Contacts of the helix formed by residues 361 - 375 (chain A) in PDB entry 4R1Z
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 LEU 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A GLU* 3.3 32.3 - - + +
343A LEU* 4.1 21.8 - - + -
346A LYS* 4.0 15.3 - - + +
347A ILE* 4.1 21.1 - - + -
357A ASP* 3.8 9.9 - - + +
358A ARG 3.1 11.0 + - - +
359A GLY 3.6 0.2 - - - -
360A ASN* 1.3 89.1 - - + +
362A PRO* 1.3 69.3 - - - +
363A TYR 3.2 3.0 + - - -
364A LEU* 3.3 7.2 + - + +
365A GLU* 3.2 18.5 + - - +
464A PHE* 3.4 37.9 - - + -
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Residues in contact with PRO 362 (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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342A GLU* 3.0 15.5 - - - +
346A LYS* 5.7 2.5 - - + -
358A ARG 5.2 0.9 - - - +
359A GLY 5.6 2.9 - - - +
360A ASN* 3.7 6.3 - - - +
361A LEU* 1.3 85.7 - - - +
363A TYR* 1.3 51.7 + - - +
365A GLU* 3.2 9.8 + - + +
366A ALA* 2.7 36.0 + - - +
429A LEU* 3.5 12.7 - - + +
433A GLY 4.0 8.1 - - - +
434A ASP 3.4 24.0 - - - +
435A GLY* 3.9 19.3 - - - -
436A LEU* 3.6 8.4 - - + +
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Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.4 35.0 - - + +
338A LYS* 3.4 40.8 - - + +
339A ILE* 3.6 16.6 - - + -
342A GLU* 3.0 21.8 + - + +
362A PRO* 1.3 79.0 - - - +
364A LEU* 1.3 53.4 + - - +
366A ALA* 3.2 4.7 + - - +
367A THR* 2.7 48.3 + - - -
425A PRO* 3.7 19.6 - - + +
426A GLY* 5.1 2.7 - - - -
429A LEU* 3.7 24.2 - - + +
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 3.7 34.7 - - + +
342A GLU* 3.4 11.3 + - - +
343A LEU* 5.2 3.8 - - + -
361A LEU* 3.3 14.0 + - + +
363A TYR* 1.3 77.7 - - - +
365A GLU* 1.3 59.2 + - - +
367A THR* 3.1 6.5 + - - -
368A ILE* 2.9 42.2 + - + +
464A PHE* 3.5 38.4 - - + +
467A LEU* 4.3 17.0 - - + -
468A ALA* 3.9 22.0 - - + -
471A LEU* 5.0 1.6 - - + -
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Residues in contact with GLU 365 (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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358A ARG* 4.3 27.6 + - - +
361A LEU 3.2 11.1 + - - +
362A PRO* 3.6 11.9 - - + +
364A LEU* 1.3 78.6 - - - +
366A ALA* 1.3 57.4 + - - +
368A ILE* 3.2 17.7 + - - +
369A ARG* 3.0 50.0 + - - +
436A LEU* 3.6 25.6 - - + -
460A LYS* 4.7 22.6 - - - +
464A PHE* 4.6 9.7 - - + +
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Residues in contact with ALA 366 (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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362A PRO 2.7 20.9 + - - +
363A TYR* 3.4 5.6 - - - +
365A GLU* 1.3 70.9 - - - +
367A THR* 1.3 66.8 + - - +
369A ARG* 3.3 5.0 + - - +
370A GLU* 2.9 24.3 + - - +
425A PRO* 3.3 25.4 - - + +
428A PHE* 4.0 11.9 - - + -
429A LEU* 3.6 21.3 - - + -
436A LEU* 4.0 7.1 - - + +
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Residues in contact with THR 367 (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 SER* 6.4 0.7 - - - -
329A LEU* 5.1 8.5 - - + -
335A VAL* 3.9 14.4 - - + -
339A ILE* 3.6 29.6 - - + +
363A TYR* 2.7 23.7 + - - -
364A LEU* 3.3 9.9 - - + -
366A ALA* 1.3 76.3 - - - +
368A ILE* 1.3 66.8 + - + +
370A GLU* 3.1 10.7 + - - +
371A VAL* 3.2 20.8 + - + +
423A PHE* 4.0 14.1 - - + -
425A PRO* 3.6 19.6 - - - +
467A LEU* 5.9 3.6 - - + -
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Residues in contact with ILE 368 (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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321A VAL* 5.6 2.2 - - + -
325A SER* 5.8 0.2 - - - +
364A LEU* 2.9 36.5 + - + +
365A GLU* 3.2 18.8 + - - +
367A THR* 1.3 77.4 - - - +
369A ARG* 1.3 64.4 + - - +
370A GLU 3.1 0.2 + - - -
371A VAL* 3.1 16.6 + - - +
