Contacts of the helix formed by residues 362 - 376 (chain K) in PDB entry 4DVQ
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 362 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343K GLU* 3.1 20.0 - - + +
344K SER* 3.5 38.4 - - - +
347K ALA* 4.2 1.1 - - + -
351K ILE* 3.4 29.6 - - + -
358K ALA* 3.2 30.5 + - + +
360K THR 3.5 1.2 - - - -
361K GLU* 1.3 84.9 - - - +
363K PRO* 1.4 65.3 - - - +
365K LEU* 3.2 22.3 + - + +
366K ARG* 3.2 17.3 + - - +
461K LEU* 4.5 6.1 - - + -
465K HIS* 4.0 18.4 - - + +
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Residues in contact with PRO 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343K GLU* 2.9 14.6 - - + +
360K THR 4.1 14.3 - - - +
361K GLU 3.4 6.1 - - - +
362K LEU* 1.4 87.1 - - - +
364K LEU* 1.3 63.7 + - + +
366K ARG* 3.2 14.0 + - + +
367K ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K ILE* 4.0 26.0 - - + +
340K LEU* 3.5 14.8 - - + +
343K GLU* 2.7 36.6 + - + +
363K PRO* 1.3 75.0 - - + +
365K LEU* 1.3 61.3 + - - +
367K ALA* 3.2 11.1 + - + +
368K ALA* 3.0 17.8 + - - +
425K PRO* 4.3 9.8 - - + +
426K GLN* 6.5 0.9 - - - -
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Residues in contact with LEU 365 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330K LEU* 5.4 1.6 - - + -
340K LEU* 3.3 18.5 - - + +
343K GLU* 2.7 17.9 + - - +
344K SER* 4.5 7.2 - - - +
362K LEU* 3.4 19.1 - - + +
364K LEU* 1.3 72.1 - - - +
366K ARG* 1.3 57.6 + - - +
368K ALA* 2.9 10.5 - - + +
369K LEU* 2.9 24.1 + - + +
461K LEU* 3.5 43.5 - - + +
464K LEU* 4.2 22.2 - - + -
465K HIS* 4.0 19.5 - - + +
468K LEU* 4.1 20.9 - - + -
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Residues in contact with ARG 366 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359K THR* 2.9 49.2 + - - +
362K LEU 3.2 10.7 + - - +
363K PRO* 3.2 14.0 + - + +
365K LEU* 1.3 72.4 - - - +
367K ALA* 1.3 55.2 + - - +
369K LEU* 3.0 15.2 + - + +
370K LYS* 2.7 59.7 + - - +
453K ARG* 4.8 0.6 - - - +
457K GLU* 3.7 30.0 + - - +
461K LEU* 3.5 27.3 - - + +
603K SO4 3.2 36.1 + - - -
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Residues in contact with ALA 367 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K PRO 3.0 12.4 + - - +
364K LEU* 3.2 13.7 + - + +
366K ARG* 1.3 75.8 - - - +
368K ALA* 1.3 52.5 + - - +
370K LYS* 3.0 13.4 + - - +
371K GLU* 2.7 36.7 + - - +
425K PRO* 3.5 28.5 - - + +
428K TRP* 3.9 17.9 - - + -
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Residues in contact with ALA 368 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326K THR* 5.2 4.9 - - + -
330K LEU* 4.8 0.9 - - + -
340K LEU* 4.0 24.0 - - + -
364K LEU 3.0 12.2 + - - +
365K LEU* 2.9 18.6 + - + +
367K ALA* 1.3 76.3 - - - +
369K LEU* 1.3 60.4 + - - +
371K GLU* 3.0 2.6 + - - +
372K THR* 2.9 21.6 + - - -
423K TYR* 3.0 27.7 + - + +
425K PRO* 3.7 12.6 - - + +
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Residues in contact with LEU 369 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326K THR* 3.8 15.5 - - - +
365K LEU 2.9 13.2 + - - +
366K ARG* 3.1 13.0 - - + +
368K ALA* 1.3 73.8 - - - +
370K LYS* 1.3 64.5 + - + +
372K THR* 3.0 8.7 + - - -
373K LEU* 3.0 29.8 + - + +
457K GLU* 4.6 13.9 - - + +
460K MET* 3.3 47.8 - - + -
461K LEU* 3.8 30.7 - - + +
464K LEU* 4.1 20.0 - - + -
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Residues in contact with LYS 370 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366K ARG* 2.7 54.3 + - - +
