Contacts of the helix formed by residues 370 - 387 (chain A) in PDB entry 1JQI
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 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A SER* 4.5 2.0 + - - +
365A GLU 3.5 4.3 - - - -
366A ILE* 3.1 25.5 + - + +
369A GLY* 1.3 77.2 - - - +
371A SER* 1.3 66.0 + - - +
372A GLU* 3.3 6.6 + - - -
373A ILE* 2.9 28.6 + - - +
374A GLN* 3.0 10.8 + - - +
399A FAD 2.6 64.6 + - - +
741B GLN* 3.7 6.1 - - - +
744B GLY* 5.2 1.6 - - - -
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Residues in contact with SER 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LYS* 4.7 1.8 + - - +
326A LEU* 3.4 25.9 - - - +
329A SER* 4.4 3.5 + - - -
330A GLU* 4.0 8.1 + - - +
365A GLU* 3.2 34.0 + - - +
370A THR* 1.3 73.0 - - - +
372A GLU* 1.3 66.8 + - - +
374A GLN* 3.3 6.2 + - - +
375A ARG* 3.0 39.0 + - - +
741B GLN* 3.7 8.7 + - - +
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A THR* 3.3 1.0 + - - -
371A SER* 1.3 81.0 - - - +
373A ILE* 1.3 64.5 + - + +
375A ARG* 3.3 16.2 + - - +
376A LEU* 3.2 25.0 + - - +
399A FAD 2.8 49.4 + - + +
685B ASN* 3.2 28.9 - - - +
686B ILE* 5.9 0.2 - - + -
689B LYS* 2.8 24.9 + - - +
741B GLN* 3.0 33.2 + - - +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A SER* 3.7 17.0 - - - +
248A ARG* 4.2 14.6 - - - +
369A GLY* 4.3 4.0 - - - -
370A THR* 2.9 27.6 + - - +
372A GLU* 1.3 79.1 - - - +
374A GLN* 1.3 65.9 + - - +
376A LEU* 3.2 9.6 + - + +
377A VAL* 3.0 28.5 + - + +
399A FAD 3.7 37.2 - - + +
400A CAA 3.8 49.4 - - + +
676B PHE* 5.8 0.2 - - + -
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 3.2 38.8 + - - +
322A ALA* 3.2 41.3 - - + +
325A LYS* 4.0 20.4 - - + +
326A LEU* 4.2 12.3 - - + -
368A GLU 3.2 5.3 + - - -
369A GLY* 3.0 27.4 + - - +
370A THR 3.0 16.9 + - - +
371A SER* 3.3 8.7 + - - +
373A ILE* 1.3 76.7 - - - +
375A ARG* 1.3 57.1 + - - +
377A VAL* 3.2 4.8 + - - +
378A ILE* 2.9 35.2 + - - +
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.7 30.2 - - + +
330A GLU* 3.2 40.2 + - - -
371A SER* 3.0 24.3 + - - +
372A GLU* 3.5 16.2 + - - +
373A ILE 3.2 0.2 - - - -
374A GLN* 1.3 78.3 - - - +
376A LEU* 1.3 63.2 + - + +
378A ILE* 3.5 8.8 + - + +
379A ALA* 3.1 24.1 + - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU 3.2 18.3 + - - +
373A ILE* 3.2 15.4 + - + +
375A ARG* 1.3 77.0 - - + +
377A VAL* 1.3 63.1 - - + +
379A ALA* 3.4 6.8 + - + +
380A GLY* 3.0 21.0 + - - -
399A FAD 3.6 40.2 - - + +
400A CAA 5.6 10.3 - - + -
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Residues in contact with VAL 377 (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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248A ARG* 4.3 15.3 - - - +
318A THR* 4.0 28.5 - - + +
319A LYS* 5.0 0.7 - - - -
322A ALA* 4.0 17.3 - - + -
373A ILE* 3.0 24.7 + - + +
374A GLN* 3.5 9.0 - - - +
376A LEU* 1.3 77.6 - - - +
378A ILE* 1.3 63.7 + - - +
380A GLY* 3.3 2.5 + - - -
381A HIS* 3.2 35.5 + - + +
400A CAA 3.9 25.8 - - + -
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Residues in contact with ILE 378 (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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319A LYS* 4.3 12.9 - - + +
322A ALA* 3.9 15.0 - - + -
323A MET* 3.7 56.5 - - + +
326A LEU* 4.1 22.2 - - + -
374A GLN 2.9 23.0 + - - +
375A ARG* 3.7 7.2 - - + +
376A LEU 3.3 0.2 - - - -
