Contacts of the helix formed by residues 886 - 902 (chain 1) 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 HIS 886 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8851 ASP* 1.3 71.2 - - - +
8871 LYS* 1.3 56.8 + - - +
8881 LEU 3.2 1.6 - - - -
8891 GLU* 2.3 33.4 + - - -
8901 GLU 3.0 4.9 + - - -
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Residues in contact with LYS 887 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8861 HIS* 1.3 70.8 - - - +
8881 LEU* 1.3 64.3 + - - +
8891 GLU 2.9 1.2 + - - -
8901 GLU* 3.0 12.9 + - - +
8911 GLN* 3.1 8.8 + - - -
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Residues in contact with LEU 888 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8851 ASP* 5.0 3.1 - - - +
8861 HIS 3.1 2.6 + - - +
8871 LYS* 1.3 73.8 - - - +
8891 GLU* 1.3 56.8 + - - +
8911 GLN* 2.9 5.3 + - - +
8921 LEU* 2.8 22.5 + - - -
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Residues in contact with GLU 889 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8851 ASP 4.3 8.5 + - - +
8861 HIS* 2.3 25.0 + - - +
8881 LEU* 1.3 64.9 - - - +
8901 GLU* 1.3 58.4 + - - +
8921 LEU* 2.5 24.0 + - - +
8931 ILE 3.0 9.9 + - - -
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Residues in contact with GLU 890 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8861 HIS 3.0 6.5 + - - -
8871 LYS* 3.0 7.7 + - - +
8891 GLU* 1.3 75.4 - - - +
8911 GLN* 1.3 64.5 + - - +
8931 ILE* 3.2 0.6 + - - +
8941 ASP* 3.0 21.8 + - - -
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Residues in contact with GLN 891 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8541 VAL* 6.1 2.9 - - - -
8871 LYS 3.1 7.2 + - - -
8881 LEU* 2.9 10.5 + - - +
8901 GLU* 1.3 75.7 - - - +
8921 LEU* 1.3 66.2 + - - +
8941 ASP* 5.2 0.7 - - - +
8951 GLY* 3.0 14.8 + - - +
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Residues in contact with LEU 892 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8881 LEU 2.8 9.2 + - - -
8891 GLU* 2.5 16.2 + - - +
8911 GLN* 1.3 68.5 - - - +
8931 ILE* 1.3 55.4 + - - +
8951 GLY* 2.4 30.1 + - - -
8961 ILE* 2.8 9.7 + - - -
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Residues in contact with ILE 893 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8891 GLU 3.0 12.5 + - - -
8901 GLU* 4.0 0.6 - - - +
8921 LEU* 1.3 70.3 - - - +
8941 ASP* 1.3 63.0 + - - +
8961 ILE* 4.1 2.9 - - - +
8971 LEU* 2.9 23.2 + - - -
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Residues in contact with ASP 894 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8901 GLU 3.0 13.6 + - - -
8911 GLN* 4.3 0.9 - - - +
8931 ILE* 1.3 74.4 - - - +
8951 GLY* 1.3 64.5 + - - +
8971 LEU* 3.6 1.0 + - - -
8981 TYR* 3.0 15.8 + - - -
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Residues in contact with GLY 895 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8541 VAL 6.1 1.3 - - - -
8571 LEU* 5.9 9.4 - - - -
8581 LYS 6.2 0.2 - - - -
8911 GLN 3.0 12.3 + - - -
8921 LEU 2.4 17.4 + - - -
8941 ASP* 1.3 67.1 - - - +
8961 ILE* 1.3 55.6 + - - -
8981 TYR* 2.3 28.7 + - - -
8991 ALA 2.8 10.4 + - - -
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Residues in contact with ILE 896 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8921 LEU 2.8 14.6 + - - -
8931 ILE* 3.0 4.0 + - - +
8951 GLY* 1.3 71.4 - - - -
8971 LEU* 1.3 60.7 + - - +
8991 ALA* 4.3 1.5 - - - +
9001 PHE* 3.0 18.4 + - - +
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Residues in contact with LEU 897 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8931 ILE 2.9 14.5 + - - -
8941 ASP 4.0 0.9 - - - -
8951 GLY 2.8 0.2 + - - -
8961 ILE* 1.3 77.2 - - - +
8981 TYR* 1.3 56.2 + - - +
9001 PHE* 2.3 28.1 + - - +
9011 GLN* 2.7 12.1 + - - -
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Residues in contact with TYR 898 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8571 LEU 5.3 1.8 - - - -
8581 LYS* 6.3 1.3 - - - -
8941 ASP 3.0 10.9 + - - -
8951 GLY* 2.3 16.0 + - - -
8971 LEU* 1.3 68.4 - - - +
8991 ALA* 1.3 63.7 + - - +
9011 GLN* 3.7 5.2 + - - +
9021 GLU* 4.0 4.3 + - - -
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Residues in contact with ALA 899 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8571 LEU* 4.6 16.9 + - - +
8951 GLY 2.8 10.8 + - - -
8961 ILE* 4.3 1.3 - - - +
8971 LEU 2.8 0.4 + - - -
8981 TYR* 1.3 77.0 - - - +
9001 PHE* 1.3 53.5 + - - +
9011 GLN 2.6 14.2 + - - -
9021 GLU 2.7 22.7 + - - +
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Residues in contact with PHE 900 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8961 ILE 3.0 15.1 + - - -
8971 LEU* 2.3 16.1 + - - +
8991 ALA* 1.3 69.3 - - - +
9011 GLN* 1.3 58.5 + - - -
9021 GLU* 3.2 4.0 + - - -
9031 GLN* 4.6 2.3 + - - -
9101 MET* 6.3 3.1 - - - +
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Residues in contact with GLN 901 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8971 LEU 2.7 10.7 + - - -
8981 TYR* 3.7 3.3 + - - +
8991 ALA 2.6 6.5 + - - -
9001 PHE* 1.3 75.8 - - - +
9021 GLU* 1.3 55.2 + - - +
9031 GLN 3.9 1.8 + - - -
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Residues in contact with GLU 902 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8981 TYR 4.0 3.9 + - - -
8991 ALA* 2.7 15.2 + - - +
9001 PHE 4.4 1.6 - - - -
9011 GLN* 1.3 79.7 - - - +
9031 GLN* 1.3 58.6 + - - +
9041 THR 4.1 1.1 + - - -
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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