Contacts of the helix formed by residues 786 - 794 (chain B) in PDB entry 4DQL
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 GLU 786 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782B GLU 5.0 5.6 - - - +
783B ALA* 3.3 17.7 + - - +
785B LEU* 1.3 82.9 - - - +
787B LYS* 1.3 59.5 + - - +
788B GLN* 3.1 3.2 + - + +
789B ALA* 3.2 7.3 + - + +
790B TYR* 2.7 34.2 + - - +
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Residues in contact with LYS 787 (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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762B ARG* 4.1 18.2 + - - +
785B LEU 3.6 2.6 + - - +
786B GLU* 1.3 73.0 + - - +
788B GLN* 1.3 56.8 + - - +
790B TYR* 3.5 2.4 + - - +
791B LYS* 3.0 27.9 + - - +
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Residues in contact with GLN 788 (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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786B GLU* 3.3 2.2 - - + +
787B LYS* 1.3 77.2 - - - +
789B ALA* 1.3 63.3 + - - +
791B LYS* 3.3 5.5 + - - +
792B GLU* 2.9 64.8 + - + +
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Residues in contact with ALA 789 (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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783B ALA* 3.3 30.3 - - + +
784B LEU* 4.2 5.8 - - + -
786B GLU* 3.2 8.6 + - + +
788B GLN* 1.3 75.4 - - - +
790B TYR* 1.3 61.5 + - - +
792B GLU* 4.9 2.7 - - - -
793B GLN* 2.8 58.7 + - - +
794B VAL 3.6 0.2 + - - -
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Residues in contact with TYR 790 (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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759B PRO* 4.8 1.6 + - - +
760B VAL 2.6 29.2 + - - -
761B THR* 3.6 9.9 - - - +
762B ARG* 3.5 53.1 + - + +
765B LEU* 4.0 15.3 - - + -
784B LEU 3.1 21.7 + - - +
786B GLU 2.7 18.7 + - - +
787B LYS 3.7 0.9 - - - +
789B ALA* 1.3 72.3 - - - +
791B LYS* 1.3 56.7 + - - +
794B VAL* 2.9 31.1 + - + +
795B LEU* 2.8 62.6 + - + +
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Residues in contact with LYS 791 (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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787B LYS 3.0 18.8 + - - +
788B GLN* 3.6 6.5 - - - +
790B TYR* 1.3 77.4 - - - +
792B GLU* 1.3 63.8 + - + +
795B LEU* 3.5 20.4 - - + +
796B ALA* 3.0 28.8 + - - +
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Residues in contact with GLU 792 (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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788B GLN* 2.9 57.1 + - + +
789B ALA* 4.3 1.9 - - - +
791B LYS* 1.3 80.8 - - + +
793B GLN* 1.3 69.5 + - + +
796B ALA* 3.5 19.7 - - - +
797B LYS* 4.0 13.3 - - - +
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Residues in contact with GLN 793 (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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784B LEU* 3.8 24.3 - - + +
789B ALA* 2.8 40.8 + - - +
792B GLU* 1.3 83.6 + - + +
794B VAL* 1.3 61.1 + - - +
797B LYS* 3.6 38.5 + - - +
799B LEU* 3.6 14.7 - - + +
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Residues in contact with VAL 794 (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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759B PRO* 3.9 8.7 - - + +
760B VAL* 3.5 46.7 - - + +
784B LEU* 4.3 23.8 - - + -
790B TYR* 2.9 36.9 + - + +
793B GLN* 1.3 79.6 - - - +
795B LEU* 1.3 61.7 + - - +
796B ALA 3.5 0.2 - - - -
797B LYS 3.4 0.3 + - - -
798B ARG* 2.8 27.4 + - - -
799B LEU* 3.1 25.4 + - + +
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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