Contacts of the helix formed by residues 371 - 387 (chain A) in PDB entry 4Z4H
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 SER 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ARG* 1.3 78.3 - - - +
372A ALA* 1.3 59.6 + - - +
373A PRO* 3.5 7.7 - - - +
374A ASP* 3.2 33.0 + - - +
375A ARG* 2.9 23.2 + - - +
726A LYS 4.5 5.2 - - - -
727A SER* 3.6 21.1 - - - +
758A GLY* 4.0 7.9 - - - +
759A THR* 3.9 1.1 - - - -
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 1.3 70.6 - - - +
373A PRO* 1.3 61.4 - - + +
375A ARG* 3.3 1.0 + - - +
376A GLN 2.9 23.4 + - - -
715A LEU 5.7 0.9 - - - +
716A PHE* 3.3 20.8 - - + -
727A SER 2.9 20.6 + - - +
728A GLY 3.4 13.7 - - - +
729A ASN* 3.5 22.9 - - - +
758A GLY 3.6 3.4 + - - -
759A THR* 3.5 16.8 - - + +
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Residues in contact with PRO 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER* 3.5 11.7 - - - +
372A ALA* 1.3 93.8 - - + +
374A ASP* 1.3 64.2 + - - +
376A GLN* 3.2 15.0 + - + +
377A GLU* 3.0 23.0 + - - +
723A ARG* 3.7 46.9 - - - +
727A SER 3.3 12.8 - - - +
728A GLY* 3.9 5.4 - - - +
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ARG* 4.1 14.4 - - + +
371A SER* 3.2 30.6 + - - +
372A ALA 3.3 0.4 - - - -
373A PRO* 1.3 81.3 - - - +
375A ARG* 1.3 57.7 + - - +
377A GLU* 3.3 7.2 + - - +
378A GLU* 3.0 33.4 + - + +
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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
----------------------------------------------------------
218A ASP* 2.6 43.0 + - - -
219A VAL* 3.5 21.0 + - + +
368A THR 5.9 0.8 + - - -
370A ARG* 4.2 14.6 + - + +
371A SER 2.9 9.4 + - - +
372A ALA 3.7 2.2 - - - +
374A ASP* 1.3 73.3 - - - +
376A GLN* 1.3 65.6 + - - +
378A GLU* 3.2 8.4 + - - +
379A ILE* 3.0 31.7 + - + +
714A ARG* 4.4 11.3 - - - +
716A PHE* 4.1 9.6 - - + -
759A THR* 3.1 47.8 + - - +
6B A 5.3 0.2 + - - -
7B U 3.8 30.3 + - - -
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Residues in contact with GLN 376 (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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41A GLN* 3.1 35.2 + - - +
372A ALA 2.9 13.1 + - - +
373A PRO* 3.3 14.4 - - - +
375A ARG* 1.3 77.3 - - - +
377A GLU* 1.3 62.2 + - - +
379A ILE 3.4 0.2 + - - -
380A SER* 3.1 30.1 + - - +
405A MET* 3.6 12.3 - - + +
716A PHE* 3.6 47.5 - - + +
717A CYS 4.2 6.2 + - - +
723A ARG* 3.9 20.4 + - - -
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Residues in contact with GLU 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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373A PRO 3.0 12.6 + - - +
374A ASP* 3.7 8.7 - - - +
375A ARG 3.2 0.2 - - - -
376A GLN* 1.3 75.1 - - - +
378A GLU* 1.3 57.8 + - + +
380A SER* 4.4 6.3 - - - -
381A LYS* 2.8 67.8 + - + +
384A ARG* 3.2 26.8 + - - -
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Residues in contact with GLU 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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219A VAL* 3.9 20.5 - - + +
370A ARG* 3.2 40.6 + - + +
374A ASP* 3.0 21.7 + - + +
375A ARG* 3.2 8.3 + - - +
377A GLU* 1.3 75.5 - - - +
379A ILE* 1.3 57.5 + - - +
381A LYS* 3.9 18.9 + - - +
382A LEU* 3.0 27.9 + - - +
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Residues in contact with ILE 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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43A ASN* 4.1 17.5 - - + +
