Contacts of the helix formed by residues 687 - 692 (chain A) in PDB entry 2JED
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 ASP 687 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685A SER 3.8 0.6 + - - -
686A MET* 1.3 83.1 - - - +
688A GLN* 1.3 68.6 + - - +
689A ASN* 3.4 22.9 + - - +
690A MET* 3.7 41.1 + - + +
691A PHE* 5.8 0.3 - - - -
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Residues in contact with GLN 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LYS* 5.0 5.4 + - - +
451A LYS* 4.5 21.4 - - - +
683A ILE 3.7 14.9 + - - +
684A ASN 5.1 7.0 + - - -
686A MET* 3.5 22.9 - - - +
687A ASP* 1.3 76.0 + - - +
689A ASN* 1.3 63.6 + - - +
690A MET 3.3 5.5 + - - -
691A PHE* 4.2 3.2 + - - +
692A ARG* 3.1 30.0 + - - +
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Residues in contact with ASN 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687A ASP* 3.4 18.4 + - - +
688A GLN* 1.3 82.8 - - - +
690A MET* 1.3 61.6 + - - +
691A PHE 3.2 2.6 + - - -
692A ARG* 3.4 38.9 + - + +
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Residues in contact with MET 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A LEU* 3.6 45.1 - - + -
422A VAL* 3.9 26.1 - - + +
426A MET* 4.5 8.3 - - - +
686A MET* 4.4 7.6 - - + -
687A ASP* 3.7 37.9 - - + +
688A GLN 3.3 1.6 - - - -
689A ASN* 1.3 77.3 - - - +
691A PHE* 1.3 88.0 + - + +
692A ARG 3.4 2.8 + - - +
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Residues in contact with PHE 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LYS* 3.7 39.0 - - + -
416A VAL* 3.8 22.4 - - + -
422A VAL* 3.7 33.0 - - + -
425A THR* 4.4 5.8 - - + -
426A MET* 4.4 16.8 - - - -
449A GLN* 2.7 43.0 + - - +
454A LEU* 3.8 35.0 - - + -
686A MET* 5.3 1.1 - - + -
687A ASP 5.8 0.4 - - - -
688A GLN 4.2 2.7 + - - -
689A ASN 3.2 0.4 - - - -
690A MET* 1.3 103.8 - - + +
692A ARG* 1.3 63.4 + - - +
694A PHE* 3.1 12.8 - - + +
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Residues in contact with ARG 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LYS* 4.5 4.8 - - - +
426A MET* 3.5 10.7 - - - +
449A GLN* 2.8 39.6 + - - +
688A GLN* 3.1 31.3 + - - +
689A ASN* 3.4 36.8 + - + +
690A MET 3.4 4.0 - - - +
691A PHE* 1.3 95.5 + - - +
693A ASN* 1.3 77.3 + - - +
694A PHE 3.1 4.7 - - - -
695A SEP 4.4 7.2 + - - -
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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