Contacts of the helix formed by residues 365 - 382 (chain A) in PDB entry 5H2U
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 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 3.5 25.0 - - - +
357A GLU* 4.9 2.4 + - - +
363A HIS 4.6 3.3 + - - -
364A TYR* 1.3 77.1 - - - +
366A THR* 1.3 63.3 + - - +
367A LYS* 3.1 23.4 + - - +
368A SER* 3.0 24.2 + - - -
369A ASP* 3.3 6.2 + - - -
428A PRO* 5.2 1.7 - - - +
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 5.8 0.7 - - + -
304A GLU* 3.4 53.4 + - + +
307A ASN* 5.0 3.3 - - - -
308A TYR 4.7 13.6 + - - +
309A ILE* 4.2 6.4 - - - +
365A SER* 1.3 73.6 - - - +
367A LYS* 1.3 60.3 + - + +
369A ASP* 3.3 12.2 - - + +
370A VAL* 2.9 26.7 + - - +
434A PHE* 3.7 15.7 - - + -
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Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 5.3 1.7 + - - +
365A SER* 3.1 11.6 - - - +
366A THR* 1.3 79.6 - - + +
368A SER* 1.3 61.9 + - - +
370A VAL* 3.4 5.4 + - + +
371A TRP 3.3 12.8 + - - -
428A PRO* 3.1 44.0 - - + +
429A GLU* 4.4 14.8 + - - +
431A ARG* 2.8 46.8 + - + +
432A PRO 3.9 3.8 + - - +
433A THR* 3.5 33.1 - - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 4.8 0.3 - - - +
354A THR* 5.9 0.2 - - - -
355A ALA* 3.6 21.5 + - - +
357A GLU* 3.9 7.6 + - - -
358A ALA* 4.0 13.5 - - - -
363A HIS 4.3 1.3 - - - -
364A TYR* 3.5 15.5 - - - -
365A SER* 3.0 34.0 + - - -
367A LYS* 1.3 73.9 - - - +
369A ASP* 1.3 64.8 + - - +
371A TRP* 3.3 5.4 - - - +
372A SER* 3.1 24.3 + - - -
431A ARG* 3.8 7.4 - - - +
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Residues in contact with ASP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 3.8 7.2 - - + +
308A TYR 4.3 1.6 - - - +
309A ILE* 3.4 11.4 - - - +
310A HIS* 2.6 35.4 + - - +
311A ARG* 3.1 25.5 + - - -
312A ASP 4.6 0.5 + - - -
313A LEU* 3.7 6.5 + - + +
365A SER 3.3 9.9 + - - +
366A THR* 3.3 15.7 + - - +
368A SER* 1.3 74.6 + - - +
370A VAL* 1.3 59.8 + - - +
372A SER* 3.2 9.2 + - - -
373A PHE* 2.8 28.4 + - - +
434A PHE* 3.6 15.6 - - + -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 4.8 1.1 - - - +
366A THR 2.9 19.7 + - - +
367A LYS* 3.5 16.4 - - + +
368A SER 3.3 0.4 - - - -
369A ASP* 1.3 75.4 - - - +
371A TRP* 1.3 61.5 + - - +
373A PHE* 3.1 13.2 + - - +
374A GLY 3.2 10.0 + - - -
423A CYS* 3.5 31.9 - - - +
431A ARG* 4.0 9.9 - - + -
432A PRO* 3.4 28.9 - - + +
433A THR* 4.7 1.3 - - - -
434A PHE* 3.6 32.8 - - + +
437A LEU* 3.9 5.6 - - + -
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Residues in contact with TRP 371 (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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352A LYS 5.0 1.4 + - - -
353A TRP 3.4 18.4 + - - -
354A THR 3.7 7.8 + - - -
355A ALA* 3.7 19.1 - - + -
356A PRO* 3.5 25.8 - - + -
367A LYS 3.3 3.6 + - - -
368A SER 3.3 10.1 - - - +
370A VAL* 1.3 78.6 - - - +
372A SER* 1.3 63.6 + - - +
374A GLY 3.1 11.1 + - - -
375A ILE* 3.3 23.1 + - + +
388A TYR* 4.6 8.7 + - - -
400A VAL* 3.6 22.9 - - + -
405A ARG* 3.6 27.8 - - - -
423A CYS 3.3 14.1 + - - +
424A TRP* 3.1 50.7 + + + -
425A CYS 3.8 5.6 - - - -
431A ARG* 3.7 20.9 - - - +
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Residues in contact with SER 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ARG 5.8 1.7 + - - -
312A ASP* 5.8 0.9 + - - -
313A LEU* 3.5 36.2 + - - +
353A TRP* 2.7 27.3 + - - +
354A THR* 4.4 3.6 - - - -
368A SER 3.1 12.3 + - - -
369A ASP* 3.2 10.9 + - - -
371A TRP* 1.3 78.6 - - - +
373A PHE* 1.3 56.6 + - - +
375A ILE* 3.2 6.5 + - - +
376A LEU* 2.9 27.4 + - - +
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA 3.8 7.9 - - - -
296A VAL* 3.6 37.7 - - + -
297A ALA* 4.1 9.6 - - + -
313A LEU* 3.7 13.2 - - + +
369A ASP 2.8 13.6 + - - +
370A VAL 3.1 10.3 + - - +
372A SER* 1.3 77.0 - - - +
374A GLY* 1.3 55.2 + - - +
376A LEU* 3.2 9.0 - - + +
377A LEU* 2.8 57.9 + - + +
380A MET* 4.7 4.0 - - + -
419A LEU* 4.7 0.9 - - + -
423A CYS* 4.2 2.2 - - - -
434A PHE* 3.6 18.4 - + + -
437A LEU* 3.7 31.4 - - + -
441A LEU* 3.7 29.6 - - + -
