Contacts of the helix formed by residues 893 - 904 (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 GLN 893 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885N GLU* 6.1 2.6 - - - +
892N GLU* 1.3 78.1 - - - +
894N GLN* 1.3 64.5 + - - +
895N GLU 3.5 2.3 + - - -
896N GLU* 3.7 3.8 + - - -
897N VAL* 3.6 15.6 + - - -
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Residues in contact with GLN 894 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892N GLU 3.4 4.2 + - - +
893N GLN* 1.3 79.0 - - - +
895N GLU* 1.3 62.0 + - - +
896N GLU 3.5 0.2 + - - -
897N VAL* 3.7 2.1 + - - -
898N ARG* 3.6 14.2 + - - -
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Residues in contact with GLU 895 (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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892N GLU 5.3 0.2 + - - -
893N GLN 3.6 0.2 - - - -
894N GLN* 1.3 75.7 - - - +
896N GLU* 1.3 62.6 + - - +
898N ARG* 3.1 14.5 + - - +
899N LYS 4.3 1.7 + - - -
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Residues in contact with GLU 896 (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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893N GLN 3.7 4.5 + - - -
894N GLN 3.4 0.8 - - - -
895N GLU* 1.3 72.1 - - - +
897N VAL* 1.3 65.5 + - - +
898N ARG 3.1 2.5 + - - -
899N LYS* 3.7 7.8 + - - -
900N ARG 4.9 0.9 + - - -
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Residues in contact with VAL 897 (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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893N GLN 3.6 12.6 + - - -
894N GLN 3.7 3.6 + - - -
895N GLU 3.4 0.6 - - - -
896N GLU* 1.3 75.7 - - - +
898N ARG* 1.3 62.7 + - - +
899N LYS 3.2 0.9 + - - -
900N ARG* 3.2 15.2 + - - -
901N CYS 3.9 2.1 + - - -
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Residues in contact with ARG 898 (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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894N GLN 3.6 9.3 + - - -
895N GLU* 3.1 11.5 + - - +
896N GLU 3.1 2.6 - - - -
897N VAL* 1.3 77.9 - - - +
899N LYS* 1.3 61.8 + - - +
901N CYS* 3.1 15.6 + - - +
902N GLU 3.7 2.8 + - - -
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Residues in contact with LYS 899 (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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895N GLU 4.3 2.2 + - - -
896N GLU 3.7 6.9 + - - -
897N VAL 3.2 1.4 + - - -
898N ARG* 1.3 74.8 - - - +
900N ARG* 1.3 64.1 + - - +
902N GLU* 2.9 14.8 + - - +
903N SER* 3.2 8.8 + - - -
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Residues in contact with ARG 900 (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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896N GLU 4.9 0.8 + - - -
897N VAL 3.2 11.0 + - - -
899N LYS* 1.3 74.2 - - - +
901N CYS* 1.3 51.9 + - - +
903N SER* 3.2 2.8 + - - +
904N ALA* 2.8 34.6 + - - +
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Residues in contact with CYS 901 (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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897N VAL 3.9 3.0 + - - -
898N ARG 3.1 11.0 + - - -
899N LYS 3.0 1.4 + - - -
900N ARG* 1.3 75.4 - - - +
902N GLU* 1.3 53.5 + - - +
904N ALA 3.9 3.1 - - - -
905N GLU* 2.0 51.8 + - - +
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Residues in contact with GLU 902 (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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898N ARG 3.7 4.9 + - - -
899N LYS* 2.9 8.2 + - - +
901N CYS* 1.3 74.9 - - - +
903N SER* 1.3 64.8 + - - +
905N GLU* 4.2 3.8 + - - +
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Residues in contact with SER 903 (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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899N LYS 3.2 11.4 + - - -
900N ARG* 3.2 3.8 + - - +
902N GLU* 1.3 76.4 - - - +
904N ALA* 1.3 55.1 + - - +
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Residues in contact with ALA 904 (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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900N ARG 2.8 13.7 + - - +
901N CYS* 2.7 6.7 - - - +
903N SER* 1.3 76.7 - - - +
905N GLU* 1.3 55.6 + - - +
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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