Contacts of the helix formed by residues 861 - 879 (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 ALA 861 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8591 ASP 3.6 3.8 - - - +
8601 GLU* 1.3 76.5 - - - +
8621 GLU* 1.3 70.3 + - - +
8631 GLN 3.7 0.2 - - - -
8641 TYR* 3.8 4.2 + - - -
8651 ARG* 3.4 9.7 + - - -
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Residues in contact with GLU 862 (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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8601 GLU 3.4 4.1 + - - -
8611 ALA* 1.3 70.3 - - - +
8631 GLN* 1.3 56.0 + - - +
8641 TYR 2.5 1.8 + - - -
8651 ARG* 2.3 34.2 + - - +
8661 LYS 2.9 9.2 + - - +
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Residues in contact with GLN 863 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8241 ALA* 5.7 9.5 - - - -
8251 LEU* 6.6 0.2 - - - +
8611 ALA 3.7 0.2 - - - -
8621 GLU* 1.3 70.9 - - - +
8641 TYR* 1.3 60.8 + - - +
8661 LYS* 3.3 4.4 + - - +
8671 MET* 2.9 19.4 + - - -
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Residues in contact with TYR 864 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8241 ALA* 6.0 5.1 - - - +
8561 ASP 5.6 0.7 - - - -
8611 ALA 3.8 4.7 + - - -
8621 GLU 2.5 5.4 + - - -
8631 GLN* 1.3 71.0 - - - +
8651 ARG* 1.3 53.9 + - - +
8671 MET* 2.6 25.0 + - - +
8681 VAL 3.0 8.7 + - - -
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Residues in contact with ARG 865 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8561 ASP 4.5 16.4 + - - -
8571 LEU* 5.1 11.1 - - - +
8591 ASP 5.2 2.6 + - - -
8611 ALA 3.4 8.4 + - - -
8621 GLU* 2.3 16.6 + - - +
8641 TYR* 1.3 67.2 - - - +
8661 LYS* 1.3 63.3 + - - +
8671 MET 2.8 1.0 + - - -
8681 VAL* 3.0 3.9 + - - +
8691 MET* 2.9 20.6 + - - -
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Residues in contact with LYS 866 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8621 GLU 2.9 10.4 + - - -
8631 GLN* 3.6 5.6 - - - +
8641 TYR 3.2 0.2 - - - -
8651 ARG* 1.3 74.3 - - - +
8671 MET* 1.3 62.8 + - - +
8691 MET* 3.1 1.3 + - - +
8701 GLU* 3.0 20.3 + - - -
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Residues in contact with MET 867 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8631 GLN 2.9 9.7 + - - -
8641 TYR* 2.6 16.3 + - - +
8661 LYS* 1.3 68.5 - - - +
8681 VAL* 1.3 66.9 + - - +
8691 MET 2.8 0.7 + - - -
8701 GLU* 3.0 10.7 + - - -
8711 THR* 3.0 11.3 + - - -
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Residues in contact with VAL 868 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8531 ILE 5.5 6.5 - - - -
8561 ASP 6.5 0.9 - - - -
8641 TYR 3.0 7.5 + - - -
8651 ARG* 3.0 6.2 + - - +
8671 MET* 1.3 75.4 - - - +
8691 MET* 1.3 64.8 + - - +
8711 THR* 3.4 1.7 + - - +
8721 ILE* 3.1 18.0 + - - -
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Residues in contact with MET 869 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8651 ARG 2.9 12.4 + - - -
8661 LYS* 3.6 3.8 - - - +
8671 MET 2.8 0.2 + - - -
8681 VAL* 1.3 79.3 - - - +
8701 GLU* 1.3 64.1 + - - +
8721 ILE* 3.3 1.2 + - - -
8731 GLU* 3.0 17.8 + - - -
9091 VAL 6.5 0.4 - - - -
9101 MET* 6.4 2.7 - - - +
9131 GLY* 5.1 7.1 - - - -
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Residues in contact with GLU 870 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8661 LYS 3.0 14.5 + - - -
8671 MET 3.0 1.3 + - - -
8691 MET* 1.3 74.2 - - - +