377A VAL* 1.3 76.6 - - - +
379A ALA* 1.3 56.4 + - - +
381A HIS* 3.3 3.3 + - - +
382A LEU* 2.9 32.4 + - + +
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Residues in contact with ALA 379 (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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375A ARG 3.1 17.9 + - - +
376A LEU* 3.8 7.4 - - + +
377A VAL 3.4 0.2 - - - -
378A ILE* 1.3 77.3 - - - +
380A GLY* 1.3 56.8 + - - +
382A LEU* 3.7 6.9 - - - +
383A LEU* 2.9 45.2 + - + +
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Residues in contact with GLY 380 (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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376A LEU 3.0 14.3 + - - -
377A VAL* 3.3 4.5 + - - -
378A ILE 3.3 0.4 - - - -
379A ALA* 1.3 76.7 - - - +
381A HIS* 1.3 58.3 + - - +
383A LEU* 4.0 6.6 - - - +
384A ARG* 3.1 35.7 + - - +
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A THR* 3.9 36.7 + - + +
319A LYS* 3.9 31.8 - - + +
377A VAL* 3.2 26.1 + - + +
378A ILE 3.9 2.9 - - - +
380A GLY* 1.3 75.1 - - - +
382A LEU* 1.3 66.5 + - - +
384A ARG* 3.3 39.7 + - - +
385A SER* 3.1 22.9 + - - -
400A CAA 5.8 5.8 - + - -
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Residues in contact with LEU 382 (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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319A LYS* 4.3 18.1 - - + +
323A MET* 6.2 1.1 - - + -
378A ILE* 2.9 23.2 + - + +
379A ALA* 3.7 7.9 - - - +
381A HIS* 1.3 76.7 - - - +
383A LEU* 1.3 75.3 + - + +
385A SER* 2.5 26.2 + - - +
386A TYR* 3.1 42.4 - - + +
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Residues in contact with LEU 383 (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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379A ALA* 2.9 30.0 + - + +
380A GLY* 4.0 6.1 - - - +
382A LEU* 1.3 87.4 - - + +
384A ARG* 1.3 65.8 + - - +
386A TYR* 3.0 19.6 + - + +
387A ARG* 3.0 47.0 + - - +
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Residues in contact with ARG 384 (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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380A GLY* 3.1 21.8 + - - +
381A HIS* 3.5 47.5 + - - +
382A LEU 3.3 0.4 - - - -
383A LEU* 1.3 74.9 - - - +
385A SER* 1.3 60.9 + - - +
387A ARG* 3.3 27.1 + - + +
400A CAA 5.6 4.9 + - - -
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Residues in contact with SER 385 (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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319A LYS* 6.2 0.3 - - - -
381A HIS 3.1 12.1 + - - -
382A LEU* 2.5 27.3 + - - +
384A ARG* 1.3 76.2 - - - +
386A TYR* 1.3 67.6 + - - +
387A ARG 3.4 1.4 - - - -
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Residues in contact with TYR 386 (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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382A LEU* 3.1 53.0 - - + +
383A LEU* 3.0 14.9 + - + +
385A SER* 1.3 84.0 + - - +
387A ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 387 (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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383A LEU* 3.0 52.1 + - - +
384A ARG* 3.3 19.0 + - + +
385A SER 4.9 2.0 - - - -
386A TYR* 1.3 82.6 - - - +
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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