Contacts of the helix formed by residues 382 - 399 (chain A) in PDB entry 5WJ9
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A MET* 3.5 22.3 - - - +
375A ILE* 3.5 11.2 - - - +
380A LEU* 4.3 6.7 - - - +
381A ALA* 1.3 75.9 - - - +
383A TYR* 1.3 65.7 + - - +
384A ASP* 3.4 15.9 - - - -
385A VAL* 3.7 9.3 + - - +
386A CYS* 3.7 16.3 + - - +
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.9 20.7 - + - -
86A SER* 3.9 28.7 + - - -
87A ASN* 3.5 32.1 - - - +
90A ALA* 3.8 25.0 - - + +
91A VAL* 5.8 1.6 - - + -
94A ARG* 5.9 4.7 - - - +
252A ASP* 4.3 14.0 + - - -
254A TYR* 4.7 5.8 - - - -
281A ILE* 4.8 13.5 - - + -
375A ILE* 3.4 35.9 + - + +
376A GLU* 6.0 0.3 - - - -
381A ALA* 5.4 2.2 - - - -
382A SER* 1.3 71.8 - - - +
384A ASP* 1.3 57.7 + - - +
385A VAL 3.3 0.2 + - - -
386A CYS* 3.3 2.3 + - - +
387A SER* 2.8 37.4 + - - -
450D TYR* 5.1 3.8 - - - +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 3.6 14.6 - - - -
383A TYR* 1.3 75.0 - - - +
385A VAL* 1.3 83.7 + - - +
387A SER* 2.7 21.1 + - - -
388A ILE* 3.1 25.1 + - + +
450D TYR* 4.0 12.9 + - - +
487D SER* 4.1 18.0 + - - -
489D LEU* 5.1 9.6 - - + +
490D VAL* 3.5 26.9 - - + -
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A MET* 3.7 22.2 - - + -
382A SER* 3.7 12.3 + - - +
383A TYR 3.3 0.6 - - - -
384A ASP* 1.3 90.2 + - - +
386A CYS* 1.3 55.2 + - - +
388A ILE* 3.3 9.4 + - + +
389A LEU* 2.8 54.0 + - + +
489D LEU* 4.1 24.2 - - + -
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Residues in contact with CYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.4 31.9 - - + -
368A GLY 3.8 17.9 - - - -
371A MET* 4.1 12.2 - - + +
372A LYS* 4.0 11.7 - - - -
375A ILE* 5.3 2.2 - - + -
380A LEU* 6.4 0.2 - - + -
382A SER 3.7 10.5 + - - +
383A TYR 3.3 3.5 + - - +
385A VAL* 1.3 80.2 - - - +
387A SER* 1.3 52.6 + - - +
389A LEU* 4.1 10.1 - - - -
390A LEU* 2.8 53.3 + - - +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 3.5 9.3 - - - -
87A ASN* 3.4 26.7 - - - -
383A TYR 2.8 18.1 + - - -
384A ASP* 2.7 26.0 + - - -
386A CYS* 1.3 71.5 - - - +
388A ILE* 1.3 60.1 + - - +
390A LEU* 5.1 0.2 - - - -
391A GLY 2.8 25.3 + - - -
445D ILE* 3.9 4.7 - - - +
446D VAL* 3.1 34.4 + - - +
450D TYR* 5.5 1.7 - - - -
490D VAL* 5.0 1.9 - - - +
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Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 3.1 19.8 + - - +
385A VAL* 3.6 6.1 - - - +
387A SER* 1.3 83.2 + - - +
389A LEU* 1.3 59.1 + - + +
392A THR* 2.7 45.1 + - - +
446D VAL* 4.5 8.5 - - + -
489D LEU* 3.4 47.8 - - + +
490D VAL* 4.1 3.6 - - + +
493D PHE* 3.7 37.7 - - + -
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.7 38.3 - - + +
367A SER* 3.7 27.4 - - - +
368A GLY* 4.2 3.4 - - - -
371A MET* 4.1 15.5 - - + -
385A VAL* 2.8 50.6 + - + +
386A CYS* 3.5 9.4 - - - +
388A ILE* 1.3 76.6 - - + +
390A LEU* 1.3 58.3 + - - +
392A THR* 3.8 1.1 - - - -
393A SER* 2.8 30.0 + - - -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL 6.0 0.7 - - - +
79A GLN* 4.6 17.0 - - + -
80A LEU* 3.5 16.6 - - + -
83A PHE* 3.9 26.5 - - + -
365A THR* 3.7 22.0 - - + +
368A GLY* 3.6 29.4 - - - -
369A THR* 3.8 8.1 - - + +
372A LYS* 4.7 6.1 - - + -
386A CYS* 2.8 39.8 + - - +
387A SER* 4.5 1.3 - - - +
389A LEU* 1.3 73.4 - - - +
391A GLY* 1.3 50.8 + - - +
393A SER* 3.3 5.4 + - - -
394A THR* 2.8 39.0 + - + +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.5 9.3 - - - +
387A SER 2.8 23.7 + - - -
390A LEU* 1.3 71.3 - - - +
392A THR* 1.3 58.6 + - - +
394A THR* 2.7 21.5 + - - -