372A LEU* 3.2 27.8 + - + +
460A LYS* 5.5 5.6 - - + +
463A LEU* 4.0 26.5 - - + +
464A PHE* 3.9 33.7 - - + +
467A LEU* 3.8 22.0 - - + -
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 3.0 44.1 + - - +
366A ALA* 3.3 11.2 - - - +
368A ILE* 1.3 77.4 - - - +
370A GLU* 1.3 55.8 + - - +
372A LEU* 3.3 5.0 + - + -
373A ARG* 2.9 17.8 + - - +
428A PHE* 3.6 33.9 + - + +
436A LEU* 3.8 33.9 - - - +
437A CYS 5.0 4.9 + - - +
438A CYS* 5.3 5.5 - - - +
443A TYR* 2.8 40.9 + - + +
460A LYS* 5.6 8.5 - - - +
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Residues in contact with GLU 370 (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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366A ALA 2.9 16.4 + - - +
367A THR 3.1 5.1 + - - +
369A ARG* 1.3 73.4 - - - +
371A VAL* 1.3 61.2 + - - +
373A ARG* 2.7 38.7 + - - +
374A ILE* 3.0 27.2 + - - +
422A LEU 3.1 2.1 - - - +
423A PHE* 3.2 25.0 - - + -
424A ASP 2.6 38.0 + - - +
425A PRO* 4.0 9.9 - - + -
427A ARG* 3.0 16.8 + - - -
428A PHE* 3.7 6.6 - - + -
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A VAL* 3.9 14.8 - - + +
324A TRP* 3.7 28.5 - - + -
325A SER* 3.6 35.9 - - - +
328A TYR* 5.0 4.3 - - + -
367A THR* 3.2 20.2 + - + +
368A ILE* 3.1 8.9 + - + +
370A GLU* 1.3 74.8 - - - +
372A LEU* 1.3 61.4 + - - +
374A ILE* 4.0 7.4 - - + -
375A ARG 3.0 32.8 + - - +
423A PHE* 3.8 17.9 - - + -
467A LEU* 6.1 0.2 - - + -
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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
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321A VAL* 4.1 30.1 - - + -
368A ILE* 3.2 31.0 + - + +
369A ARG* 3.4 8.7 - - + +
371A VAL* 1.3 81.6 - - - +
373A ARG* 1.3 60.8 + - - +
375A ARG 4.8 3.6 - - - +
376A PRO* 3.5 15.9 - - - +
377A VAL 5.4 3.4 - - - +
411A HIS* 3.5 10.4 - - - -
443A TYR* 3.6 16.6 - - - +
445A PRO* 4.0 9.6 - - + +
446A PHE* 4.1 23.8 - - + -
460A LYS* 5.8 3.8 - - + -
463A LEU* 4.8 3.8 - - + -
600A HEM 4.0 31.2 - - + -
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Residues in contact with ARG 373 (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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369A ARG 2.9 14.3 + - - +
370A GLU* 2.7 55.4 + - - +
371A VAL 3.1 0.4 - - - -
372A LEU* 1.3 78.0 - - - +
374A ILE* 1.3 83.4 + - - +
375A ARG 3.6 0.3 + - - -
376A PRO* 3.7 4.9 - - - +
411A HIS* 2.7 55.0 + - + +
412A HIS* 4.4 2.4 + - - -
417A TRP* 3.6 44.3 - - + -
420A PRO* 3.3 13.7 - - - +
421A GLU 3.1 30.7 - - - +
422A LEU 3.4 7.5 + - - -
427A ARG* 3.1 13.2 - - - +
428A PHE* 4.1 1.8 - - + -
443A TYR* 3.7 10.3 - - + -
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Residues in contact with ILE 374 (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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328A TYR* 3.7 41.3 - - + +
370A GLU 3.0 18.5 + - - +
371A VAL* 3.6 9.0 - - - +
373A ARG* 1.3 99.4 - - - +
375A ARG* 1.3 79.6 + - - +
376A PRO* 3.6 1.8 - - - +
408A TRP* 3.9 0.3 - - - -
412A HIS* 3.3 26.2 - - - +
421A GLU* 4.3 10.3 - - - -
422A LEU 3.8 31.2 - - - +
423A PHE* 4.0 12.8 - - + +
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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
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321A VAL* 5.7 1.9 - - - +
324A TRP* 3.5 63.9 + - + -
328A TYR* 3.4 31.3 + - + -
371A VAL* 3.0 16.8 + - - +
372A LEU* 4.8 1.4 - - - +
374A ILE* 1.3 96.6 + - + +
376A PRO* 1.3 70.7 - - - +
377A VAL* 3.3 5.2 + - - +
408A TRP* 3.7 20.4 - - - -
412A HIS* 4.8 0.2 + - - -
421A GLU* 4.6 12.1 + - - +
487A LEU* 2.4 38.8 + - - +
488A GLN* 4.4 5.7 + - - +
495A LEU* 4.2 13.0 - - + -
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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