N GLY* 3.2 5.6 + - - -
737N LYS* 1.3 78.8 - - - +
739N CYS* 1.3 58.1 + - - +
740N PRO 3.8 0.3 - - - -
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Residues in contact with CYS 739 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735N GLY 2.8 14.0 + - - -
736N LEU* 3.4 3.1 - - - -
738N LYS* 1.3 76.9 - - - +
740N PRO* 1.4 66.6 - - - +
741N HIS* 3.0 5.5 + - - -
742N SER 3.9 6.2 + - - +
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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