Contacts of the helix formed by residues 357 - 377 (chain A) in PDB entry 5KJH
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 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.5 35.9 - - + +
267A LEU* 6.1 0.7 - - + -
318A PHE* 4.1 20.4 - - + -
333A MET* 3.7 25.1 - - + -
341A PRO* 2.9 26.1 + - + +
343A LEU* 4.2 5.2 - - + -
355A TRP* 4.0 13.5 - - + +
356A ASP* 1.3 71.4 - - - +
358A ALA* 1.4 59.4 + - - +
360A PHE* 3.3 46.4 - - + +
361A GLY 4.2 1.7 + - - -
225B LEU* 4.1 23.9 - - + +
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Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 4.0 4.9 - - + -
340A HIS* 3.7 30.1 - - + +
341A PRO* 4.0 3.0 - - + +
356A ASP* 3.1 13.5 + - - +
357A LEU* 1.4 74.2 - - - +
359A ARG* 1.4 62.5 + - - +
360A PHE 3.3 0.4 - - - -
361A GLY* 3.5 9.7 + - - +
362A GLU* 3.6 17.8 + - - +
229B GLU* 3.9 24.7 - - - +
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.4 43.9 + - + +
11A LEU* 3.9 17.8 - - - +
356A ASP* 3.2 25.4 + - + +
358A ALA* 1.4 74.4 - - - +
360A PHE* 1.3 59.8 + - - +
361A GLY 3.4 0.2 + - - -
362A GLU 3.4 1.0 + - - -
363A TYR* 3.0 29.1 + - - +
411A TRP* 3.3 53.2 + - + +
502A TYR* 2.8 50.8 + - + -
514A HIS* 3.7 22.0 + - - +
515A ARG* 5.9 1.8 - - - +
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Residues in contact with PHE 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PHE* 3.8 32.1 - + - -
355A TRP* 4.4 0.7 - + + -
356A ASP 4.3 0.4 - - - -
357A LEU* 3.3 40.2 - - + +
358A ALA 3.3 0.2 - - - -
359A ARG* 1.3 75.7 - - - +
361A GLY* 1.3 55.9 + - - +
363A TYR* 3.5 5.6 + - - +
364A ALA* 2.9 25.6 + - - +
501A MET 3.3 22.0 - - - -
502A TYR* 3.5 25.3 - + - +
504A LEU* 3.6 32.1 - - + -
511A ILE* 3.8 13.2 - - + -
514A HIS* 3.6 20.0 - + - -
222B ASN* 3.3 11.1 + - - +
225B LEU* 3.8 16.4 - - + -
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Residues in contact with GLY 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU 4.2 1.4 + - - -
358A ALA* 3.5 7.7 + - - +
359A ARG 3.3 0.6 - - - -
360A PHE* 1.3 77.0 - - - +
362A GLU* 1.3 57.5 + - - +
364A ALA* 3.5 3.8 + - - +
365A ARG* 3.0 34.0 + - - +
222B ASN* 3.4 12.5 + - - -
226B GLU* 3.9 24.5 - - - -
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Residues in contact with GLU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.3 31.5 - - + -
358A ALA 3.6 15.1 + - - +
359A ARG 3.4 1.0 + - - +
361A GLY* 1.3 71.1 - - - +
363A TYR* 1.3 59.3 - - - +
365A ARG* 3.4 9.2 + - - +
366A PHE* 2.9 30.4 + - - +
386A GLN* 5.1 8.9 + - - +
409A PRO* 4.0 15.0 - - + +
411A TRP* 3.5 19.7 + - + -
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Residues in contact with TYR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG 3.0 18.4 + - - +
360A PHE 3.7 2.7 - - - +
362A GLU* 1.3 74.0 - - - +
364A ALA* 1.3 60.1 + - + +
366A PHE* 3.2 6.1 + - - +
367A MET* 2.8 77.1 + - + +
411A TRP* 4.3 8.0 - - + -
412A LEU* 3.9 20.2 - - + -
495A LEU 4.6 1.0 + - - -
498A TRP* 3.8 25.4 - + + +
499A ALA* 3.6 22.3 + - - +
502A TYR* 3.3 39.3 - + + -
503A ASP* 3.8 25.7 + - + +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PHE 2.9 18.8 + - - +
361A GLY* 3.6 6.1 - - - +
363A TYR* 1.3 80.6 - - + +
365A ARG* 1.3 57.2 + - - +
367A MET* 3.4 3.9 + - - +
368A ALA* 2.9 31.1 + - - +
218B SER* 4.7 6.3 - - - +
222B ASN* 3.6 28.3 - - + +
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Residues in contact with ARG 365 (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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361A GLY 3.0 23.2 + - - +
362A GLU* 3.7 11.7 - - - +
363A TYR 3.3 0.2 - - - -
364A ALA* 1.3 76.0 - - - +
366A PHE* 1.3 60.4 + - - +
368A ALA* 3.5 10.2 + - - +
369A ASP* 3.1 44.8 + - - +
226B GLU* 4.6 17.2 + - - -
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Residues in contact with PHE 366 (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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362A GLU 2.9 17.9 + - - +
363A TYR* 3.6 2.9 - - - +
365A ARG* 1.3 76.1 - - - +
367A MET* 1.3 77.8 + - + +
369A ASP* 3.4 7.0 + - - +
370A LEU* 2.9 40.4 + - + +
383A VAL* 3.7 13.9 - - + -
406A VAL* 3.6 12.6 - - + -
407A MET 3.6 20.6 - - - +
408A LYS* 3.7 21.8 - - + -
409A PRO* 3.9 14.8 - - + -
412A LEU* 3.6 20.6 - - + -
490A PHE* 3.8 24.7 - + - -
498A TRP* 3.8 20.4 - + - -
