Contacts of the helix formed by residues 384 - 401 (chain D) in PDB entry 5ZR1
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 384 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D SER 4.4 0.4 + - - -
383D LEU* 1.3 77.6 - - - +
385D ASP* 1.3 65.5 + - - +
386D LEU 3.5 0.2 - - - -
387D GLU* 3.4 32.2 + - - +
388D LEU* 3.0 26.2 + - - +
248E HIS* 3.9 38.9 + - - -
249E SER* 3.7 15.0 + - - -
252E GLY* 4.4 3.4 - - - -
253E ASN* 4.9 1.8 + - - -
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Residues in contact with ASP 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D LEU 5.4 0.2 - - - +
384D SER* 1.3 77.2 - - - +
386D LEU* 1.3 60.6 + - - +
388D LEU* 3.5 8.4 + - - +
389D ALA* 3.0 21.8 + - - +
521D ASN* 5.4 4.2 - - - +
522D MET* 4.4 18.7 - - + +
523D TYR* 3.2 30.2 - - + +
249E SER* 4.6 7.4 + - - +
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Residues in contact with LEU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D SER* 3.5 0.8 + - - -
385D ASP* 1.3 76.5 - - - +
387D GLU* 1.3 61.5 + - - +
389D ALA* 3.3 2.6 + - - +
390D ILE* 3.0 43.1 + - + +
415D TYR* 3.3 39.5 - - + +
451D TRP* 3.5 37.0 - - + -
455D ASP 5.0 1.1 - - - +
456D VAL* 4.2 11.4 - - + -
459D VAL* 3.7 20.6 - - + -
523D TYR* 5.4 0.7 - - - -
249E SER* 3.2 34.3 + - - +
250E TYR* 4.6 1.1 - - - -
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D SER 4.7 0.2 - - - +
383D LEU* 3.3 33.7 - - + +
384D SER* 3.4 28.5 + - - +
385D ASP 3.3 0.2 - - - -
386D LEU* 1.3 77.1 - - - +
388D LEU* 1.3 61.5 + - - +
390D ILE 3.8 0.2 + - - -
391D LEU* 3.2 23.6 + - - +
459D VAL* 3.7 29.2 - - + +
462D ASN* 3.9 18.2 + - - +
463D LEU* 3.8 12.5 - - + +
466D LEU* 6.0 0.9 - - - -
191E ARG* 4.4 9.3 + - - -
249E SER 4.8 0.4 - - - +
250E TYR 4.8 0.5 - - - +
251E THR 3.3 24.1 - - - +
252E GLY* 3.4 11.2 + - - -
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D LEU* 3.8 21.5 - - + +
383D LEU* 4.4 9.8 - - + +
384D SER 3.0 18.8 + - - +
385D ASP* 3.9 9.4 - - - +
386D LEU 3.3 0.2 - - - -
387D GLU* 1.3 77.5 - - - +
389D ALA* 1.3 57.4 + - - +
391D LEU* 3.3 4.6 + - + +
392D ILE* 3.0 47.2 + - + +
513D LEU* 5.1 0.4 - - + -
517D ILE* 3.8 38.8 - - + -
521D ASN* 4.2 17.5 - - - +
523D TYR* 4.3 16.6 - - + -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D ASP 3.0 18.6 + - - +
386D LEU* 3.3 5.6 + - - +
388D LEU* 1.3 77.7 - - - +
390D ILE* 1.3 53.9 + - - +
392D ILE* 3.6 5.1 + - - +
393D SER* 2.6 37.0 + - - -
415D TYR* 3.9 22.7 - - + -
418D MET* 4.7 6.2 - - - +
419D ILE* 5.3 0.2 - - + -
523D TYR* 3.6 28.9 - - + +
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Residues in contact with ILE 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D LEU* 3.0 25.4 + - + +
389D ALA* 1.3 73.1 - - - +
391D LEU* 1.3 59.9 + - - +
393D SER* 3.8 2.1 - - - -
394D ALA* 2.9 30.0 + - - +
411D ALA* 4.4 6.5 - - + +
412D TYR* 4.9 1.6 - - + -
415D TYR* 3.5 39.9 - - + -
456D VAL* 3.7 29.6 - - + -
459D VAL* 4.1 12.1 - - + -
460D TRP* 3.6 33.9 - - + -
463D LEU* 4.0 12.6 - - + -
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D LEU* 3.7 31.2 - - + -
383D LEU* 3.8 12.1 - - + -
387D GLU 3.2 18.0 + - - +
388D LEU* 3.7 5.8 - - + +
389D ALA 3.3 0.2 - - - -
390D ILE* 1.3 78.1 - - - +
392D ILE* 1.3 60.8 + - - +
394D ALA 4.0 0.2 - - - -
395D ALA* 3.2 23.2 + - - +
463D LEU* 4.1 7.5 - - + +
468D PHE* 3.7 43.7 - - + -
469D PHE* 3.7 11.2 - - + -
506D MET* 3.7 24.9 - - + +
508D ILE* 4.7 1.3 - - + -
513D LEU* 4.2 13.2 - - + -
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Residues in contact with ILE 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D LEU* 3.0 36.7 + - + +
389D ALA* 3.9 4.7 - - - +
391D LEU* 1.3 76.4 - - - +
393D SER* 1.3 56.9 + - - +
395D ALA* 3.0 16.3 + - - +
396D ARG* 3.0 15.5 + - - +
418D MET* 4.0 14.6 - - + -
510D LEU* 4.4 3.6 - - + -
513D LEU* 3.7 23.6 - - + -
517D ILE* 5.2 3.4 - - + -