8711 THR* 1.3 68.0 + - - +
8731 GLU* 2.9 11.2 + - - +
8741 LYS* 2.9 10.2 + - - -
9091 VAL* 6.1 5.0 - - - +
9131 GLY* 5.7 3.6 - - - -
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Residues in contact with THR 871 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8341 VAL* 5.6 12.3 - - - +
8671 MET 3.0 12.6 + - - -
8681 VAL* 3.8 3.1 - - - +
8701 GLU* 1.3 77.2 - - - +
8721 ILE* 1.3 64.8 + - - +
8741 LYS* 2.9 8.8 + - - -
8751 ILE* 3.0 9.7 + - - -
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Residues in contact with ILE 872 (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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8501 ILE* 6.4 2.2 - - - +
8681 VAL 3.1 13.3 + - - -
8691 MET 3.7 2.9 - - - -
8711 THR* 1.3 72.0 - - - +
8731 GLU* 1.3 66.0 + - - +
8751 ILE* 2.7 15.0 + - - +
8761 MET* 3.0 12.1 + - - -
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Residues in contact with GLU 873 (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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8691 MET 3.0 10.6 + - - -
8701 GLU* 2.9 8.8 + - - +
8721 ILE* 1.3 74.3 - - - +
8741 LYS* 1.3 62.8 + - - +
8761 MET* 3.7 0.9 + - - -
8771 GLY* 2.9 17.7 + - - -
9131 GLY* 4.6 23.3 - - - -
9161 THR* 5.9 5.0 - - - +
9171 VAL 5.9 1.3 - - - +
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Residues in contact with LYS 874 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8701 GLU 2.9 13.2 + - - -
8711 THR 3.6 2.5 - - - -
8731 GLU* 1.3 74.1 - - - +
8751 ILE* 1.3 54.2 + - - +
8771 GLY* 2.2 34.9 + - - -
8781 ASN 2.8 4.6 + - - -
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Residues in contact with ILE 875 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8381 VAL* 6.0 6.0 - - - +
8711 THR 3.0 9.0 + - - -
8721 ILE* 2.7 12.8 + - - +
8741 LYS* 1.3 67.6 - - - +
8761 MET* 1.3 57.9 + - - +
8781 ASN* 2.7 21.6 + - - +
8791 LEU* 2.9 14.2 + - - -
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Residues in contact with MET 876 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8721 ILE 3.0 11.3 + - - -
8731 GLU 3.7 2.0 - - - -
8751 ILE* 1.3 71.9 - - - +
8771 GLY* 1.3 63.6 + - - +
8801 GLY* 3.8 26.6 + - - +
8811 ALA* 4.4 4.1 + - - +
9161 THR 5.5 5.4 - - - +
9201 ALA* 5.5 5.7 - - - -
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Residues in contact with GLY 877 (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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8731 GLU 2.9 11.2 + - - -
8741 LYS* 2.2 25.0 + - - -
8761 MET* 1.3 72.7 - - - +
8781 ASN* 1.3 62.8 + - - +
8801 GLY* 4.2 2.6 + - - -
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Residues in contact with ASN 878 (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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8741 LYS 2.8 5.3 + - - -
8751 ILE* 2.7 10.0 + - - +
8771 GLY* 1.3 73.8 - - - +
8791 LEU* 1.3 62.0 + - - +
8801 GLY* 3.4 0.5 + - - -
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Residues in contact with LEU 879 (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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8421 ASN* 6.6 0.4 - - - +
8461 ALA* 6.6 0.2 - - - +
8751 ILE* 2.9 13.1 + - - +
8761 MET* 5.4 0.2 - - - +
8781 ASN* 1.3 73.1 - - - +
8801 GLY* 1.3 65.1 + - - +
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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