Contacts of the helix formed by residues 389 - 407 (chain A) in PDB entry 5WRS
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 ASN 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A TYR* 5.0 4.2 - - - -
386A PRO* 3.0 29.3 + - - +
387A TYR 3.7 9.2 - - - +
388A ASN* 1.3 87.5 + - - +
390A SER* 1.3 66.1 + - - +
392A ARG* 3.2 13.3 + - - +
393A LEU* 3.9 5.7 + - - +
422A ASP* 4.6 11.7 + - - +
423A ASP* 2.8 32.0 + - - +
603A NAG 4.0 26.9 + - + -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASN 4.0 1.3 + - - -
389A ASN* 1.3 73.4 - - - +
391A GLN* 1.3 65.3 + - - +
392A ARG 3.3 0.3 + - - -
393A LEU* 3.4 6.1 + - - +
394A LEU* 3.1 36.4 + - - +
454A MET* 5.8 4.2 - - - +
523A VAL* 5.3 8.8 - - - +
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Residues in contact with GLN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASN* 3.4 0.6 - - - +
390A SER* 1.3 80.1 - - - +
392A ARG* 1.3 57.8 + - - +
394A LEU* 3.3 10.7 + - - +
395A ASN* 2.9 53.4 + - - +
423A ASP* 3.2 46.9 + - + +
456A LYS* 3.7 19.5 - - - +
525A GLY* 5.8 4.3 - - - -
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 3.8 17.4 - - - +
386A PRO* 3.5 39.5 - - + +
387A TYR* 3.9 15.9 - - + -
389A ASN* 3.2 21.0 + - - +
390A SER 3.3 0.8 - - - -
391A GLN* 1.3 78.9 - - - +
393A LEU* 1.3 62.5 + - - +
395A ASN* 3.3 6.2 + - - +
396A VAL* 3.1 23.3 + - - +
414A TYR* 3.1 30.5 + - - -
416A MET* 3.3 35.7 - - - +
422A ASP* 3.7 25.1 + - - +
423A ASP* 3.7 7.3 + - - +
424A GLY 5.3 0.9 - - - -
426A LEU* 4.4 14.8 - - - -
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Residues in contact with LEU 393 (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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359A TRP* 3.6 33.4 - - + -
378A CYS* 4.1 9.2 - - - -
381A VAL* 5.0 0.9 - - + -
382A LYS* 3.7 30.5 - - + -
387A TYR* 4.3 31.1 - - + +
389A ASN 3.9 4.2 + - - +
390A SER* 3.4 7.5 + - - +
391A GLN 3.4 0.2 - - - -
392A ARG* 1.3 78.5 - - - +
394A LEU* 1.3 57.8 + - - +
396A VAL* 3.3 6.9 + - + +
397A ILE* 3.0 43.3 + - + +
452A CYS* 4.1 7.2 - - - -
454A MET* 4.1 21.5 - - - -
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A SER* 3.1 28.0 + - - +
391A GLN* 3.7 13.5 - - - +
393A LEU* 1.3 76.7 - - - +
395A ASN* 1.3 58.2 + - - +
397A ILE* 3.3 5.8 + - + +
398A ASP* 2.9 30.7 + - - +
454A MET* 3.9 24.0 - - + +
455A ILE* 3.9 35.9 - - - +
456A LYS* 3.8 24.7 + - + +
523A VAL* 3.9 32.5 - - + -
524A ASP 5.7 0.9 - - - +
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Residues in contact with ASN 395 (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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277A ARG* 5.2 3.7 + - - +
391A GLN* 2.9 27.4 + - - +
392A ARG* 3.6 7.0 - - - +
393A LEU 3.3 0.2 - - - -
394A LEU* 1.3 77.0 - - - +
396A VAL* 1.3 56.0 + - - +
398A ASP* 3.2 5.6 + - - +
399A MET* 2.9 27.0 + - - +
423A ASP 3.7 9.1 + - - -
424A GLY 2.9 29.7 + - - -
425A PHE* 3.7 13.0 - - - +
426A LEU* 3.8 21.1 - - + +
428A HIS* 5.0 1.2 + - - -
456A LYS* 2.7 36.7 + - - +
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Residues in contact with VAL 396 (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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357A ASN* 4.5 9.0 - - - +
