Contacts of the strand formed by residues 722 - 727 (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 ALA 722 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704E TYR 4.6 7.9 - - - +
708E LEU* 3.9 19.5 - - + -
713E LEU* 5.3 0.9 - - + -
716E LEU* 3.4 29.1 - - + +
721E LYS* 1.3 78.4 - - - +
723E ASN* 1.3 63.0 + - - +
733E LEU* 3.5 9.5 - - - +
734E VAL* 3.0 38.1 + - + +
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Residues in contact with ASN 723 (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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700E GLU* 3.5 16.9 + - - +
701E ASP 3.0 46.1 + - - -
702E ARG* 4.4 0.2 - - - +
704E TYR* 4.2 8.7 + - - +
705E GLY 3.0 22.9 + - - +
706E PRO 4.2 2.0 + - - +
707E ALA* 3.4 11.3 - - - -
708E LEU* 2.7 36.2 + - - +
722E ALA* 1.3 75.1 - - - +
724E VAL* 1.3 54.0 + - - +
731E VAL* 3.8 14.8 - - + -
732E VAL 3.4 2.9 - - - +
733E LEU* 3.3 15.7 - - - +
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Residues in contact with VAL 724 (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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707E ALA* 4.3 0.4 - - - -
708E LEU* 3.3 12.3 - - + +
709E SER 3.5 24.5 - - - +
710E ILE* 4.5 1.8 - - + +
713E LEU* 3.1 36.1 - - + -
723E ASN* 1.3 70.8 - - - +
725E LEU* 1.3 60.8 + - - +
726E ILE* 3.5 21.3 + - + +
731E VAL* 3.3 7.6 - - - -
732E VAL 2.9 36.3 + - - +
734E VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 725 (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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707E ALA* 4.1 7.6 - - + +
708E LEU 3.0 15.5 + - - +
709E SER* 5.1 2.9 - - - -
710E ILE* 3.8 22.2 + - - +
724E VAL* 1.3 70.0 - - - +
726E ILE* 1.3 59.4 + - - +
727E GLY* 3.3 24.2 - - - +
728E GLN 3.8 16.6 - - - +
729E GLY* 4.7 1.6 - - - -
730E ASP 3.7 2.5 - - - +
731E VAL* 3.3 27.8 - - + -
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Residues in contact with ILE 726 (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 46.8 - - - +
691E LEU* 3.2 40.2 - - + -
696E ILE* 5.8 3.4 - - + -
710E ILE* 3.9 11.9 - - + -
724E VAL* 3.9 14.8 - - + +
725E LEU* 1.3 72.8 - - - +
727E GLY* 1.3 55.5 + - - +
730E ASP* 2.9 27.2 + - - +
732E VAL* 4.0 29.4 - - + -
734E VAL* 5.4 0.2 - - + -
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Residues in contact with GLY 727 (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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725E LEU* 3.3 13.0 + - - +
726E ILE* 1.3 82.1 - - - +
728E GLN* 1.3 78.0 + - - +
730E ASP* 2.8 20.7 + - - +
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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