367K ALA* 3.0 11.8 + - - +
369K LEU* 1.3 74.3 - - + +
371K GLU* 1.3 57.4 + - - +
373K LEU* 3.5 2.9 + - - +
374K ARG* 2.9 27.4 + - - +
428K TRP* 4.0 33.6 - - + -
440K HIS* 3.5 55.3 + - + +
457K GLU* 5.3 2.2 + - - -
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Residues in contact with GLU 371 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367K ALA 2.7 17.5 + - - +
368K ALA* 3.4 7.4 - - - +
370K LYS* 1.3 77.2 - - - +
372K THR* 1.3 61.5 + - - +
374K ARG* 2.6 49.0 + - - +
375K LEU* 3.4 23.6 + - - +
422K ARG 3.3 0.3 - - - +
423K TYR* 3.7 16.4 - - + -
424K ASN 3.2 40.7 + - - +
425K PRO 3.8 2.7 - - - -
427K ARG* 3.2 8.8 + - - +
428K TRP* 2.7 32.4 + - + +
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Residues in contact with THR 372 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322K PRO* 3.5 33.7 - - + +
325K MET* 3.7 21.7 - - + -
326K THR* 2.8 23.0 + - - +
329K GLU* 5.8 0.2 - - + -
368K ALA 2.9 15.2 + - - -
369K LEU* 3.0 8.7 + - - -
371K GLU* 1.3 76.4 - - - +
373K LEU* 1.3 52.4 + - - +
374K ARG 3.2 0.4 - - - -
375K LEU 3.2 1.0 + - - -
376K TYR* 2.6 43.4 + - + +
423K TYR* 3.5 17.8 + - - -
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Residues in contact with LEU 373 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322K PRO* 3.7 28.9 - - + -
369K LEU* 3.0 22.3 + - + +
370K LYS* 3.7 4.7 - - - +
372K THR* 1.3 73.8 - - - +
374K ARG* 1.3 62.8 + - - +
376K TYR 4.1 12.6 - - - +
377K PRO* 3.4 24.3 - - + +
378K VAL* 4.1 19.3 - - + -
407K LEU* 5.8 0.9 - - - +
440K HIS* 4.5 5.2 - - + -
442K PRO* 3.9 25.5 - - + +
443K PHE* 3.8 33.4 - - + -
460K MET* 4.9 8.3 - - + -
601K HEM 4.3 9.0 - - + -
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Residues in contact with ARG 374 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370K LYS 2.9 17.4 + - - +
371K GLU* 2.6 45.0 + - - +
372K THR 3.2 0.2 - - - -
373K LEU* 1.3 79.4 - - - +
375K LEU* 1.3 79.3 + - - +
377K PRO* 4.2 6.2 - - - +
407K LEU 4.5 3.8 - - - +
411K GLY* 2.9 54.8 + - - +
412K ARG* 4.2 7.9 - - - +
417K PHE* 3.8 29.1 - - + +
420K PRO* 2.8 39.6 + - - +
422K ARG 2.8 13.7 + - - -
427K ARG* 3.6 10.0 - - - +
428K TRP* 4.2 8.3 - - + -
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Residues in contact with LEU 375 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329K GLU* 5.1 1.3 - - - +
371K GLU 3.4 11.3 + - - +
372K THR 3.2 2.7 + - - +
374K ARG* 1.3 104.2 - - - +
376K TYR* 1.3 86.7 + - + +
377K PRO* 3.4 8.2 - - - +
408K TYR* 4.1 5.7 - - - -
412K ARG* 2.8 59.8 + - + +
420K PRO 3.6 19.1 - - - +
421K GLU* 4.4 10.1 - - - +
422K ARG 4.5 1.6 - - - +
423K TYR* 4.2 30.1 - - + +
483K MET* 5.3 0.2 - - - +
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Residues in contact with TYR 376 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322K PRO* 4.8 6.8 - - - +
325K MET* 3.7 37.7 - - + -
328K PHE* 4.8 2.6 - + - -
329K GLU* 2.3 44.3 + - + -
332K ARG* 3.8 8.1 + - - -
372K THR* 2.6 28.7 + - + +
373K LEU* 4.1 8.5 - - - +
375K LEU* 1.3 95.8 - - + +
377K PRO* 1.3 64.3 - - - +
378K VAL* 3.2 4.9 + - - +
412K ARG* 4.2 14.6 - - - -
421K GLU* 5.2 2.3 + - - -
480K ASP* 3.9 9.1 + - - -
481K ILE* 4.7 9.5 + - + -
483K MET* 3.6 45.9 - - + +
489K LEU* 4.6 2.0 - - - -
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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