45A PHE* 4.0 16.6 - - + -
217A ILE* 3.9 23.1 - - + +
218A ASP* 3.7 24.7 - - - +
219A VAL* 4.3 18.8 - - + +
375A ARG* 3.0 24.2 + - + +
378A GLU* 1.3 73.9 - - - +
380A SER* 1.3 65.8 + - - +
382A LEU* 3.2 4.9 + - - +
383A MET* 3.0 22.3 + - - +
405A MET* 3.7 19.1 - - + -
714A ARG* 5.1 0.2 - - + -
716A PHE* 4.0 23.3 - - + -
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 5.4 3.6 - - - -
376A GLN* 3.1 19.4 + - - +
377A GLU* 3.7 10.0 + - - -
379A ILE* 1.3 79.6 - - - +
381A LYS* 1.3 62.9 + - - +
383A MET* 3.2 6.5 + - - +
384A ARG* 3.1 48.3 + - - +
403A ASP 5.1 1.9 - - - +
405A MET* 3.8 16.4 + - - +
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Residues in contact with LYS 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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377A GLU* 2.8 47.5 + - + +
378A GLU* 3.9 19.2 + - - +
380A SER* 1.3 72.8 - - - +
382A LEU* 1.3 63.4 + - - +
384A ARG* 3.4 24.0 + - - +
385A SER* 3.1 25.1 + - - -
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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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201A GLY 5.0 0.7 - - - +
202A PHE* 3.4 47.8 - - + -
217A ILE* 3.8 21.1 - - + -
219A VAL* 3.7 19.7 - - + -
378A GLU 3.0 18.7 + - - +
379A ILE* 3.2 4.7 + - - +
381A LYS* 1.3 76.4 - - - +
383A MET* 1.3 54.1 + - - +
385A SER* 3.4 6.0 + - - -
386A ALA* 2.6 43.1 + - + +
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Residues in contact with MET 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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45A PHE* 3.5 50.3 - - + -
215A LEU* 4.8 0.7 - - + -
217A ILE* 3.7 27.8 - - + -
379A ILE 3.0 14.4 + - - +
380A SER* 3.2 5.4 + - - +
382A LEU* 1.3 75.4 - - - +
384A ARG* 1.3 65.8 + - - +
386A ALA* 3.2 14.8 + - - +
387A ASP* 3.4 6.4 + - - -
388A PHE* 3.4 39.2 - - + -
401A VAL* 4.0 10.1 - - + +
402A LYS 3.9 11.4 - - - +
403A ASP* 4.4 14.3 - - + +
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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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377A GLU* 3.2 26.9 + - - -
380A SER* 3.1 32.6 + - - +
381A LYS* 3.4 26.6 - - - +
382A LEU 3.4 0.2 - - - -
383A MET* 1.3 77.4 - - - +
385A SER* 1.3 62.1 + - - +
387A ASP* 3.6 16.3 + - - +
403A ASP* 4.6 22.8 + - + +
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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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381A LYS 3.1 17.6 + - - -
382A LEU* 3.5 5.4 - - - -
384A ARG* 1.3 74.4 - - - +
386A ALA* 1.3 65.3 + - - +
387A ASP* 3.3 5.2 + - - +
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Residues in contact with ALA 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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202A PHE* 6.5 0.9 - - + -
382A LEU* 2.6 29.7 + - + +
383A MET* 3.2 11.8 + - - +
385A SER* 1.3 76.2 - - - +
387A ASP* 1.3 70.8 + - - +
388A PHE* 3.3 32.1 + - + -
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Residues in contact with ASP 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 MET 3.4 8.2 + - - -
384A ARG 3.6 11.2 + - - +
385A SER 3.3 8.2 - - - +
386A ALA* 1.3 81.8 - - - +
388A PHE* 1.3 62.9 + - - +
389A ASN* 3.2 7.9 + - - +
390A THR* 2.6 49.4 + - - +
391A ASP* 3.9 3.1 + - - +
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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