358A PRO* 5.3 1.1 - - + -
359A TRP* 4.0 30.7 - - + -
387A TYR* 3.9 22.9 - - + -
392A ARG* 3.1 15.4 + - - +
393A LEU* 3.3 8.7 + - + +
395A ASN* 1.3 75.3 - - - +
397A ILE* 1.3 58.0 + - - +
399A MET* 3.1 12.1 + - + +
400A ALA* 2.8 27.5 + - + +
414A TYR* 4.3 13.5 - - + +
426A LEU* 3.9 18.6 - - + -
448A PRO* 4.4 8.7 - - + -
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Residues in contact with ILE 397 (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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393A LEU* 3.0 28.1 + - + +
394A LEU* 3.6 10.5 - - + +
395A ASN 3.2 0.2 - - - -
396A VAL* 1.3 72.7 - - + +
398A ASP* 1.3 66.6 + - - +
400A ALA* 3.3 6.8 + - - +
401A ILE* 3.0 31.7 + - + +
448A PRO* 3.9 32.3 - - + +
449A LEU* 3.9 24.9 - - + -
452A CYS* 4.1 6.5 - - + -
454A MET* 3.2 46.4 - - + +
455A ILE* 4.7 6.7 - - + -
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Residues in contact with ASP 398 (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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275A PHE* 3.5 20.2 - - + -
277A ARG* 3.1 26.8 + - - +
394A LEU 2.9 15.3 + - - +
395A ASN* 3.2 11.2 + - - +
397A ILE* 1.3 77.1 - - - +
399A MET* 1.3 56.9 + - - +
401A ILE* 3.2 5.7 + - - +
402A PHE* 3.0 24.1 + - - +
428A HIS* 4.8 0.2 - - - -
455A ILE* 5.1 1.2 - - - +
456A LYS* 2.9 31.1 + - - +
459A THR* 2.8 39.5 + - - +
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Residues in contact with MET 399 (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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357A ASN* 4.6 12.1 - - - +
395A ASN 2.9 11.8 + - - +
396A VAL* 3.1 22.0 + - + +
398A ASP* 1.3 76.3 - - - +
400A ALA* 1.3 57.6 + - - +
402A PHE* 3.4 2.0 + - - +
403A ASP* 2.9 43.7 + - - +
411A ARG* 3.5 32.3 - - + +
414A TYR* 3.6 42.0 - - + -
426A LEU* 4.2 7.0 - - + -
427A ILE 5.4 0.2 - - - +
428A HIS* 3.5 39.6 - - + +
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Residues in contact with ALA 400 (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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396A VAL* 2.8 19.4 + - + +
397A ILE 3.7 4.7 - - - +
398A ASP 3.2 0.2 - - - -
399A MET* 1.3 72.9 - - + +
401A ILE* 1.3 59.6 + - - +
403A ASP* 3.7 6.0 - - - +
404A PHE* 2.8 31.9 + - - +
445A ILE* 3.4 24.9 - - - +
446A LEU* 4.2 8.2 - - + +
448A PRO* 3.7 23.1 - - + -
449A LEU 5.2 0.9 - - - +
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Residues in contact with ILE 401 (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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273A LEU* 5.5 0.4 - - + -
275A PHE* 4.9 8.3 - - + -
397A ILE* 3.0 25.9 + - + +
398A ASP* 3.2 8.3 + - - +
400A ALA* 1.3 76.6 - - - +
402A PHE* 1.3 63.3 + - - +
404A PHE* 3.4 2.6 + - - +
405A LEU* 3.0 29.0 + - + +
446A LEU* 4.0 21.5 - - + -
449A LEU* 4.3 4.3 - - + -
455A ILE* 3.7 32.1 - - + -
459A THR* 4.0 13.5 - - + -
463A LEU* 4.2 22.2 - - + -
505A ILE* 3.6 24.7 - - + +
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Residues in contact with PHE 402 (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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266A ALA* 3.5 38.8 - - + -
