Contacts of the helix formed by residues 808 - 825 (chain 3) 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 THR 808 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8073 TYR* 1.3 78.6 - - - +
8093 GLU* 1.3 59.9 + - - +
8103 ALA 3.4 2.2 - - - -
8113 THR* 2.6 28.2 + - - +
8123 LYS* 3.0 4.9 + - - -
8623 TRP 3.9 10.1 + - - -
8633 ALA* 4.6 10.3 - - - +
8643 SER 5.9 0.2 - - - +
8823 LEU 6.1 0.7 - - - -
8843 GLN* 5.6 0.8 + - - +
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Residues in contact with GLU 809 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8073 TYR 4.5 0.4 - - - -
8083 THR* 1.3 73.7 - - - +
8103 ALA* 1.3 61.2 + - - +
8123 LYS* 3.1 4.6 + - - +
8133 ALA* 3.0 15.1 + - - -
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Residues in contact with ALA 810 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8083 THR 3.4 0.6 - - - -
8093 GLU* 1.3 73.6 - - - +
8113 THR* 1.3 57.4 + - - +
8133 ALA* 2.9 6.5 + - - +
8143 GLN* 2.9 22.5 + - - -
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Residues in contact with THR 811 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8073 TYR* 4.9 3.1 - - - +
8083 THR* 2.6 22.2 + - - +
8103 ALA* 1.3 67.6 - - - +
8123 LYS* 1.3 55.9 + - - +
8133 ALA 2.8 3.6 - - - -
8143 GLN* 2.8 20.0 + - - +
8153 ARG* 2.9 11.6 + - - -
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Residues in contact with LYS 812 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8073 TYR* 4.6 6.0 + - - +
8083 THR 3.0 10.3 + - - -
8093 GLU 3.1 5.1 + - - -
8113 THR* 1.3 74.3 - - - +
8133 ALA* 1.3 56.8 + - - +
8153 ARG* 5.1 1.3 - - - +
8163 LYS* 2.8 25.8 + - - +
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Residues in contact with ALA 813 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8093 GLU 3.0 8.5 + - - -
8103 ALA* 2.9 12.3 + - - +
8113 THR 2.8 3.2 - - - -
8123 LYS* 1.3 76.7 - - - +
8143 GLN* 1.3 59.3 + - - +
8163 LYS* 4.5 0.4 - - - +
8173 GLN* 2.8 27.9 + - - -
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Residues in contact with GLN 814 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8103 ALA 2.9 8.8 + - - -
8113 THR* 2.8 12.2 + - - +
8133 ALA* 1.3 72.7 - - - +
8153 ARG* 1.3 56.0 + - - +
8173 GLN* 3.9 0.7 - - - +
8183 GLN* 2.9 25.8 + - - -
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Residues in contact with ARG 815 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8113 THR 2.9 12.0 + - - -
8123 LYS* 4.8 2.2 - - - +
8143 GLN* 1.3 75.7 - - - +
8163 LYS* 1.3 65.1 + - - +
8183 GLN* 4.5 1.8 - - - +
8193 MET* 2.9 18.2 + - - -
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Residues in contact with LYS 816 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8123 LYS* 2.8 26.3 + - - +
8133 ALA* 3.0 4.0 + - - +
8153 ARG* 1.3 79.0 - - - +
8173 GLN* 1.3 63.0 + - - +
8183 GLN 2.8 0.2 + - - -
8193 MET* 3.1 1.2 + - - -
8203 ALA* 3.0 16.1 + - - -
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Residues in contact with GLN 817 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8133 ALA 2.8 15.3 + - - -
8143 GLN* 3.9 0.9 - - - +
8163 LYS* 1.3 70.6 - - - +
8183 GLN* 1.3 57.1 + - - +
8203 ALA* 3.5 4.5 - - - +
8213 GLU* 2.8 27.0 + - - -
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Residues in contact with GLN 818 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8143 GLN 2.9 16.7 + - - -
8153 ARG* 3.4 5.8 - - - +
8163 LYS 2.8 2.0 + - - -
8173 GLN* 1.3 78.6 - - - +
8193 MET* 1.3 57.3 + - - +
8213 GLU* 3.8 0.5 - - - -
8223 GLU* 2.9 27.0 + - - -
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Residues in contact with MET 819 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8153 ARG 2.9 13.0 + - - -
8163 LYS 3.8 1.8 - - - -
8183 GLN* 1.3 74.3 - - - +
8203 ALA* 1.3 61.9 + - - +
8223 GLU* 4.5 2.2 - - - +
8233 MET* 2.9 21.2 + - - +
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Residues in contact with ALA 820 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8163 LYS 3.0 14.2 + - - -
8173 GLN* 3.5 6.7 - - - +
8183 GLN 3.1 0.4 - - - -
8193 MET* 1.3 79.8 - - - +
8213 GLU* 1.3 64.2 + - - +
8233 MET* 3.3 7.1 + - - -
8243 VAL 3.8 3.3 + - - -
8393 ALA* 5.6 10.8 - - - +
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Residues in contact with GLU 821 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8173 GLN 2.8 16.9 + - - -
8183 GLN 3.8 1.6 - - - -
8203 ALA* 1.3 70.0 - - - +
8223 GLU* 1.3 64.1 + - - +
8243 VAL* 2.8 19.4 + - - -
8253 GLU* 3.7 3.8 + - - -
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Residues in contact with GLU 822 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8183 GLN 2.9 19.5 + - - -
8193 MET* 3.9 2.0 - - - +
8213 GLU* 1.3 70.7 - - - +
8233 MET* 1.3 64.7 + - - +
8253 GLU* 3.5 10.9 + - - +
8263 ALA 4.4 1.4 + - - -
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Residues in contact with MET 823 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8193 MET 2.9 19.3 + - - -
8203 ALA 3.8 2.9 - - - -
8213 GLU 2.8 1.6 + - - -
8223 GLU* 1.3 78.5 - - - +
8243 VAL* 1.3 63.3 + - - +
8253 GLU 2.9 1.7 + - - -
8263 ALA* 3.2 10.9 + - - -
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Residues in contact with VAL 824 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8203 ALA 3.8 4.8 + - - -
8213 GLU 2.8 13.5 + - - -
8233 MET* 1.3 70.1 - - - +
8253 GLU* 1.3 56.4 + - - +
8263 ALA* 2.9 7.4 + - - -
8273 ALA* 3.1 13.7 + - - -
8343 LEU 4.3 15.9 + - - +
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Residues in contact with GLU 825 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8213 GLU 3.7 4.7 + - - -
8223 GLU* 3.5 9.1 + - - +
8233 MET 2.9 3.0 + - - -
8243 VAL* 1.3 72.3 - - - +
8263 ALA* 1.3 63.9 + - - +
8273 ALA* 3.1 3.3 + - - +
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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