Contacts of the helix formed by residues 487 - 496 (chain N) in PDB entry 2JA7
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 THR 487 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486N TYR* 1.3 79.1 + - - +
488N TYR* 1.3 72.7 + - + +
489N SER* 3.6 23.8 - - - +
490N SER* 2.7 22.2 + - - -
491N THR* 3.2 4.7 + - - -
774N GLY 4.6 7.0 - - - +
775N LYS 5.8 0.2 - - - -
777N ALA 2.6 28.7 + - - -
778N MET 3.6 0.3 - - - -
779N GLY* 3.5 14.0 + - - -
780N VAL 5.0 1.1 - - - +
781N PHE* 4.1 10.3 - - - +
814N PHE* 5.6 1.1 - - + -
817N LEU 5.0 2.5 - - - +
818N PRO 4.7 6.3 - - - +
819N ALA* 4.1 19.3 - - + -
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Residues in contact with TYR 488 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N LEU* 5.6 1.3 - - + +
197N PHE* 2.9 33.7 + - + -
199N MET* 3.5 32.4 - - + +
487N THR* 1.3 75.9 - - + +
489N SER* 1.3 56.2 + - - +
490N SER 2.7 12.3 + - - -
491N THR* 2.8 19.0 + - - -
492N LEU* 3.1 28.1 + - + +
780N VAL 4.1 6.7 + - - +
781N PHE* 3.5 28.3 - - - +
782N LEU* 4.6 3.1 - - + -
812N LEU 3.7 24.9 - - - -
813N LYS* 3.9 28.9 - - + +
814N PHE* 6.4 1.8 - + + -
817N LEU* 3.7 31.2 - - + +
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Residues in contact with SER 489 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487N THR* 3.4 16.1 - - - +
488N TYR* 1.3 78.5 - - - +
490N SER* 1.3 60.8 + - - +
492N LEU* 3.6 15.5 - - - +
493N SER* 3.2 22.7 + - - -
751N VAL* 3.8 8.2 - - - +
752N ALA* 6.0 0.8 - - - -
755N ILE* 4.0 26.4 - - - +
774N GLY* 4.1 13.9 + - - -
775N LYS* 5.6 1.2 - - - +
812N LEU* 5.8 3.4 - - - -
814N PHE* 4.7 15.9 - - - -
819N ALA* 5.4 1.6 - - - +
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Residues in contact with SER 490 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484N ASN* 3.3 29.9 + - - +
486N TYR* 4.7 2.3 - - - +
487N THR* 2.7 32.5 + - - -
489N SER* 1.3 74.0 + - - +
491N THR* 1.3 65.0 + - - -
493N SER* 3.0 8.4 + - - -
494N HIS* 2.8 23.0 + - - +
497N ARG* 4.9 0.7 + - - -
775N LYS* 4.1 34.7 + - - +
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Residues in contact with THR 491 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199N MET* 3.8 20.9 - - + -
483N LEU* 3.2 38.1 - - + -
484N ASN 2.7 21.1 + - - -
485N ARG* 3.5 25.1 + - - +
487N THR 3.8 5.9 + - - -
488N TYR* 2.8 17.3 + - - -
490N SER* 1.3 75.3 - - - +
492N LEU* 1.3 67.0 + - - +
494N HIS* 3.3 3.9 + - - +
495N LEU* 3.1 25.0 + - + +
781N PHE* 4.8 0.9 + - - +
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Residues in contact with LEU 492 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43N LEU* 3.7 23.8 - - + -
44N VAL* 5.3 1.1 - - + -
199N MET* 3.4 35.2 - - + -
488N TYR* 3.1 38.5 + - + +
489N SER* 3.6 10.8 - - - +
490N SER 3.1 0.4 - - - -
491N THR* 1.3 76.9 - - - +
493N SER* 1.3 55.1 + - - +
495N LEU* 2.5 39.4 + - + +
496N ARG* 3.3 10.7 + - - +
751N VAL* 3.8 11.0 - - + -
812N LEU* 3.5 36.3 - - + +
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Residues in contact with SER 493 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489N SER 3.2 11.3 + - - -
490N SER* 3.0 9.3 + - - -
492N LEU* 1.3 78.0 - - - +
494N HIS* 1.3 63.8 + - - +
495N LEU 3.0 1.2 + - - -
496N ARG* 3.0 11.5 + - - +
497N ARG* 2.9 17.5 + - - +
526N GLU* 2.7 29.9 + - - -
538N ASN* 3.3 17.2 + - - +
751N VAL* 4.0 19.4 - - - +
752N ALA* 5.0 2.0 - - - -
775N LYS* 3.5 6.9 - - - -
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Residues in contact with HIS 494 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76 A 6.0 3.3 - - - -
211N VAL* 4.0 8.3 - - + +
213N ILE* 3.5 22.4 - - + +
481N GLN* 2.6 34.4 + - + +
482N VAL 3.6 20.4 - - - -
483N LEU* 3.7 8.9 - - + -
484N ASN* 3.2 43.8 + - + -
490N SER 2.8 15.8 + - - +
491N THR* 3.6 10.5 - - - +
493N SER* 1.3 73.4 - - - +
495N LEU* 1.3 60.5 + - - +
497N ARG* 3.5 33.8 + - - +
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Residues in contact with LEU 495 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N VAL* 3.9 18.8 - - + -
46N GLN* 3.5 14.2 - - - +
47N GLN* 3.8 20.4 + - + +
199N MET* 3.7 31.4 - - + -
200N GLY 3.8 9.0 - - - +
201N GLY* 4.1 18.4 - - - +
202N TYR* 4.4 7.0 - - + -
211N VAL* 3.8 25.1 - - + -
213N ILE* 5.0 1.7 - - - +
483N LEU* 4.1 12.8 - - + -
491N THR* 3.1 23.6 - - + +
492N LEU* 2.5 17.8 + - - +
494N HIS* 1.3 71.4 - - - +
496N ARG* 1.3 56.2 + - + +
497N ARG 3.2 9.8 + - - +
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Residues in contact with ARG 496 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N PHE* 5.8 0.2 - - - -
43N LEU* 2.9 39.7 + - - +
44N VAL* 5.8 0.7 - - + -
45N SER* 4.9 4.8 + - - -
46N GLN* 3.6 24.4 - - - +
492N LEU* 3.8 12.1 - - - +
493N SER* 3.0 5.2 + - - +
495N LEU* 1.3 78.9 - - + +
497N ARG* 1.3 58.4 + - - +
538N ASN* 3.2 10.0 - - + +
539N LEU* 3.1 50.8 + - + +
540N SER 3.0 22.4 + - - -
541N LEU* 3.4 25.9 + - - +
543N SER 3.7 13.5 + - - -
751N VAL* 3.2 32.9 - - + +
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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