Contacts of the helix formed by residues 371 - 383 (chain A) in PDB entry 4JS2
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 PRO 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A TRP* 4.4 5.6 - - + -
308A LEU* 3.8 18.2 - - + -
316A ILE* 4.2 15.3 - - + -
317A GLN* 3.4 24.0 - - + +
319A ASN 3.6 14.1 - - - +
320A PRO 3.4 17.3 - - - +
321A PRO* 4.3 2.2 - - + -
369A TYR 3.9 2.7 - - - +
370A HIS* 1.3 80.0 - - + +
372A LEU* 1.3 62.3 + - - +
373A LEU* 3.2 3.4 - - + -
374A TYR* 3.1 26.0 + - + +
375A GLU* 3.1 21.7 + - - +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLN* 5.4 0.2 - - - +
322A SER* 3.2 30.3 - - - +
343A PHE* 3.9 12.3 - - + -
363A ALA 4.2 0.2 - - - +
364A CYS* 3.0 28.9 - - - +
365A THR 3.2 18.6 - - - +
367A GLY* 3.7 19.7 - - - +
370A HIS* 2.8 14.4 + - + +
371A PRO* 1.3 72.8 - - - +
373A LEU* 1.3 64.0 + - - +
375A GLU* 3.2 14.4 + - - +
376A LYS* 2.9 40.8 + - - +
511A C 3.6 17.5 - - + +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.6 29.1 - - + -
100A SER* 4.0 16.4 - - - +
101A SER* 3.6 34.1 - - - +
102A SER 4.3 0.2 - - - +
104A ASN* 6.2 0.4 - - + -
105A LEU* 4.3 17.9 - - + -
317A GLN* 6.3 1.3 - - - +
366A MET* 3.6 39.8 + - + +
371A PRO 3.2 0.4 - - - -
372A LEU* 1.3 80.5 - - - +
374A TYR* 1.3 81.1 + - + +
376A LYS* 3.4 3.7 + - - +
377A ASN* 3.1 29.3 + - - +
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Residues in contact with TYR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER 4.5 7.6 - - - -
101A SER* 4.9 0.2 - - - -
102A SER* 4.1 4.3 + - - -
105A LEU* 5.9 0.2 - - - +
113A TRP* 3.7 15.5 + + - -
308A LEU* 3.8 12.8 - - + +
312A SER* 3.3 30.3 - - - +
313A PRO* 4.8 4.7 - - + -
314A GLU* 2.7 39.4 + - + +
316A ILE* 3.4 30.3 - - + -
317A GLN* 3.7 18.6 - - - -
371A PRO* 3.1 17.0 + - + +
373A LEU* 1.3 95.3 - - + +
375A GLU* 1.3 64.8 + - - +
377A ASN* 3.5 19.8 + - + +
378A LEU* 3.2 20.8 + - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.7 23.3 - - + -
321A PRO* 3.1 10.7 - - - +
322A SER* 2.5 49.0 + - - -
325A MET* 3.2 29.8 - - + +
343A PHE* 4.0 8.0 - - + -
371A PRO* 3.1 24.8 + - - +
372A LEU* 3.3 15.8 + - - +
374A TYR* 1.3 77.7 - - - +
376A LYS* 1.3 62.0 + - - +
378A LEU* 3.0 15.4 + - - +
379A VAL* 3.0 17.0 + - - +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TRP* 3.5 40.2 - - + -
343A PHE* 2.8 47.4 + - + +
344A LEU* 3.3 18.0 - - + +
345A PRO* 4.9 0.4 - - - +
365A THR* 3.1 35.3 + - - +
372A LEU* 2.9 31.1 + - - +
375A GLU* 1.3 73.0 - - - +
377A ASN* 1.3 65.7 + - - +
379A VAL 3.1 1.3 + - - +
380A LYS* 3.0 21.7 + - - +
511A C 2.8 30.7 + - - -
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Residues in contact with ASN 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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96A TRP* 2.8 31.8 + - - +
97A ASN 3.1 9.7 - - - +
98A LYS* 3.3 29.1 + - - +
99A ASP* 4.4 0.8 - - - +
100A SER* 3.2 29.6 + - - -