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Residues in contact with MET 367 (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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363A TYR* 2.8 66.8 + - + +
364A ALA* 4.0 3.6 - - - +
366A PHE* 1.3 89.3 - - + +
368A ALA* 1.4 56.2 + - - +
370A LEU* 3.7 11.8 - - - -
371A LYS* 2.8 35.0 + - - +
478A VAL* 3.7 32.8 - - + +
495A LEU* 4.6 16.8 - - + +
498A TRP* 5.0 1.8 - - - -
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA 2.9 18.3 + - - +
365A ARG* 3.7 13.5 - - - +
366A PHE 3.4 0.2 - - - -
367A MET* 1.4 73.7 - - - +
369A ASP* 1.4 55.6 + - - +
371A LYS* 3.4 6.3 + - - +
372A GLU* 2.9 38.6 + - - +
219B ARG* 4.8 16.2 - - - +
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Residues in contact with ASP 369 (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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365A ARG* 3.1 36.3 + - - +
366A PHE* 3.6 6.0 - - - +
368A ALA* 1.4 74.2 - - - +
370A LEU* 1.4 56.1 + - - +
372A GLU* 3.6 6.9 - - - +
373A ALA* 2.9 35.7 + - - +
406A VAL* 3.8 20.3 - - + +
407A MET 5.4 1.9 + - - +
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 2.9 41.8 + - + +
367A MET* 3.7 17.3 - - - +
369A ASP* 1.4 73.6 - - - +
371A LYS* 1.3 59.7 + - - +
373A ALA* 3.5 0.9 + - - +
374A GLN* 3.0 51.0 + - - +
381A VAL* 4.1 21.5 - - + -
383A VAL* 4.1 16.8 - - + -
406A VAL* 4.0 7.5 - - + +
478A VAL* 3.7 27.6 - - + -
489A GLY* 5.5 3.6 - - - -
490A PHE* 4.5 14.4 - - + -
495A LEU* 4.8 2.0 - - + -
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Residues in contact with LYS 371 (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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367A MET 2.8 21.0 + - - +
368A ALA* 3.7 6.1 - - - +
370A LEU* 1.3 72.5 - - - +
372A GLU* 1.4 63.0 + - - +
374A GLN* 3.3 7.2 + - - +
375A GLN* 3.1 57.9 + - + +
478A VAL* 3.7 32.2 - - + +
215B GLN* 3.7 32.6 + - + +
219B ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 372 (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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368A ALA 2.9 22.8 + - - +
369A ASP* 3.6 8.1 - - - +
371A LYS* 1.4 70.3 - - - +
373A ALA* 1.3 56.8 + - - +
375A GLN* 3.3 13.7 + - - +
376A SER* 3.0 42.7 + - - -
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Residues in contact with ALA 373 (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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369A ASP 2.9 21.5 + - - +
370A LEU 3.9 1.1 - - - +
371A LYS 3.4 0.2 - - - -
372A GLU* 1.3 72.9 - - - +
374A GLN* 1.3 56.5 + - - +
376A SER* 4.6 0.2 - - - -
377A TYR* 2.9 53.5 + - + +
381A VAL* 3.5 29.4 - - + +
404A GLY* 4.8 3.8 - - - -
405A VAL 5.3 0.2 - - - +
406A VAL* 3.9 8.5 - - + -
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Residues in contact with GLN 374 (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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370A LEU* 3.0 37.9 + - + +
371A LYS* 3.3 5.7 + - + +
373A ALA* 1.3 74.3 - - - +
375A GLN* 1.3 57.6 + - + +
378A ASN* 3.0 11.3 + - - -
379A GLY* 2.8 34.8 + - - +
381A VAL* 3.7 18.0 - - + +
478A VAL* 3.8 13.1 - - - +
479A SER* 2.9 55.4 + - - +
480A ALA 5.7 0.2 - - - -
489A GLY* 4.7 12.5 - - - -
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Residues in contact with GLN 375 (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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371A LYS* 3.1 47.2 + - + +
372A GLU* 3.8 11.2 - - - +
374A GLN* 1.3 78.0 - - + +
376A SER* 1.3 60.0 + - - +
377A TYR 3.6 0.2 + - - -
378A ASN* 3.9 5.9 + - - +
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A GLU* 3.0 30.6 + - - -
373A ALA* 4.6 0.2 - - - -
375A GLN* 1.3 75.6 - - - +
377A TYR* 1.3 79.1 + - - +
378A ASN 3.6 0.6 + - - -
380A ARG* 5.4 0.3 + - - -
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Residues in contact with TYR 377 (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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373A ALA* 2.9 33.9 + - + +
376A SER* 1.3 91.1 - - - +
378A ASN* 1.3 67.8 + - - +
379A GLY 3.3 1.6 - - - -
380A ARG* 3.0 49.4 + - - +
396A GLN* 6.0 0.5 + - - -
401A PRO 3.6 19.9 + - - -
402A GLY* 3.5 20.4 - - - +
403A VAL 3.9 7.2 + - - -
404A GLY* 3.6 25.1 - - - -
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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