Contacts of the helix formed by residues 857 - 873 (chain A) 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 ASN 857 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856A LEU* 1.3 76.3 - - - +
858A GLN* 1.3 65.2 + - - +
859A SER 3.3 2.7 - - - -
860A GLN* 3.2 6.6 + - - +
861A ARG* 3.0 20.1 + - - -
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Residues in contact with GLN 858 (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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857A ASN* 1.3 72.8 - - - +
859A SER* 1.3 56.6 + - - +
861A ARG* 3.3 2.3 + - - +
862A GLU* 2.9 26.2 + - - -
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Residues in contact with SER 859 (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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857A ASN 3.3 0.6 - - - -
858A GLN* 1.3 75.9 - - - +
860A GLN* 1.3 56.9 + - - +
862A GLU* 3.4 2.3 + - - +
863A GLU* 3.0 24.3 + - - -
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Residues in contact with GLN 860 (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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856A LEU* 5.7 2.7 - - - +
857A ASN* 3.2 11.1 + - - +
858A GLN 3.2 0.2 - - - -
859A SER* 1.3 74.5 - - - +
861A ARG* 1.3 63.3 + - - +
863A GLU* 3.3 2.1 + - - +
864A LEU* 3.1 19.6 + - - -
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Residues in contact with ARG 861 (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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856A LEU* 5.4 1.2 - - - +
857A ASN 3.0 13.8 + - - -
858A GLN* 3.3 4.4 + - - +
860A GLN* 1.3 75.2 - - - +
862A GLU* 1.3 60.9 + - - +
864A LEU* 3.4 1.7 + - - +
865A GLY* 3.0 20.6 + - - -
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Residues in contact with GLU 862 (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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858A GLN 2.9 14.2 + - - -
859A SER* 3.4 3.8 + - - +
860A GLN 3.2 0.2 - - - -
861A ARG* 1.3 74.5 - - - +
863A GLU* 1.3 58.0 + - - +
865A GLY* 3.2 3.4 + - - -
866A LEU* 2.9 26.0 + - - -
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Residues in contact with GLU 863 (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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859A SER 3.0 15.4 + - - -
860A GLN* 3.7 3.6 - - - +
861A ARG 3.2 0.4 - - - -
862A GLU* 1.3 76.5 - - - +
864A LEU* 1.3 60.6 - - - +
866A LEU* 3.2 3.2 + - - +
867A ILE* 3.0 19.8 + - - -
913A PRO* 5.6 10.3 - - - -
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Residues in contact with LEU 864 (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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860A GLN 3.1 13.6 + - - -
861A ARG* 3.9 3.1 - - - +
863A GLU* 1.3 75.4 - - - +
865A GLY* 1.3 55.8 + - - +
867A ILE* 3.2 3.0 + - - +
868A GLU* 2.9 25.3 + - - -
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Residues in contact with GLY 865 (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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861A ARG 3.0 14.9 + - - -
862A GLU* 3.2 4.5 + - - -
864A LEU* 1.3 74.9 - - - +
866A LEU* 1.3 56.7 + - - +
868A GLU* 3.2 3.2 + - - -
869A GLN* 2.9 25.1 + - - -
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Residues in contact with LEU 866 (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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862A GLU 2.9 12.8 + - - -
863A GLU* 3.2 4.2 + - - +
865A GLY* 1.3 75.7 - - - +
867A ILE* 1.3 57.0 - - - +
869A GLN* 3.2 3.3 + - - +
870A ALA* 2.9 25.3 + - - -
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Residues in contact with ILE 867 (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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863A GLU 3.0 13.6 + - - -
864A LEU* 3.2 4.4 + - - +
866A LEU* 1.3 74.9 - - - +
868A GLU* 1.3 62.6 + - - +
870A ALA* 3.2 3.5 + - - +
871A TYR* 3.1 18.0 + - - -
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Residues in contact with GLU 868 (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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864A LEU 2.9 14.6 + - - -
865A GLY* 3.2 3.8 + - - -
867A ILE* 1.3 75.4 - - - +
869A GLN* 1.3 57.6 + - - +
871A TYR* 3.1 4.9 + - - +
872A ASP* 2.9 23.9 + - - -
289N ASN* 4.8 4.5 - - - +
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Residues in contact with GLN 869 (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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865A GLY 2.9 14.2 + - - -
866A LEU* 3.6 3.8 - - - +
868A GLU* 1.3 77.5 - - - +
870A ALA* 1.3 54.7 + - - +
872A ASP* 3.1 3.0 + - - +
873A ASN* 2.9 28.6 + - - +
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Residues in contact with ALA 870 (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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866A LEU 2.9 14.1 + - - -
867A ILE* 3.2 5.3 + - - +
869A GLN* 1.3 75.4 - - - +
871A TYR* 1.3 61.7 + - - +
873A ASN 3.4 4.4 - - - -
874A PRO* 3.2 28.6 - - - +
877A ALA* 5.3 8.7 - - - +
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Residues in contact with TYR 871 (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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867A ILE 3.1 12.5 + - - -
868A GLU* 3.1 3.8 + - - +
870A ALA* 1.3 77.8 - - - +
872A ASP* 1.3 61.9 + - - +
874A PRO* 4.5 2.4 - - - +
289N ASN* 2.5 31.1 + - - +
290N ASP* 3.3 1.6 + - - -
291N ILE 4.4 2.4 + - - -
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Residues in contact with ASP 872 (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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868A GLU 2.9 14.1 + - - -
869A GLN* 3.1 4.9 + - - +
871A TYR* 1.3 79.0 - - - +
873A ASN* 1.3 57.0 + - - +
290N ASP* 2.9 31.8 - - - +
291N ILE 4.3 3.1 + - - -
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Residues in contact with ASN 873 (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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869A GLN 2.9 12.0 + - - +
870A ALA* 3.4 5.0 - - - +
872A ASP* 1.3 79.3 - - - +
874A PRO* 1.3 63.4 - - - +
875A HIS 3.2 3.7 + - - +
876A GLU* 3.3 6.1 + - - +
877A ALA* 3.2 17.3 + - - -
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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