311A ILE* 6.6 0.4 - - + -
313A PRO* 5.7 3.4 - - - +
373A LEU 3.1 16.1 + - - +
374A TYR* 3.6 23.0 - - + +
375A GLU 3.3 0.6 - - - -
376A LYS* 1.3 75.6 - - - +
378A LEU* 1.3 56.8 + - - +
380A LYS* 3.6 0.5 + - - +
381A HIS* 3.0 29.0 + - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.4 36.8 - - + -
144A LEU* 4.4 18.4 - - + -
304A LEU* 5.0 3.8 - - + -
307A ILE* 5.6 3.6 - - + -
308A LEU* 4.1 20.2 - - + -
311A ILE* 5.4 9.6 - - + -
325A MET* 4.0 29.2 - - + -
374A TYR 3.2 9.5 + - - +
375A GLU 3.0 7.3 + - - +
377A ASN* 1.3 77.4 - - - +
379A VAL* 1.3 66.4 + - - +
381A HIS* 3.2 6.2 + - - +
382A LEU* 3.0 39.2 + - + +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MET* 4.0 13.2 - - + -
328A ILE* 4.0 12.6 - - + -
340A ILE* 4.7 5.6 - - + -
343A PHE* 3.5 26.9 - - + -
344A LEU* 3.9 23.6 - - + -
375A GLU 3.0 17.4 + - - +
376A LYS 3.1 5.6 + - - +
378A LEU* 1.3 73.8 - - - +
380A LYS* 1.3 65.5 + - - +
382A LEU* 3.1 5.8 + - - +
383A ASN* 2.9 22.2 + - - +
396A ALA* 4.1 16.4 - - + -
398A LEU* 4.0 18.5 - - + +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.6 5.8 - - - -
96A TRP* 3.3 40.6 - - + +
98A LYS* 4.2 28.9 + - - +
344A LEU* 3.5 21.4 - - + +
376A LYS 3.0 16.1 + - - +
377A ASN 3.8 4.3 - - - +
379A VAL* 1.3 77.3 - - - +
381A HIS* 1.3 62.5 + - - +
383A ASN* 3.2 18.0 + - + +
387A ASP* 3.4 26.0 + - - -
390A ILE* 4.4 13.5 - - + -
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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
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98A LYS* 3.5 37.6 + - + +
135A PHE* 2.9 28.8 + - + +
136A SER* 3.8 9.2 + - - -
137A ALA* 3.6 24.2 + - + +
140A LEU* 3.4 27.6 - - + -
311A ILE* 6.0 3.4 - - + -
377A ASN 3.0 19.1 + - - +
378A LEU* 3.5 6.5 - - + +
379A VAL 3.1 0.6 - - - -
380A LYS* 1.3 77.7 - - - +
382A LEU* 1.3 61.2 + - + +
383A ASN 4.9 1.6 - - - +
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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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137A ALA* 3.3 38.6 - - + +
140A LEU* 4.2 15.3 - - + -
141A ARG* 2.7 44.0 + - + +
144A LEU* 3.7 28.7 - - + -
332A MET* 5.5 4.0 - - + -
378A LEU* 3.0 30.3 + - + +
379A VAL* 3.6 3.6 - - - +
381A HIS* 1.3 77.4 - - - +
383A ASN* 1.3 66.0 + - - +
384A GLN 3.4 1.6 + - - -
397A THR 4.0 1.4 - - - +
398A LEU* 3.7 27.9 - - + +
399A PRO* 4.5 0.2 - - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 5.9 0.2 + - - -
344A LEU* 5.2 0.2 - - + -
379A VAL 2.9 11.3 + - - +
380A LYS* 3.2 22.5 + - + +
381A HIS 4.9 1.6 - - - +
382A LEU* 1.3 79.1 - - - +
384A GLN* 1.3 62.7 + - - +
385A GLY* 3.2 31.4 + - - +
386A THR 4.0 2.8 + - - -
387A ASP* 5.7 0.4 + - - -
390A ILE* 3.8 26.0 - - - +
395A LYS 4.7 0.6 + - - -
396A ALA* 3.2 12.2 - - + +
397A THR 2.6 35.8 + - - -
398A LEU* 3.9 2.2 - - + -
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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