Contacts of the helix formed by residues 374 - 392 (chain A) in PDB entry 4X4W
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ILE* 4.1 1.0 - - - +
373A SER* 1.3 78.5 - - - +
375A GLY* 1.3 57.9 + - - +
376A LYS* 3.4 9.0 + - - +
377A GLU* 3.3 31.2 + - - +
378A ILE* 2.9 31.7 + - - +
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A SER 3.5 3.8 + - - -
374A SER* 1.3 70.9 + - - +
376A LYS* 1.3 63.0 + - - +
378A ILE* 3.3 11.1 + - - +
379A GLY* 2.9 21.0 + - - -
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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
----------------------------------------------------------
374A SER* 3.3 7.4 + - - +
375A GLY* 1.3 74.9 - - - +
377A GLU* 1.3 58.8 + - - +
379A GLY* 3.2 2.0 + - - -
380A ALA* 2.9 29.7 + - - +
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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
----------------------------------------------------------
372A ILE* 3.5 38.3 - - + +
373A SER 5.3 0.2 + - - -
374A SER* 3.3 22.4 + - - +
376A LYS* 1.3 78.8 - - - +
378A ILE* 1.3 62.4 + - - +
380A ALA* 3.3 7.1 + - + +
381A LEU* 3.0 34.6 + - + +
409A LEU* 4.8 6.9 - - - +
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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
----------------------------------------------------------
364A GLY* 3.9 17.9 - - - +
367A ILE* 3.9 20.6 - - + +
368A ARG* 3.7 28.9 - - + -
372A ILE* 3.9 20.2 - - + +
373A SER 4.2 5.4 - - - +
374A SER 2.9 27.0 + - - +
375A GLY* 3.6 9.0 - - - +
377A GLU* 1.3 76.7 - - - +
379A GLY* 1.3 57.6 + - - +
381A LEU* 3.4 1.7 + - - +
382A LEU* 2.9 46.9 + - + +
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLY 2.9 15.3 + - - -
376A LYS* 3.7 2.7 - - - -
378A ILE* 1.3 77.4 - - - +
380A ALA* 1.3 62.3 + - - +
382A LEU* 3.5 9.1 + - - +
383A GLN* 3.0 24.3 + - - +
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Residues in contact with ALA 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 LYS 2.9 16.7 + - - +
377A GLU* 3.6 9.6 - - + +
379A GLY* 1.3 76.1 - - - +
381A LEU* 1.3 60.8 + - + +
383A GLN* 3.3 8.1 + - - +
384A GLN* 3.1 35.3 + - - +
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.8 15.9 - - + -
370A VAL* 5.7 0.2 - - + -
372A ILE* 3.8 32.8 - - + -
377A GLU* 3.0 32.6 + - + +
378A ILE 3.8 3.6 - - - +
380A ALA* 1.3 73.4 - - + +
382A LEU* 1.3 65.8 + - - +
384A GLN* 3.2 22.0 + - - +
385A LEU* 2.9 28.2 + - - +
405A ILE* 3.5 33.6 - - + +
408A THR* 4.9 2.0 - - + -
409A LEU* 4.1 20.4 - - + -
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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
----------------------------------------------------------
360A PHE* 3.7 12.6 - - + -
362A VAL* 3.8 42.6 - - + +
363A SER* 3.9 3.6 - - - +
364A GLY* 4.1 12.6 - - - +
367A ILE* 3.9 13.9 - - + -
378A ILE* 2.9 38.7 + - + +
379A GLY* 3.9 7.4 - - - +
381A LEU* 1.3 76.0 - - - +
383A GLN* 1.3 57.4 + - - +
385A LEU* 3.2 5.0 + - - +
386A ARG* 2.8 34.6 + - - +
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Residues in contact with GLN 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 GLY 3.0 17.9 + - - +
380A ALA* 3.5 7.6 - - - +
381A LEU 3.2 0.2 - - - -
382A LEU* 1.3 77.3 - - - +
384A GLN* 1.3 64.1 + - + +
386A ARG* 3.3 17.4 + - - +
387A GLU* 2.8 58.3 + - - +
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Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA* 3.1 27.2 + - - +
