Contacts of the helix formed by residues 686 - 692 (chain E) in PDB entry 2JDQ
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 VAL 686 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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687E GLU* 1.3 73.2 + - + +
688E SER* 4.6 5.3 + - - +
689E ALA* 3.8 22.6 - - - +
690E VAL* 3.5 24.4 + - - +
710E ILE* 4.7 2.2 - - - +
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Residues in contact with GLU 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E VAL* 1.3 84.3 - - + +
688E SER* 1.3 61.8 + - - +
690E VAL* 3.2 6.2 + - - +
691E LEU* 2.9 41.3 + - + +
710E ILE* 4.0 24.6 - - + +
726E ILE* 2.9 47.9 - - - +
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Residues in contact with SER 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E VAL* 5.0 4.7 + - - +
687E GLU* 1.3 77.9 + - - +
689E ALA* 1.3 60.3 + - - +
690E VAL 3.2 0.9 - - - -
691E LEU* 3.8 9.6 - - - +
692E ARG* 2.8 29.6 + - - +
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Residues in contact with ALA 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E VAL* 3.8 23.6 - - - +
687E GLU 3.3 0.6 - - - -
688E SER* 1.3 79.8 + - - +
690E VAL* 1.3 61.4 + - + +
692E ARG* 4.0 14.6 - - - +
693E GLY 4.9 0.2 + - - -
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Residues in contact with VAL 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686E VAL 3.5 15.5 + - - +
687E GLU 3.2 7.7 + - - +
689E ALA* 1.3 76.8 - - + +
691E LEU* 1.3 66.2 + - + +
692E ARG 3.1 1.6 - - - -
693E GLY* 3.1 13.5 + - - -
694E PHE* 3.2 32.3 - - + -
710E ILE* 3.9 25.8 - - + +
713E LEU* 4.0 18.2 - - + -
714E SER* 5.4 5.2 - - - +
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Residues in contact with LEU 691 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687E GLU* 2.9 39.3 + - + +
688E SER* 4.2 6.5 - - - -
690E VAL* 1.3 73.6 - - - +
692E ARG* 1.3 67.7 + - - +
694E PHE* 2.9 34.7 + - + +
696E ILE* 5.0 16.4 - - + -
710E ILE* 4.3 2.7 - - + -
713E LEU* 3.6 30.3 - - + -
726E ILE* 3.2 37.5 - - + -
734E VAL* 4.8 8.1 - - + -
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Residues in contact with ARG 692 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 5.2 2.8 + - - +
368A GLY 3.1 27.7 + - - -
369A ASN* 3.5 17.6 - - - +
370A ARG* 3.6 19.2 - - - +
373A ILE* 4.3 0.2 - - - +
409A SER* 4.4 11.9 + - - +
410A GLY* 2.7 45.5 + - - -
688E SER 2.8 20.4 + - - +
689E ALA* 4.0 13.7 - - - +
691E LEU* 1.3 77.6 - - - +
693E GLY* 1.3 57.4 + - - +
737E ARG* 3.3 22.9 + - - -
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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