523D TYR* 3.7 37.2 - - + +
526D TRP* 3.4 30.7 - - + +
527D THR* 3.9 13.2 - - + -
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Residues in contact with SER 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ALA 2.6 23.8 + - - -
390D ILE* 3.4 4.2 + - - -
392D ILE* 1.3 76.5 - - - +
394D ALA* 1.3 60.4 + - - +
396D ARG* 3.4 1.3 + - - -
397D VAL* 3.3 29.0 + - - +
411D ALA* 3.5 22.9 - - - -
414D GLU* 3.8 11.7 - - - +
415D TYR* 3.4 26.1 - - - +
418D MET* 3.6 15.5 - - - +
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Residues in contact with ALA 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D ILE 2.9 17.4 + - - +
391D LEU 4.2 0.9 - - - +
393D SER* 1.3 76.5 - - - +
395D ALA* 1.3 58.2 + - - +
396D ARG 3.4 0.2 - - - -
397D VAL* 4.0 2.5 - - - +
398D ALA* 3.2 26.5 + - - +
406D PHE* 3.6 27.2 - - + -
411D ALA* 3.9 17.2 - - + +
469D PHE* 3.6 28.3 - - + -
506D MET* 4.2 1.6 - - - -
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D LEU 3.2 16.9 + - - +
392D ILE 3.0 7.8 + - - +
394D ALA* 1.3 78.3 - - - +
396D ARG* 1.3 58.8 + - - +
398D ALA* 4.0 4.5 - - - +
399D LEU* 3.5 20.6 + - - +
506D MET* 4.1 15.7 - - + -
508D ILE 4.5 1.1 - - - +
509D ILE* 6.0 0.2 - - - +
510D LEU* 3.7 35.8 + - + +
513D LEU* 3.8 11.9 - - + -
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Residues in contact with ARG 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D ILE 3.0 14.9 + - - +
393D SER 3.4 4.9 + - - +
394D ALA 3.4 0.2 - - - -
395D ALA* 1.3 79.0 - - - +
397D VAL* 1.3 64.2 + - - +
399D LEU* 3.4 2.9 + - - +
400D ARG* 3.3 42.9 + - - +
414D GLU* 2.4 39.8 + - + -
418D MET* 4.0 15.9 - - - -
510D LEU* 4.0 10.1 - - + -
526D TRP* 3.2 53.8 + - - +
528D GLN 3.9 5.3 + - - -
529D LEU* 3.7 46.4 + - + +
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Residues in contact with VAL 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D SER 3.3 16.7 + - - +
394D ALA* 4.3 2.5 - - - +
396D ARG* 1.3 76.1 - - - +
398D ALA* 1.3 57.3 + - - +
400D ARG* 3.5 15.8 + - - +
401D ALA* 3.1 29.2 + - + +
405D SER 4.3 2.5 - - - +
406D PHE* 3.7 24.7 - - + -
410D LEU* 3.5 48.9 - - + +
411D ALA* 4.3 1.3 - - - -
414D GLU* 3.7 12.6 - - + -
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Residues in contact with ALA 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394D ALA 3.2 20.8 + - - +
395D ALA* 4.3 5.8 - - - +
396D ARG 3.3 0.2 - - - -
397D VAL* 1.3 77.1 - - - +
399D LEU* 1.3 59.2 + - - +
401D ALA 3.9 4.8 - - - +
404D GLY* 3.3 37.4 - - - +
405D SER 4.4 0.9 - - - -
406D PHE* 3.7 20.1 - - + -
506D MET* 4.3 13.0 - - + -
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Residues in contact with LEU 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D ALA 3.5 14.4 + - - +
396D ARG* 3.4 5.8 + - - +
397D VAL 3.2 1.0 - - - -
398D ALA* 1.3 79.7 - - - +
400D ARG* 1.3 63.4 + - - +
401D ALA 3.4 4.6 - - - +
509D ILE* 6.0 2.0 - - + -
510D LEU* 3.9 13.7 - - + +
511D GLN* 3.4 40.4 - - - +
529D LEU* 3.7 32.8 - - + +
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Residues in contact with ARG 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D ARG* 3.3 38.5 + - - +
397D VAL* 3.9 22.8 - - - +
399D LEU* 1.3 78.3 - - - +
401D ALA* 1.3 63.3 + - - +
402D LYS* 3.7 3.3 + - - -
414D GLU* 2.4 35.3 + - - +
417D LYS* 6.3 0.4 - - - -
529D LEU* 3.8 28.1 - - + +
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Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397D VAL* 3.1 18.7 + - + +
398D ALA 3.9 3.5 - - - +
399D LEU 3.4 7.5 - - - +
400D ARG* 1.3 80.4 - - - +
402D LYS* 1.3 64.9 + - - +
403D ASP 4.3 1.6 - - - +
404D GLY* 3.6 7.4 + - - +
405D SER* 3.5 33.9 - - - +
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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
------------------------------------------------------------
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