395A LEU* 2.8 17.3 + - - +
442D CYS* 3.4 22.9 - - - -
446D VAL* 4.1 3.6 - - - -
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Residues in contact with THR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.5 23.1 - - + -
388A ILE* 2.7 31.8 + - - +
391A GLY* 1.3 68.6 - - - -
393A SER* 1.3 58.7 + - - +
395A LEU* 3.6 11.8 - - + +
396A LEU* 2.8 48.7 + - + +
442D CYS* 4.1 2.8 - - - -
493D PHE* 3.2 23.8 - - + -
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 4.9 0.9 - - - +
361A SER* 3.8 8.9 - - - -
364A LEU* 3.8 6.0 - - - +
365A THR* 2.6 52.5 + - - +
389A LEU 2.8 19.2 + - - -
390A LEU* 3.3 9.1 + - - -
392A THR* 1.3 77.7 - - - +
394A THR* 1.3 59.0 + - - +
396A LEU* 3.7 1.2 - - - +
397A VAL* 2.8 36.7 + - - +
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Residues in contact with THR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.6 38.8 - - + +
77A THR* 4.2 7.0 - - - +
80A LEU* 3.2 34.3 - - + +
390A LEU* 2.8 22.9 + - + +
391A GLY* 2.7 19.9 + - - -
393A SER* 1.3 70.7 - - - +
395A LEU* 1.3 57.1 + - - +
397A VAL* 4.2 5.8 - - - -
398A TRP* 2.8 41.7 + - - +
438D GLY* 4.9 1.6 - - - -
441D PHE* 5.3 2.5 - - - -
442D CYS* 4.5 4.0 + - - -
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Residues in contact with LEU 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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391A GLY 2.8 20.6 + - - +
392A THR* 3.6 15.3 - - + +
394A THR* 1.3 75.3 + - - +
396A LEU* 1.3 66.6 + - + +
398A TRP* 4.1 1.9 - - - +
399A VAL* 3.3 27.6 + - + +
435D ILE 4.4 1.8 - - - +
438D GLY* 3.6 33.7 + - - +
439D TYR* 3.6 47.8 - - + +
442D CYS* 4.2 12.3 - - + -
493D PHE* 5.3 4.7 - - + -
497D TYR* 5.1 2.9 - - + -
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.6 38.8 - - + +
358A LEU* 5.8 0.2 - - - -
360A THR* 5.0 8.1 - - + -
361A SER* 3.5 31.1 + - - +
364A LEU* 4.2 10.1 - - + -
392A THR* 2.8 42.6 + - + +
395A LEU* 1.3 77.9 - - + +
397A VAL* 1.3 60.8 + - - +
399A VAL* 3.1 23.9 - - + +
400A GLY* 3.4 5.5 + - - -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 6.1 2.5 - - - +
72A LYS* 4.5 23.3 - - + +
73A ILE* 3.5 41.5 - - + +
76A VAL* 3.8 15.5 - - + -
358A LEU* 6.2 2.9 - - + -
361A SER* 4.2 15.5 - - - +
365A THR* 4.5 3.4 - - - +
393A SER* 2.8 36.7 + - - +
394A THR* 3.9 6.1 - - - +
396A LEU* 1.3 71.7 - - - +
398A TRP* 1.3 60.8 - - + +
400A GLY* 2.8 24.1 + - - -
401A VAL 3.9 1.6 + - - -
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Residues in contact with TRP 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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73A ILE* 3.4 23.1 - - + +
77A THR* 3.2 27.0 + - + +
394A THR* 2.8 29.0 + - - +
395A LEU 4.1 0.2 - - - +
397A VAL* 1.3 73.7 - - + +
399A VAL* 1.3 60.7 + - - +
401A VAL* 3.1 33.2 + - + +
434D VAL* 3.0 51.2 - - + +
437D LEU* 4.3 24.5 - - + -
438D GLY* 3.9 17.0 - - - -
441D PHE* 3.9 30.3 - + + -
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A TRP* 5.0 6.3 + - + -
357A LEU* 4.2 15.3 - - + -
395A LEU* 3.3 19.9 + - + +
396A LEU* 3.1 30.5 - - + +
398A TRP* 1.3 75.1 - - + +
400A GLY* 1.3 60.0 + - - +
401A VAL 3.2 0.4 - - - -
402A ILE* 3.3 29.1 + - + +
403A ARG 4.1 1.4 + - - -
434D VAL* 4.0 7.0 - - - -
435D ILE* 3.6 40.2 - - + +
439D TYR* 5.9 0.2 - - + -
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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
------------------------------------------------------------
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