Contacts of the helix formed by residues 383 - 401 (chain D) in PDB entry 1OKW
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 THR 383 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D TRP* 4.2 1.1 - - - -
377D ILE* 4.3 16.4 - - + -
381D GLY 4.0 4.1 + - - +
382D TYR* 1.3 74.1 - - - +
384D LEU* 1.3 64.2 + - - +
385D GLU* 3.3 14.7 + - + +
386D SER* 2.6 52.4 + - - -
387D LEU* 3.2 8.7 + - - +
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D HIS* 2.8 51.8 - - + +
371D SER* 3.7 11.9 - - - +
372D TRP* 3.7 22.4 - - + +
377D ILE* 4.5 6.1 - - + +
383D THR* 1.3 70.2 - - - +
385D GLU* 1.3 66.3 + - - +
387D LEU* 3.1 16.3 + - + +
388D LYS* 3.3 9.5 + - - +
391D LEU* 4.1 10.4 - - + +
432D LEU* 4.0 20.0 - - + +
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D THR* 3.0 13.2 + - + +
384D LEU* 1.3 77.8 - - - +
386D SER* 1.3 60.7 + - - +
388D LYS* 2.9 46.5 + - - +
389D PRO* 4.0 2.4 - - - +
432D LEU* 4.8 9.0 - - - +
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Residues in contact with SER 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D VAL* 5.5 3.1 - - - +
381D GLY 5.1 0.2 + - - -
382D TYR* 3.6 14.4 - - - +
383D THR* 2.6 47.4 + - - -
385D GLU* 1.3 74.1 - - - +
387D LEU* 1.3 62.1 + - - +
389D PRO* 3.5 12.8 - - - +
390D CYS* 6.0 0.2 - - - +
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D VAL* 4.3 28.0 - - + +
357D GLY* 4.2 2.7 - - - -
358D ALA* 4.2 17.9 - - + +
361D HIS* 5.2 1.3 - - + -
372D TRP* 3.7 41.7 - - + +
382D TYR* 4.1 29.4 - - + -
383D THR 3.5 9.2 - - - +
384D LEU* 3.1 13.9 + - + +
385D GLU 3.1 0.4 - - - -
386D SER* 1.3 80.3 - - - +
388D LYS* 1.3 64.3 + - - +
389D PRO 3.4 0.2 - - - -
390D CYS* 3.0 10.1 + - - +
391D LEU* 3.0 32.0 + - + +
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Residues in contact with LYS 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D LEU 3.3 6.5 + - - +
385D GLU* 2.9 41.2 + - - +
387D LEU* 1.3 68.6 - - - +
389D PRO* 1.3 58.6 - - + +
391D LEU* 3.1 10.0 + - + -
392D MET* 2.6 70.7 + - + +
432D LEU* 3.8 44.4 - - + -
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Residues in contact with PRO 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D TYR* 3.6 19.5 - - + +
385D GLU 4.0 2.7 - - - +
386D SER* 3.5 13.2 - - - +
387D LEU 3.5 4.3 - - - -
388D LYS* 1.3 94.5 - - + +
390D CYS* 1.3 60.9 + - - +
392D MET* 3.2 9.7 + - + +
393D ASP* 3.0 26.9 + - - -
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Residues in contact with CYS 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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347D TYR* 4.6 6.2 - - - -
350D TYR* 3.7 37.9 + - + -
354D VAL* 3.9 19.1 - - + -
355D ILE* 3.9 25.6 - - - -
358D ALA* 3.7 18.4 - - + -
387D LEU 3.0 7.8 + - - +
389D PRO* 1.3 79.5 - - - +
391D LEU* 1.3 53.6 + - - +
393D ASP* 3.5 2.8 + - - +
394D LEU* 2.7 38.1 + - - +
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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
----------------------------------------------------------
358D ALA* 3.3 33.8 - - + +
361D HIS* 4.0 28.7 - - + -
362D LEU* 4.2 21.1 - - + -
384D LEU* 4.1 9.9 - - + +
387D LEU* 3.0 30.5 + - + +
388D LYS* 3.2 14.8 - - + +
390D CYS* 1.3 75.2 - - - +
392D MET* 1.3 66.5 + - + +
394D LEU* 3.8 2.9 - - + +
395D HIS* 2.9 25.3 + - - +
430D LEU* 4.2 13.8 - - + +
432D LEU* 4.8 9.2 - - + -
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Residues in contact with MET 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 LYS* 2.6 55.3 + - + +
389D PRO* 3.4 10.8 - - + +
391D LEU* 1.3 74.8 - - + +
393D ASP* 1.3 66.9 + - - +
395D HIS* 3.1 12.4 + - - +
396D GLN* 3.2 20.3 + - - +
430D LEU* 5.2 4.7 - - + -
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Residues in contact with ASP 393 (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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346D PRO* 4.2 19.0 - - + +
347D TYR* 3.2 24.1 + - + +
349D LYS* 5.0 3.1 - - - -
350D TYR* 2.7 29.3 + - - +
