Contacts of the helix formed by residues 361 - 375 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLU* 3.4 28.0 - - + +
343B LEU* 3.4 30.7 - - + -
346B LYS* 3.8 21.8 - - + -
347B ILE* 4.0 16.6 - - + -
357B ASP* 3.6 12.1 - - + +
358B ARG 3.1 12.3 + - - +
360B ASN* 1.3 87.0 - - + +
362B PRO* 1.3 59.9 - - - +
363B TYR 3.4 2.2 - - - -
364B LEU* 3.5 10.7 + - + +
365B GLU* 3.0 25.5 + - - +
464B PHE* 3.9 26.8 - - + -
468B ALA* 5.2 0.9 - - + -
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Residues in contact with PRO 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLU* 3.1 9.2 - - - +
346B LYS* 5.1 3.8 - - - +
358B ARG 4.3 1.1 - - - +
359B GLY* 4.5 7.6 - - - +
360B ASN* 3.0 17.5 - - - +
361B LEU* 1.3 85.5 - - - +
363B TYR* 1.3 55.0 + - - +
365B GLU* 3.0 8.0 + - + +
366B ALA* 2.7 37.2 + - - +
429B LEU* 4.1 16.6 - - + -
433B GLY 4.4 8.5 - - - +
434B ASP* 3.7 27.6 - - - +
435B GLY* 4.5 3.8 - - - +
436B LEU* 3.7 10.1 - - + +
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Residues in contact with TYR 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B VAL* 3.6 29.8 - - + +
338B LYS* 3.5 54.3 - - + +
339B ILE* 3.8 14.1 - - + -
342B GLU* 3.0 20.9 + - + +
362B PRO* 1.3 77.6 - - - +
364B LEU* 1.3 54.1 + - - +
366B ALA* 3.2 5.2 + - - +
367B THR* 2.8 52.9 + - - -
424B ASP* 5.4 1.0 + - - -
425B PRO* 3.7 17.1 - - + +
426B GLY* 5.1 2.4 + - - -
429B LEU* 3.7 26.7 - - + +
433B GLY 5.4 0.8 + - - -
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B ILE* 4.1 37.0 - - + +
342B GLU* 3.3 10.8 + - - +
343B LEU* 5.2 0.9 - - + -
361B LEU* 3.7 17.7 - - + +
362B PRO 3.2 0.2 - - - -
363B TYR* 1.3 77.7 - - - +
365B GLU* 1.3 65.6 + - - +
367B THR* 4.2 5.8 - - + -
368B ILE* 3.0 36.9 + - + +
464B PHE* 3.6 35.7 - - + +
467B LEU* 4.3 16.6 - - + -
468B ALA* 4.0 25.6 - - + -
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Residues in contact with GLU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ARG* 4.2 28.1 + - + +
361B LEU 3.0 14.5 + - - +
362B PRO* 3.0 11.7 + - + +
364B LEU* 1.3 78.2 - - - +
366B ALA* 1.3 58.3 + - - +
368B ILE* 3.3 19.6 + - - +
369B ARG* 3.1 45.1 + - - +
436B LEU* 3.5 29.2 - - + -
460B LYS* 4.8 15.6 + - - +
464B PHE* 4.4 12.5 - - + +
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Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B PRO 2.7 19.7 + - - +
363B TYR 3.6 3.8 - - - +
365B GLU* 1.3 72.4 - - - +
367B THR* 1.3 64.2 + - - +
369B ARG* 3.3 5.9 + - - +
370B GLU* 3.1 22.7 + - - +
425B PRO* 3.5 22.3 - - - +
428B PHE* 3.7 20.4 - - + +
429B LEU* 3.7 20.4 - - + -
436B LEU* 3.9 4.9 - - + +
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 4.8 7.4 - - + -
335B VAL* 3.9 11.6 - - + +
339B ILE* 4.0 21.6 - - + +
363B TYR* 2.8 44.8 + - - -
364B LEU* 3.6 7.2 - - + +
365B GLU 3.4 0.2 - - - -
366B ALA* 1.3 69.0 - - - +
368B ILE* 1.3 69.9 + - + +
370B GLU* 3.0 13.7 + - - +
371B VAL* 3.2 15.3 + - + +
423B PHE* 4.3 13.4 - - + -
425B PRO* 3.4 14.2 - - - +
467B LEU* 6.0 3.1 - - + -
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 5.7 0.8 - - + +
325B SER* 5.9 0.7 - - - +
364B LEU* 3.0 28.8 + - + +
365B GLU* 3.3 23.8 - - - +
367B THR* 1.3 76.4 - - + +
369B ARG* 1.3 64.4 + - + +
371B VAL* 3.1 18.7 + - - +
372B LEU* 3.4 21.3 + - + +