269A LEU* 3.9 21.1 - - + -
270A ASP* 4.1 9.2 - - + -
273A LEU* 3.9 18.6 - - + -
275A PHE* 4.1 15.9 - + + -
278A VAL* 4.3 6.7 - - + -
398A ASP 3.0 12.5 + - - +
399A MET* 3.6 8.7 - - - +
401A ILE* 1.3 78.7 - - - +
403A ASP* 1.3 72.3 + - - +
405A LEU* 3.2 16.8 + - - +
406A ILE* 3.3 26.4 + - + +
411A ARG* 4.0 3.4 - - - -
428A HIS* 3.8 22.4 - + + +
431A ASN* 3.5 22.7 - - - -
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Residues in contact with ASP 403 (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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357A ASN* 5.6 0.9 + - - -
399A MET* 2.9 26.4 + - - +
400A ALA* 4.4 1.3 - - - -
402A PHE* 1.3 78.0 - - - +
404A PHE* 1.3 59.1 + - - +
406A ILE* 3.4 6.1 + - - +
407A GLY 2.7 24.6 + - - -
408A ASN* 2.8 34.8 + - + +
411A ARG* 2.6 52.6 + - - +
445A ILE* 3.6 19.9 - - + +
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Residues in contact with PHE 404 (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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400A ALA 2.8 18.5 + - - +
401A ILE 3.8 2.9 - - - +
402A PHE 3.3 0.2 - - - -
403A ASP* 1.3 78.1 - - - +
405A LEU* 1.3 60.6 + - - +
407A GLY* 3.2 10.4 + - - -
441A ASP* 4.2 9.0 - - + -
442A GLU 3.4 37.9 - - - -
443A ILE* 3.8 17.3 - - + -
445A ILE* 3.5 12.9 - - + +
446A LEU* 3.6 23.6 - - + -
501A ARG* 3.3 49.7 - - + -
504A THR* 3.8 22.4 - - + -
505A ILE* 3.6 25.8 - - + -
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Residues in contact with LEU 405 (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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269A LEU* 4.1 12.6 - - + -
273A LEU* 3.9 36.3 - - + -
401A ILE* 3.0 26.8 + - + +
402A PHE* 3.2 6.9 + - - +
404A PHE* 1.3 76.3 - - - +
406A ILE* 1.3 52.4 + - - +
463A LEU* 4.8 4.0 - - + -
473A LEU* 4.3 11.0 - - + -
498A LEU* 3.4 32.5 - - + +
501A ARG* 2.7 34.7 + - + +
502A LEU* 3.8 29.4 - - + +
505A ILE* 3.9 14.1 - - + -
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Residues in contact with ILE 406 (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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266A ALA* 4.8 2.9 - - + -
269A LEU* 3.6 22.0 - - + -
402A PHE* 3.3 35.8 + - + +
403A ASP* 3.5 14.1 - - - +
405A LEU* 1.3 75.6 - - - +
407A GLY* 1.3 58.9 + - - +
408A ASN* 3.7 22.0 - - + -
431A ASN* 4.4 15.9 - - + +
434A GLY* 4.2 9.0 - - - -
435A PHE* 2.8 70.7 + - + -
436A GLY 4.6 0.5 + - - -
501A ARG* 3.6 6.4 + - - +
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Residues in contact with GLY 407 (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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403A ASP 2.7 8.8 + - - -
404A PHE 3.2 11.2 + - - -
405A LEU 3.4 0.2 - - - -
406A ILE* 1.3 79.1 - - - +
408A ASN* 1.3 58.6 + - - -
409A MET* 3.6 7.2 + - - +
433A ARG 4.0 8.3 - - - +
434A GLY* 4.6 0.6 - - - -
435A PHE 4.9 0.3 + - - -
436A GLY 5.3 2.1 + - - -
437A ARG* 5.2 8.6 + - - -
440A HIS 5.8 1.6 - - - -
442A GLU* 5.9 3.8 - - - -
445A ILE* 4.0 11.7 - - - -
501A ARG* 3.7 10.4 - - - +
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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