Contacts of the helix formed by residues 781 - 796 (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 ASP 781 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7791 SER* 3.3 8.7 - - - +
7801 PRO* 1.3 77.2 - - - +
7821 GLU* 1.3 61.4 + - - +
7831 GLU 3.6 1.6 - - - +
7841 MET* 3.7 7.7 + - - +
7851 LYS* 3.3 17.5 + - - -
161G U 4.2 14.3 + - - -
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Residues in contact with GLU 782 (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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7801 PRO 3.2 4.3 + - - -
7811 ASP* 1.3 70.5 - - - +
7831 GLU* 1.3 71.5 + - - +
7841 MET 3.0 0.9 - - - -
7851 LYS* 3.0 2.4 + - - +
7861 LYS* 3.0 19.4 + - - -
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Residues in contact with GLU 783 (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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7811 ASP 3.6 0.2 - - - -
7821 GLU* 1.3 74.4 - - - +
7841 MET* 1.3 66.7 + - - +
7861 LYS* 3.3 1.9 + - - -
7871 ILE* 3.0 13.9 + - - -
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Residues in contact with MET 784 (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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7441 ALA* 6.0 6.7 - - - +
7811 ASP* 3.7 11.2 + - - +
7821 GLU 3.0 1.4 - - - -
7831 GLU* 1.3 73.6 - - - +
7851 LYS* 1.3 52.7 + - - +
7871 ILE* 2.3 30.0 + - - +
7881 VAL 2.9 10.9 + - - -
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Residues in contact with LYS 785 (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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7771 PHE 5.7 5.2 - - - -
7811 ASP 3.3 11.9 + - - -
7821 GLU* 3.0 6.2 + - - +
7841 MET* 1.3 72.7 - - - +
7861 LYS* 1.3 67.4 + - - +
7881 VAL* 4.6 1.8 - - - +
7891 LEU* 3.1 17.7 + - - +
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Residues in contact with LYS 786 (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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7821 GLU 3.0 12.9 + - - -
7831 GLU 3.7 4.3 - - - -
7851 LYS* 1.3 79.8 - - - +
7871 ILE* 1.3 65.1 + - - +
7891 LEU* 3.5 0.5 - - - -
7901 LYS* 3.0 15.4 + - - -
8291 ASN* 6.6 0.7 - - - +
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Residues in contact with ILE 787 (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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7441 ALA 5.6 5.6 - - - -
7481 LYS* 5.8 8.6 - - - +
7831 GLU 3.0 8.0 + - - -
7841 MET* 2.3 19.4 + - - +
7861 LYS* 1.3 68.0 - - - +
7881 VAL* 1.3 61.8 + - - +
7901 LYS* 2.9 14.6 + - - +
7911 VAL* 2.9 11.1 + - - -
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Residues in contact with VAL 788 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7731 LEU* 6.4 2.2 - - - +
7841 MET 2.9 11.0 + - - -
7851 LYS* 4.4 1.3 - - - +
7871 ILE* 1.3 74.5 - - - +
7891 LEU* 1.3 64.7 + - - +
7911 VAL* 3.4 2.7 + - - +
7921 VAL* 3.0 16.5 + - - -
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Residues in contact with LEU 789 (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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7851 LYS 3.1 15.4 + - - -
7861 LYS 3.5 4.0 - - - -
7871 ILE 2.9 1.8 + - - -
7881 VAL* 1.3 77.4 - - - +
7901 LYS* 1.3 63.1 + - - +
7921 VAL* 2.8 14.8 + - - +
7931 LYS 3.2 8.1 + - - -
8361 THR* 5.8 3.1 - - - -
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Residues in contact with LYS 790 (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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7861 LYS 3.0 8.8 + - - -
7871 ILE 2.9 9.2 + - - -
7891 LEU* 1.3 70.8 - - - +
7911 VAL* 1.3 65.7 + - - +
7931 LYS* 3.0 12.1 + - - +
7941 GLN 3.2 6.4 + - - -
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Residues in contact with VAL 791 (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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7511 GLY* 4.8 19.0 - - - -
7871 ILE 2.9 11.9 + - - -
7881 VAL* 3.7 4.7 - - - +
7901 LYS* 1.3 73.5 - - - +
7921 VAL* 1.3 52.3 + - - +
7941 GLN* 2.2 32.7 + - - +
7951 CYS* 2.8 10.6 + - - -
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Residues in contact with VAL 792 (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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7881 VAL 3.0 9.6 + - - -
7891 LEU 2.8 11.2 + - - -
7911 VAL* 1.3 69.4 - - - +
7931 LYS* 1.3 65.7 + - - +
7951 CYS* 4.3 3.1 - - - +
7961 CYS* 3.0 24.3 + - - +
7971 GLY 3.3 1.9 + - - -
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Residues in contact with LYS 793 (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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7891 LEU 3.2 7.6 + - - -
7901 LYS* 3.0 9.1 + - - +
7911 VAL 2.8 2.4 + - - -
7921 VAL* 1.3 75.4 - - - +
7941 GLN* 1.3 50.5 + - - +
7971 GLY* 2.5 33.8 - - - -
8361 THR* 5.1 16.6 - - - +
8391 GLU* 6.4 1.6 - - - +
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Residues in contact with GLN 794 (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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7511 GLY* 5.5 8.5 - - - -
7551 PRO 6.3 1.3 - - - -
7901 LYS 3.2 5.8 + - - -
7911 VAL* 2.2 20.3 + - - +
7931 LYS* 1.3 69.6 - - - +
7951 CYS* 1.3 58.5 + - - +
7971 GLY* 2.7 27.2 + - - +
7981 THR* 3.4 2.3 + - - -
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Residues in contact with CYS 795 (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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7511 GLY* 6.2 1.2 - - - -
7661 THR* 6.4 1.8 - - - +
7911 VAL 2.8 14.9 + - - -
7921 VAL* 4.8 2.0 - - - +
7941 GLN* 1.3 72.9 - - - +
7961 CYS* 1.3 58.5 + - - +
7971 GLY 3.1 1.6 + - - -
7981 THR* 3.6 9.2 + - - -
8011 VAL* 5.6 4.7 - - - -
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Residues in contact with CYS 796 (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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7921 VAL* 3.0 14.6 + - - +
7951 CYS* 1.3 73.5 - - - +
7971 GLY* 1.3 54.7 + - - +
7981 THR 3.1 10.1 + - - +
8011 VAL* 6.3 2.0 - - - +
8391 GLU 5.2 6.1 - - - +
8401 LEU* 5.7 2.3 - - - -
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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