460B LYS* 5.5 6.1 - - + +
463B LEU* 3.9 28.7 - - + +
464B PHE* 3.7 38.4 - - + +
467B LEU* 3.9 19.7 - - + -
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Residues in contact with ARG 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B GLU* 3.1 39.4 + - - +
366B ALA* 3.5 15.0 - - - +
367B THR 3.2 0.2 - - - -
368B ILE* 1.3 76.1 - - + +
370B GLU* 1.3 58.2 + - - +
372B LEU* 3.3 5.5 + - + -
373B ARG* 3.0 20.6 + - - +
428B PHE* 3.7 30.7 - - + -
436B LEU* 3.7 33.1 - - - +
437B CYS 4.9 6.3 + - - -
438B CYS* 5.5 6.9 - - - +
443B TYR* 2.9 40.6 + - + +
460B LYS* 4.5 15.3 - - - +
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Residues in contact with GLU 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B ALA 3.1 12.0 + - - +
367B THR 3.0 10.7 + - - +
369B ARG* 1.3 75.7 - - - +
371B VAL* 1.3 56.5 + - - +
373B ARG* 2.3 48.7 + - - -
374B ILE* 3.1 26.6 + - - +
422B LEU 3.6 1.4 - - - +
423B PHE* 3.3 27.7 - - + -
424B ASP 3.3 21.2 + - - +
425B PRO* 4.2 10.1 - - + -
427B ARG* 2.8 17.4 + - - -
428B PHE* 3.3 11.4 - - + -
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B VAL* 4.0 14.8 - - + +
324B TRP* 3.8 29.6 - - + -
325B SER* 3.9 32.1 - - - +
328B TYR* 4.7 7.2 - - + -
367B THR* 3.2 13.6 + - + +
368B ILE* 3.1 10.8 + - - +
370B GLU* 1.3 78.4 - - - +
372B LEU* 1.3 56.5 + - - +
374B ILE* 4.3 4.7 - - - -
375B ARG* 3.1 30.7 + - + +
423B PHE* 3.8 20.9 - - + -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 3.7 38.6 - - + -
368B ILE* 3.6 26.9 - - + +
369B ARG* 3.3 3.9 + - + -
371B VAL* 1.3 72.8 - - - +
373B ARG* 1.3 66.7 + - - +
375B ARG 4.6 4.0 - - - +
376B PRO* 3.4 18.2 - - - +
377B VAL* 5.5 1.6 - - + +
411B HIS* 3.5 10.7 + - - -
443B TYR* 3.7 15.7 - - - +
445B PRO* 3.6 18.6 - - + +
446B PHE* 4.0 25.6 - - + -
460B LYS* 5.9 2.7 - - + -
463B LEU* 4.5 6.1 - - + -
600B HEM 4.5 16.8 - - + -
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Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ARG 3.0 16.9 + - - +
370B GLU* 2.3 48.2 + - - +
372B LEU* 1.3 78.5 - - - +
374B ILE* 1.3 83.1 + - - +
376B PRO* 3.4 4.9 - - - +
411B HIS* 2.8 50.6 + - - +
412B HIS* 3.8 8.1 - - - -
417B TRP* 3.8 40.2 - - + -
420B PRO* 3.5 12.4 - - - +
421B GLU 3.1 28.9 - - - +
422B LEU 3.6 3.2 + - - -
427B ARG* 2.9 21.6 - - - +
428B PHE* 4.2 1.1 - - + -
443B TYR* 3.7 12.7 - - + -
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B TYR* 3.6 39.5 - - + +
370B GLU* 3.1 17.4 + - - +
371B VAL* 3.9 8.1 - - - +
373B ARG* 1.3 112.5 - - - +
375B ARG* 1.3 81.0 + - + +
376B PRO* 3.5 1.9 - - - +
408B TRP* 3.7 0.2 - - - -
412B HIS* 3.2 27.1 - - - +
421B GLU* 3.6 27.1 - - - +
423B PHE* 4.1 22.0 - - + -
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Residues in contact with ARG 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B VAL* 5.8 0.5 - - - +
324B TRP* 3.5 65.0 + - + +
328B TYR* 3.2 32.7 + - + -
371B VAL* 3.1 16.5 + - + +
372B LEU* 4.6 1.9 - - - +
374B ILE* 1.3 93.8 + - + +
376B PRO* 1.3 70.8 - - - +
377B VAL* 3.5 5.9 + - - +
408B TRP* 3.5 19.5 - - - -
421B GLU* 2.4 34.1 + - - -
487B LEU* 2.6 41.8 + - - +
488B GLN* 5.0 0.2 - - - +
489B GLY 5.5 0.9 - - - +
495B LEU* 4.2 11.7 - - + -
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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