Contacts of the helix formed by residues 694 - 701 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743C ALA* 3.7 15.0 - - + +
744C GLY 3.9 7.6 - - - -
745C SER* 4.0 2.0 - - - +
689D THR* 3.5 35.9 - - + +
692D LYS 3.4 2.3 + - - +
693D PRO* 1.3 75.7 - - - +
695D ALA* 1.3 65.2 + - - +
696D ILE* 3.2 5.0 + - + -
697D ASN* 3.3 15.9 + - - +
698D TRP* 3.6 9.2 + - - +
746D ILE* 4.8 5.0 - - - +
776D ASN* 4.8 3.4 + - - +
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Residues in contact with ALA 695 (chain D).
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* 3.5 32.8 - - + -
699A ILE* 3.9 4.5 - - + -
746A ILE* 5.3 0.2 - - + -
744B GLY* 5.4 0.2 - - - -
743C ALA 3.1 4.8 + - - +
744C GLY* 3.0 22.0 + - - +
694D ALA* 1.3 72.8 - - - +
696D ILE* 1.3 58.2 + - - +
698D TRP* 3.2 2.8 + - - +
699D ILE* 2.9 34.6 + - + +
746D ILE* 3.9 23.6 - - + +
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Residues in contact with ILE 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A ILE* 3.5 26.2 - - + +
743C ALA* 3.0 20.8 + - + +
635D HIS* 4.4 5.2 - - + -
646D ARG* 3.7 28.2 + - - +
687D TYR* 3.5 44.0 - - + +
689D THR* 3.7 23.1 - - - +
694D ALA* 4.2 2.0 - - + -
695D ALA* 1.3 78.3 - - - +
697D ASN* 1.3 68.1 + - - +
699D ILE* 4.8 1.3 - - - -
700D GLU* 2.8 44.0 + - + +
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Residues in contact with ASN 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646D ARG* 3.2 16.7 + - - +
688D CYS 3.4 0.2 - - - +
689D THR* 2.8 53.1 + - - +
692D LYS 4.3 9.7 + - - -
694D ALA* 3.3 10.3 + - - +
695D ALA 3.3 0.8 - - - -
696D ILE* 1.3 77.9 - - - +
698D TRP* 1.3 58.7 + - - +
701D GLY* 2.8 31.1 + - - -
702D ARG* 3.7 10.4 - - - +
773D GLY* 5.0 9.3 - - - -
776D ASN* 4.4 4.5 - - - +
798D PRO* 4.3 1.0 - - - +
799D SER* 4.1 22.6 - - - +
801D GLU* 4.5 4.9 + - - -
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Residues in contact with TRP 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A SER* 5.6 1.6 + - - -
741B ALA 2.9 26.8 + - - -
742B MET* 3.7 44.2 + - + +
744B GLY* 4.6 3.6 - - - -
694D ALA 3.6 6.3 + - - +
695D ALA* 3.2 12.0 + - - +
697D ASN* 1.3 82.0 - - - +
699D ILE* 1.3 66.3 + - + +
746D ILE* 4.5 16.2 - - + +
747D GLY* 3.6 29.0 - - - +
749D TYR* 4.4 8.1 - + - -
776D ASN* 3.7 21.0 + - + +
777D CYS* 3.7 24.5 - - - -
778D ILE* 3.8 32.1 - - + -
798D PRO* 3.7 38.9 - - + +
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Residues in contact with ILE 699 (chain D).
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* 3.1 29.6 - - + -
636A THR 5.3 0.3 - - - +
637A SER* 5.4 4.2 + - - -
687A TYR* 4.3 3.2 + - - +
695A ALA* 3.8 13.7 - - + +
696A ILE* 3.5 52.5 - - + +
699A ILE* 4.3 6.1 - - + -
700A GLU* 4.0 1.6 - - - +
742B MET 3.8 18.4 - - - +
743B ALA 3.7 10.5 - - - +
744B GLY* 4.7 0.2 - - - -
695D ALA* 2.9 20.3 + - + +
696D ILE* 4.3 1.6 - - - +
698D TRP* 1.3 84.6 - - + +
700D GLU* 1.3 75.5 + - - +
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Residues in contact with GLU 700 (chain D).
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* 2.8 29.8 + - - -
699A ILE* 4.1 8.3 - - - +
700A GLU* 2.8 32.7 - - - +
585D ALA* 5.9 2.4 - - - +
635D HIS* 4.7 19.8 + - + +
646D ARG* 3.4 23.1 + - - +
648D GLN* 4.8 9.5 + - - +
696D ILE* 2.8 24.7 + - + +
699D ILE* 1.3 81.9 - - - +
701D GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D ALA* 6.3 0.4 - - - -
646D ARG* 2.9 26.9 + - - -
648D GLN* 4.4 5.8 + - - -
697D ASN 2.8 19.6 + - - -
698D TRP 4.4 1.0 + - - -
699D ILE 3.6 1.6 - - - -
700D GLU* 1.3 81.4 - - - +
702D ARG* 1.3 59.9 + - - -
705D SER* 3.8 9.0 - - - -
798D PRO* 3.2 18.4 - - - +
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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