389D PRO 3.0 8.2 + - - +
390D CYS* 3.6 8.7 - - - +
392D MET* 1.3 81.6 - - - +
394D LEU* 1.3 62.3 + - - +
395D HIS 3.2 0.3 + - - -
396D GLN* 3.5 8.0 + - - +
397D THR* 3.0 19.4 + - - -
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D LEU* 3.9 35.2 - - + +
339D LEU* 5.7 0.4 - - + -
340D SER* 4.7 6.7 - - - -
347D TYR* 3.2 26.2 + - + +
355D ILE* 4.5 6.3 - - + +
358D ALA* 4.1 7.2 - - + +
359D ALA* 3.5 42.0 - - + +
362D LEU* 4.0 8.7 - - + +
390D CYS* 2.7 23.5 + - - +
391D LEU* 3.3 6.5 + - - +
393D ASP* 1.3 74.3 - - - +
395D HIS* 1.3 57.2 - - - +
397D THR* 3.4 7.9 + - + -
398D TYR* 2.8 27.7 + - - +
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Residues in contact with HIS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D LEU* 3.9 19.7 - - + +
391D LEU 2.9 16.9 + - - +
392D MET* 3.4 6.1 - - - +
394D LEU* 1.3 74.6 - - - +
396D GLN* 1.3 61.9 + - - +
398D TYR* 2.9 8.7 + + - +
399D LEU* 2.7 50.2 + - + +
426D PRO* 5.5 0.2 - - + -
427D PRO* 3.2 34.4 + - + +
428D GLU 3.6 26.5 - - - -
429D THR* 3.9 9.4 - - - -
430D LEU* 3.7 26.8 - - + +
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Residues in contact with GLN 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 MET 3.2 12.3 + - - +
393D ASP* 3.5 10.1 - - - +
395D HIS* 1.3 82.8 + - - +
397D THR* 1.3 64.8 + - - +
399D LEU* 2.9 26.6 + - - +
400D LYS* 2.9 55.3 + - - +
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Residues in contact with THR 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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339D LEU* 4.3 27.6 - - + +
343D ASP* 4.4 16.5 + - - +
346D PRO* 5.6 0.5 - - - +
347D TYR* 2.5 38.6 + - + +
393D ASP 3.0 10.3 + - - -
394D LEU* 3.6 7.6 - - + -
396D GLN* 1.3 76.4 - - - +
398D TYR* 1.3 65.3 + - - +
400D LYS* 3.2 13.6 + - - +
401D ALA* 3.2 14.4 + - + +
404D HIS* 5.9 3.6 - - - +
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Residues in contact with TYR 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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332D LEU* 3.4 29.0 - - + +
335D PHE* 4.4 17.7 - + - -
336D LEU* 3.8 26.2 - - + -
339D LEU* 5.1 2.7 - - + -
362D LEU* 4.0 20.0 - - + -
366D THR* 4.1 13.0 - - + +
394D LEU 2.8 17.9 + - - +
395D HIS* 2.9 15.5 + + - +
397D THR* 1.3 75.8 - - - +
399D LEU* 1.3 61.5 + - - +
401D ALA* 3.6 12.4 + - + +
402D PRO* 4.3 2.4 - - - +
421D VAL 4.6 2.0 + - - -
422D SER 6.0 2.2 - - - -
424D LEU* 4.3 11.4 - - - +
426D PRO* 3.5 51.0 - - + +
427D PRO* 3.9 12.3 - - + -
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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
----------------------------------------------------------
395D HIS* 2.7 38.4 + - + +
396D GLN* 2.9 33.0 + - - +
398D TYR* 1.3 75.4 - - - +
400D LYS* 1.3 62.1 + - + +
401D ALA 3.3 0.2 - - - -
402D PRO* 3.2 16.3 - - - +
403D GLN* 4.5 3.3 + - - -
426D PRO* 4.2 17.9 - - + +
427D PRO 4.1 16.6 - - - +
428D GLU* 4.9 9.6 - - + +
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Residues in contact with LYS 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D GLN* 2.9 57.2 + - - +
397D THR* 3.2 4.5 + - - +
399D LEU* 1.3 75.1 - - + +
401D ALA* 1.3 64.0 + - - +
402D PRO* 3.2 4.7 - - - -
403D GLN* 2.9 28.0 + - + +
404D HIS* 3.4 11.3 + - + +
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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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335D PHE* 5.2 2.7 - - + -
339D LEU* 4.1 23.8 - - + -
397D THR* 3.2 15.8 + - + +
398D TYR* 3.8 7.6 - - + +
399D LEU 3.3 0.2 - - - -
400D LYS* 1.3 77.3 - - - +
402D PRO* 1.3 65.8 - - + +
403D GLN 3.0 0.2 - - - -
404D HIS* 3.1 15.0 + - - +
406D GLN 4.5 0.5 - - - +
407D GLN* 2.7 23.7 + - - -
410D ARG* 3.5 18.3 - - + -
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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
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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