Contacts of the helix formed by residues 737 - 743 (chain B) 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 LEU 737 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B ASN* 3.4 9.1 + - - +
733B ILE* 3.2 26.6 + - + +
735B LYS 3.3 0.2 - - - -
736B ASN* 1.3 86.3 - - - +
738B VAL* 1.3 60.7 + - - +
740B SER* 3.6 1.6 + - - -
741B ALA* 3.0 30.2 + - - +
749B TYR* 4.0 10.9 - - + -
778B ILE* 3.9 29.8 - - + -
779B THR 4.7 2.9 - - - +
780B LEU* 4.1 16.6 - - + -
733D ILE* 4.5 11.7 - - + -
737D LEU* 4.5 26.5 - - + -
738D VAL* 4.0 25.8 - - + +
741D ALA* 5.5 0.4 - - + -
749D TYR* 5.4 0.5 - - - -
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Residues in contact with VAL 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639A ALA* 3.9 24.9 - - + -
642A ASN* 4.4 2.9 - - - +
644A TYR* 3.2 21.3 - - + +
733B ILE* 3.0 21.3 + - + +
734B ASN* 3.9 13.7 - - - +
737B LEU* 1.3 68.7 - - - +
739B GLY* 1.3 66.5 + - - +
741B ALA* 3.1 6.1 + - - +
742B MET* 2.9 23.2 + - + +
737D LEU* 3.9 15.7 - - + -
778D ILE* 3.9 13.9 - - + -
780D LEU* 3.7 26.0 - - + -
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Residues in contact with GLY 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A TYR* 3.6 16.4 - - - -
685A GLY 3.3 19.7 - - - -
686A ASN* 4.0 5.0 - - - +
687A TYR* 4.6 1.4 - - - -
734B ASN 3.1 11.7 + - - -
735B LYS 3.1 11.8 + - - -
738B VAL* 1.3 74.4 - - - +
740B SER* 1.3 62.7 + - - +
742B MET* 3.0 14.6 + - - +
743B ALA* 3.0 13.2 + - - +
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Residues in contact with SER 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ASN* 2.9 26.3 + - - +
689A THR* 5.9 1.4 - - - +
735B LYS 3.1 4.2 + - - -
736B ASN 3.4 19.0 + - - -
737B LEU 3.6 0.2 + - - -
738B VAL 3.3 0.4 - - - -
739B GLY* 1.3 74.4 - - - +
741B ALA* 1.3 60.6 + - - +
743B ALA* 3.4 5.5 + - - +
744B GLY 3.2 4.3 + - - -
745B SER* 2.9 35.8 + - - -
748B GLY 2.8 27.0 + - - -
749B TYR* 3.6 14.1 - - - -
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Residues in contact with ALA 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B LEU 3.0 19.3 + - - +
738B VAL* 3.4 8.7 - - - +
739B GLY 3.1 0.2 - - - -
740B SER* 1.3 75.2 - - - +
742B MET* 1.3 63.6 + - - +
744B GLY* 3.0 11.3 + - - -
745B SER 4.8 1.1 - - - +
749B TYR* 4.2 1.9 - - + -
698D TRP* 2.9 19.7 + - - -
737D LEU* 5.5 0.4 - - + -
746D ILE* 6.1 0.5 - - - -
749D TYR* 3.6 49.8 - - + -
778D ILE* 4.4 8.1 - - + -
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Residues in contact with MET 742 (chain B).
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* 3.4 22.0 + - - +
638A ILE 3.5 17.5 - - - +
639A ALA* 4.1 6.3 - - + -
644A TYR* 3.9 26.7 - - + -
687A TYR* 3.7 25.8 - - + -
738B VAL* 2.9 16.7 + - + +
739B GLY* 3.0 7.8 + - - +
741B ALA* 1.3 76.8 - - - +
743B ALA* 1.3 60.0 + - - +
744B GLY 3.2 0.9 + - - -
698D TRP* 3.7 44.2 + - + +
699D ILE* 3.8 13.5 - - - +
778D ILE* 4.1 24.9 - - + -
796D THR* 5.3 0.7 - - + -
798D PRO* 5.2 8.3 - - + -
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Residues in contact with ALA 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A ASN 3.5 13.5 - - - +
687A TYR* 4.0 10.3 - - + -
689A THR* 3.2 27.1 - - + +
694A ALA* 3.7 6.2 - - + +
695A ALA 3.2 2.1 + - - -
696A ILE* 3.0 38.8 + - + -
739B GLY 3.0 8.8 + - - +
740B SER* 3.7 7.9 - - - +
741B ALA 3.2 0.2 - - - -
742B MET* 1.3 74.9 - - - +
744B GLY* 1.3 61.7 + - - +
745B SER* 5.1 0.2 - - - -
699D ILE* 3.7 4.6 - - - +
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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