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A VAL 3.2 6.9 + - - -
371A TRP 3.1 9.1 + - - -
373A PHE* 1.3 76.1 - - - +
375A ILE* 1.3 58.2 + - - +
377A LEU* 3.4 16.8 + - - +
378A HIS 3.1 20.3 + - - -
420A MET* 3.5 5.5 - - - +
423A CYS* 4.0 12.1 - - - -
424A TRP* 3.3 24.9 - - - -
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS 3.8 13.2 - - - +
353A TRP* 3.3 34.8 - - + +
371A TRP* 3.3 28.9 + - + +
372A SER 3.2 7.5 + - - +
374A GLY* 1.3 72.9 - - - +
376A LEU* 1.3 60.9 + - - +
378A HIS* 3.2 6.0 + - - +
379A GLU* 3.0 27.4 + - - +
387A PRO* 3.6 21.3 - - + -
388A TYR* 3.7 23.6 - - + +
406A MET* 3.8 11.4 - - + -
424A TRP* 3.5 21.8 - - + +
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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
----------------------------------------------------------
272A LEU* 4.4 10.3 - - + -
296A VAL* 4.2 11.7 - - + -
313A LEU* 3.4 34.8 - - + -
314A ALA* 3.6 21.1 - - - +
315A ALA* 3.7 12.8 - - - +
318A ILE* 3.9 12.1 - - + -
353A TRP* 4.7 0.6 - - - +
372A SER 2.9 12.7 + - - +
373A PHE* 3.2 12.1 - - + +
375A ILE* 1.3 77.2 - - - +
377A LEU* 1.3 59.4 + - - +
379A GLU* 3.2 14.6 + - - +
380A MET* 2.9 67.6 + - + +
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Residues in contact with LEU 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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293A ALA* 3.8 20.2 - - + -
373A PHE* 2.8 53.6 + - + +
374A GLY* 3.5 9.9 - - - +
375A ILE 3.3 0.2 - - - -
376A LEU* 1.3 73.7 - - - +
378A HIS* 1.3 58.4 + - - +
380A MET* 3.2 22.5 + - + -
381A PHE* 3.1 46.1 + - + +
416A VAL* 4.6 8.1 - - + +
419A LEU* 3.9 16.8 - - + -
420A MET* 3.7 28.1 - - + +
423A CYS* 4.7 0.9 - - - -
441A LEU* 4.7 4.7 - - + -
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Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.1 9.5 + - - +
375A ILE 3.2 9.8 + - - +
377A LEU* 1.3 73.4 - - - +
379A GLU* 1.3 59.8 + - - +
381A PHE 3.9 0.4 - - - +
382A SER* 2.6 51.3 + - - -
385A GLN* 4.7 5.8 - - - +
386A VAL 5.3 2.0 + - - -
387A PRO* 4.6 11.2 - - + +
389A PRO* 5.5 3.4 - - - +
406A MET* 3.5 47.9 - - + +
407A PRO* 4.0 14.3 + - + -
409A PRO* 3.7 26.1 - - + +
420A MET* 3.8 22.6 - - + +
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Residues in contact with GLU 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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273A LEU* 3.8 18.2 - - - +
276A LEU* 3.5 4.1 - - + +
315A ALA* 3.0 38.8 + - + +
316A ARG 4.8 0.2 + - - -
353A TRP* 2.8 45.6 + - + +
375A ILE 3.0 15.0 + - - +
376A LEU* 3.2 14.5 + - - +
378A HIS* 1.3 75.2 - - + +
380A MET* 1.3 61.2 + - - +
382A SER* 3.7 5.2 - - - -
383A ARG 3.2 3.1 + - - -
384A GLY* 2.8 31.8 + - - -
385A GLN 4.0 16.8 - - - +
387A PRO* 4.6 4.9 - - + -
502A GOL 4.7 1.7 + - - -
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Residues in contact with MET 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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272A LEU* 3.9 27.4 - - + -
276A LEU* 3.5 27.9 - - + +
289A LEU* 3.8 21.1 - - + +
292A ILE* 4.2 15.3 - - - -
293A ALA* 4.2 17.5 - - + -
296A VAL* 5.0 1.6 - - + -
315A ALA* 5.2 0.2 - - + -
373A PHE* 4.7 3.6 - - + -
376A LEU* 2.9 40.6 + - + +
377A LEU* 3.4 45.5 - - + +
378A HIS 3.1 0.4 - - - -
379A GLU* 1.3 76.9 - - + +
381A PHE* 1.3 67.5 + - + +
382A SER 3.3 0.2 - - - -
383A ARG* 3.2 14.0 + - - +
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL* 4.1 6.3 - - + -
289A LEU* 3.6 46.4 - - + -
290A LEU* 3.7 27.1 - - + -
293A ALA* 4.8 2.0 - - + -
377A LEU* 3.1 39.3 + - + +
380A MET* 1.3 83.2 - - + +
382A SER* 1.3 56.9 + - - +
383A ARG* 3.4 5.8 - - - +
409A PRO* 3.3 17.2 - - + +
411A GLU* 4.0 24.6 + - + +
412A CYS* 3.5 26.0 - - + +
413A PRO* 4.0 23.3 - - + -
416A VAL* 3.9 21.1 - - + -
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS* 2.6 38.0 + - - -
379A GLU* 3.4 7.3 + - - -
381A PHE* 1.3 77.1 - - - +
383A ARG* 1.3 68.4 + - - +
385A GLN* 3.4 51.0 + - - +
409A PRO* 4.1 10.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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