381A LEU* 3.5 25.7 - - - +
383A GLN* 1.3 79.2 - - + +
385A LEU* 1.3 63.0 + - + +
387A GLU* 3.4 13.5 + - - +
388A GLN* 3.1 26.7 + - - +
404A TYR* 5.5 5.6 - - + -
405A ILE* 4.1 8.7 - - + +
408A THR* 3.6 25.7 + - - +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PHE* 3.7 14.6 - - + -
362A VAL* 4.1 24.9 - - + -
367A ILE* 4.2 11.0 - - + -
381A LEU 2.9 20.0 + - - +
382A LEU* 3.7 4.5 - - - +
384A GLN* 1.3 74.3 - - - +
386A ARG* 1.3 63.9 + - - +
388A GLN* 3.3 4.1 + - + +
389A TRP* 2.9 24.6 + - - +
401A LEU* 3.1 47.8 - - + +
402A LEU* 4.8 0.9 - - + +
404A TYR* 3.8 23.8 - - + -
405A ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PHE* 3.5 60.1 - - + +
382A LEU* 2.8 19.1 + - - +
383A GLN* 3.7 22.0 - - - +
385A LEU* 1.3 72.0 - - - +
387A GLU* 1.3 57.9 + - + +
389A TRP* 3.3 14.6 + - + +
390A LYS* 2.9 31.0 + - - +
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Residues in contact with GLU 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 GLN* 2.8 46.9 + - - +
384A GLN* 3.6 14.1 - - - +
385A LEU 3.2 0.4 - - - -
386A ARG* 1.3 76.0 - - - +
388A GLN* 1.3 64.2 + - - +
390A LYS* 3.4 6.7 + - - +
391A LYS* 2.9 30.6 + - - +
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Residues in contact with GLN 388 (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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384A GLN 3.1 14.5 + - - +
385A LEU* 3.6 8.1 - - - +
387A GLU* 1.3 78.2 - - - +
389A TRP* 1.3 58.8 + - - +
391A LYS* 3.1 34.2 + - - +
392A SER 2.9 24.9 + - - -
396A MET* 3.4 19.9 - - + +
401A LEU* 4.1 12.6 - - + -
404A TYR* 3.3 55.4 + - + -
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Residues in contact with TRP 389 (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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325A ILE* 4.4 11.0 - - + -
358A PRO* 3.5 35.2 - - + +
359A PRO 3.7 9.6 + - - -
360A PHE* 3.7 34.8 - + + -
361A PRO* 3.7 16.8 - - + +
385A LEU 2.9 18.2 + - - +
386A ARG* 3.5 21.1 - - + +
388A GLN* 1.3 77.2 - - - +
390A LYS* 1.3 59.8 + - + +
392A SER* 2.7 22.7 + - - -
394A TYR* 2.9 65.6 + + - +
395A GLN 4.3 0.2 - - - -
396A MET* 3.3 27.9 + - - -
401A LEU* 4.0 11.6 - - + +
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Residues in contact with LYS 390 (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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318A LYS* 2.9 35.2 - - - +
322A ASP* 3.9 14.7 + - - +
326A ASP* 4.2 20.2 + - - -
386A ARG 2.9 17.6 + - - +
387A GLU* 3.8 6.1 - - - +
389A TRP* 1.3 77.2 - - + +
391A LYS* 1.3 62.6 + - - +
393A GLY* 3.2 8.0 + - - -
394A TYR* 3.8 37.9 + - + +
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Residues in contact with LYS 391 (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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318A LYS* 4.5 10.7 - - - +
387A GLU 2.9 17.8 + - - +
388A GLN* 3.1 34.7 + - - +
390A LYS* 1.3 74.4 - - - +
392A SER* 1.3 55.7 + - - +
393A GLY 3.1 8.9 + - - -
396A MET* 6.4 0.2 - - + -
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 4.9 4.8 - - - +
388A GLN 2.9 4.6 + - - -
389A TRP* 2.7 19.4 + - - -
391A LYS* 1.3 75.7 - - - +
393A GLY* 1.3 58.3 + - - +
395A GLN* 3.2 29.3 + - - +
396A MET* 3.3 41.1 + - - +
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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