Contacts of the helix formed by residues 694 - 701 (chain A) in PDB entry 1DQ8
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 694 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689A THR* 3.5 35.7 - - + +
692A LYS 3.3 2.7 + - - +
693A PRO* 1.3 77.6 - - - +
695A ALA* 1.3 66.2 + - - +
696A ILE* 3.1 4.8 + - + -
697A ASN* 3.2 16.9 + - - +
698A TRP* 3.6 8.7 + - - +
746A ILE* 4.8 3.8 - - - +
776A ASN* 4.9 4.1 + - - +
743B ALA* 3.7 15.0 - - + +
744B GLY 3.8 6.1 - - - -
745B SER* 4.6 1.6 - - - -
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Residues in contact with ALA 695 (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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694A ALA* 1.3 70.8 - - - +
696A ILE* 1.3 56.9 + - - +
698A TRP* 3.3 2.5 + - - +
699A ILE* 2.9 35.6 + - + +
746A ILE* 3.9 24.7 - - + +
743B ALA 3.2 0.4 + - - -
744B GLY* 2.9 21.9 + - - +
744C GLY* 5.4 0.2 - - - -
695D ALA* 3.5 32.3 - - + -
699D ILE* 3.8 8.7 - - + -
746D ILE* 5.0 1.8 - - + -
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Residues in contact with ILE 696 (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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635A HIS* 4.3 0.2 - - - +
646A ARG* 3.9 24.7 - - - +
687A TYR* 3.5 48.7 - - + +
689A THR* 3.6 24.2 - - - +
694A ALA* 3.0 2.6 - - + -
695A ALA* 1.3 78.7 - - - +
697A ASN* 1.3 67.2 + - - +
699A ILE* 4.6 1.1 - - - +
700A GLU* 2.8 47.4 + - - +
743B ALA* 3.0 20.1 + - + +
699D ILE* 3.5 27.8 - - + +
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Residues in contact with ASN 697 (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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646A ARG* 3.2 15.3 + - - +
689A THR* 2.9 49.1 + - - -
691A LYS 5.7 0.2 - - - +
692A LYS 4.5 9.1 + - - -
694A ALA* 3.2 10.8 + - - +
696A ILE* 1.3 76.4 - - - +
698A TRP* 1.3 61.8 + - - +
701A GLY* 2.9 29.8 + - - +
702A ARG* 3.7 12.1 - - + +
773A GLY* 4.9 9.9 - - - -
776A ASN* 4.2 4.9 - - - +
798A PRO* 4.2 1.4 - - - +
799A SER* 3.9 21.2 - - - +
801A GLU* 4.4 5.5 + - - -
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Residues in contact with TRP 698 (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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694A ALA 3.6 4.9 + - - +
695A ALA* 3.3 13.2 + - - +
697A ASN* 1.3 81.9 - - - +
699A ILE* 1.3 66.5 + - + +
701A GLY 4.4 0.2 + - - -
746A ILE* 4.4 16.2 - - + -
747A GLY* 3.6 29.9 - - - +
749A TYR* 4.4 9.9 - + - -
776A ASN* 3.7 16.3 - - + +
777A CYS* 3.7 17.9 - - - -
778A ILE* 3.9 30.7 - - + -
798A PRO* 3.6 51.3 - - + +
741C ALA 2.9 25.9 + - - -
742C MET* 3.7 42.9 + - + +
744C GLY* 4.6 3.8 - - - -
637D SER* 5.4 1.4 + - - -
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Residues in contact with ILE 699 (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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695A ALA* 2.9 19.2 + - + +
696A ILE* 4.2 1.8 - - - +
698A TRP* 1.3 84.5 - - + +
700A GLU* 1.3 74.0 + - - +
742C MET 3.9 17.7 - - - +
743C ALA 3.7 10.5 - - - +
744C GLY* 4.6 0.7 - - - +
635D HIS* 3.1 24.1 + - - +
636D THR 5.2 0.2 - - - +
637D SER* 4.0 8.9 + - - -
687D TYR* 4.4 2.7 - - - +
695D ALA* 3.9 13.2 - - + +
696D ILE* 3.5 54.7 - - + +
699D ILE* 4.3 5.8 - - + -
700D GLU* 4.1 2.9 - - - +
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Residues in contact with GLU 700 (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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635A HIS* 3.2 28.4 + - + -
646A ARG* 3.3 25.1 + - - +
648A GLN* 4.7 8.4 + - - +
696A ILE* 2.8 27.5 + - + +
699A ILE* 1.3 83.8 - - - +
701A GLY* 1.3 60.4 - - - +
705A SER* 5.1 0.3 + - - -
635D HIS* 4.0 11.4 - - + -
699D ILE* 4.0 2.6 - - - +
700D GLU* 2.8 40.6 - - - +
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Residues in contact with GLY 701 (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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585A ALA* 6.4 0.2 - - - -
646A ARG* 3.0 24.8 + - - -
648A GLN* 4.3 5.7 + - - -
697A ASN 2.9 19.1 + - - -
698A TRP 4.4 0.6 + - - -
699A ILE 3.5 1.6 - - - -
700A GLU* 1.3 82.2 - - - +
702A ARG* 1.3 59.5 + - - -
705A SER* 3.9 8.1 - - - -
798A PRO* 3.2 18.8 - - - -
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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