Contacts of the helix formed by residues 360 - 382 (chain G) in PDB entry 2QJK
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 ARG 360 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LYS* 2.7 31.1 - - - +
350G ASP* 3.1 19.2 + - - -
352G SER* 3.2 27.1 + - - +
354G VAL* 4.0 18.8 - - + -
355G ARG 5.1 0.2 + - - -
356G SER 3.9 16.8 - - - +
357G GLY* 3.3 13.0 + - - +
358G ARG 3.5 1.2 + - - -
359G TYR* 1.3 84.5 - - - +
361G PRO* 1.3 59.8 - - - +
363G PHE* 3.2 35.8 + - + +
364G LYS* 2.9 32.7 + - - +
408G LEU* 4.6 3.8 + - - +
411G LEU* 4.2 22.0 - - - +
412G GLY 4.8 0.4 - - - +
415G GLU* 2.9 28.3 + - - +
417G PRO* 5.3 0.9 - - + -
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Residues in contact with PRO 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359G TYR 3.8 6.3 - - - +
360G ARG* 1.3 85.7 - - - +
362G MET* 1.3 62.4 + - + +
364G LYS* 3.8 22.0 - - + +
365G ILE* 4.0 11.1 + - - +
415G GLU* 3.3 10.3 - - - +
416G LYS 4.0 15.9 - - - +
418G VAL* 4.0 22.7 - - + -
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Residues in contact with MET 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G PRO* 1.3 69.8 - - + +
363G PHE* 1.3 67.2 + - - +
365G ILE* 2.9 22.0 + - - +
366G TYR* 3.5 26.9 + - + +
411G LEU* 3.6 32.5 - - + -
414G ILE* 4.1 20.9 - - + -
415G GLU* 2.4 39.5 + - + +
416G LYS 5.2 0.9 - - - +
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Residues in contact with PHE 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU 3.6 20.2 - - - -
117G TYR* 4.3 15.5 - + - -
121G TYR* 4.4 2.2 - - - -
122G LYS* 5.8 0.2 - - - -
350G ASP* 4.1 4.3 - - - -
357G GLY* 4.4 14.1 - - - -
360G ARG* 3.2 61.2 - - + +
362G MET* 1.3 74.8 - - - +
364G LYS* 1.3 72.6 + - + +
365G ILE 2.8 2.3 + - - -
366G TYR* 2.9 14.8 + - - +
367G PHE* 2.9 34.1 + + + -
403G TYR* 3.3 26.4 - + - -
408G LEU* 3.6 15.9 - - + -
411G LEU* 3.5 13.3 - - + +
415G GLU* 3.0 5.7 + - - +
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Residues in contact with LYS 364 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TYR* 3.7 18.6 - - + +
357G GLY 3.3 16.6 - - - +
358G ARG* 2.5 41.2 + - - +
360G ARG 2.9 22.0 + - - +
361G PRO* 3.8 14.0 - - + +
363G PHE* 1.3 79.6 - - - +
365G ILE* 1.3 67.5 + - + +
367G PHE* 3.3 2.6 + - - +
368G TRP* 3.0 41.1 + - + +
504G LOP 5.3 1.6 + - - -
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Residues in contact with ILE 365 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G PRO 4.0 12.3 - - - +
362G MET* 2.9 12.9 + - - +
363G PHE 2.8 4.0 + - - -
364G LYS* 1.3 77.5 - - + +
366G TYR* 1.3 74.2 + - + +
368G TRP* 3.5 6.5 + - + +
369G LEU* 3.2 36.3 + - + +
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Residues in contact with TYR 366 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362G MET* 3.6 32.1 - - + +
363G PHE* 2.9 6.8 + - - +
365G ILE* 1.3 81.6 - - + +
367G PHE* 1.3 66.5 + - - +
369G LEU* 3.2 12.2 + - + -
370G LEU* 2.9 16.3 + - - +
399G TYR* 2.7 33.0 + + - +
403G TYR* 3.9 11.0 - - + -
407G ILE* 3.3 45.1 - - + -
411G LEU* 3.7 20.6 - - + -
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Residues in contact with PHE 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G PHE* 3.7 24.5 - + - -
116G LEU* 4.0 8.7 - - + -
117G TYR* 3.3 53.8 - + + -
363G PHE* 2.9 40.6 + + + +
364G LYS* 3.5 7.0 - - - +
366G TYR* 1.3 76.4 - - - +
368G TRP* 1.3 88.3 + + - +
370G LEU* 2.8 29.2 + - + +
371G ALA* 3.0 7.4 + - + +
403G TYR* 3.9 18.9 - + - -
504G LOP 3.6 21.3 - - + -
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Residues in contact with TRP 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G TYR* 4.2 12.8 + + - -
364G LYS* 3.0 36.0 + - + +
365G ILE* 4.0 7.0 - - + +
367G PHE* 1.3 94.0 - + - +
369G LEU* 1.3 56.3 + - - +
371G ALA* 3.3 16.0 + - + +
372G ALA* 2.8 28.9 + - - +
504G LOP 3.7 75.4 - - + -
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Residues in contact with LEU 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365G ILE* 3.2 28.3 + - + +
366G TYR* 3.4 16.8 - - + +
367G PHE 3.1 0.2 - - - -
368G TRP* 1.3 73.4 - - - +
370G LEU* 1.3 57.3 + - - +
372G ALA* 3.4 9.5 - - + +
373G ASP* 2.6 37.2 + - - +
399G TYR* 3.3 36.1 - - + +
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Residues in contact with LEU 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G PHE* 4.1 20.9 - - + -
116G LEU* 4.3 7.4 - - + -
366G TYR 2.9 12.5 + - - +
367G PHE* 2.8 18.3 + - + +
369G LEU* 1.3 76.8 - - - +
371G ALA* 1.3 55.1 + - - +
373G ASP* 3.1 5.1 + - - +
374G PHE* 2.8 28.6 + - - +
399G TYR* 3.6 12.1 - - + -
400G TRP* 3.5 34.1 - - + -
403G TYR* 3.3 51.4 - - + +
404G PHE* 3.9 13.7 - - + -
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Residues in contact with ALA 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G PHE* 4.2 17.4 - - + -
367G PHE* 3.0 9.6 + - + +
368G TRP* 3.5 26.5 - - + +
370G LEU* 1.3 76.5 - - - +
372G ALA* 1.3 66.3 + - - +
374G PHE* 3.0 13.3 + - - +
375G VAL* 3.0 18.9 + - + +
504G LOP 4.3 24.6 - - + +
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Residues in contact with ALA 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368G TRP 2.8 20.2 + - - +
369G LEU* 3.4 12.8 - - + +
371G ALA* 1.3 74.3 - - - +
373G ASP* 1.3 58.0 + - - +
375G VAL* 3.2 9.6 + - - +
376G ILE* 2.8 41.8 + - + +
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Residues in contact with ASP 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369G LEU 2.6 17.5 + - - +
370G LEU* 3.1 13.9 - - + +
372G ALA* 1.3 72.2 - - - +
374G PHE* 1.3 54.4 + - - +
376G ILE* 2.8 14.4 + - - +
377G LEU* 2.5 45.8 + - - +
396G ALA* 2.7 50.8 - - - +
399G TYR* 3.8 13.2 - - + +
400G TRP* 3.6 16.7 + - + +
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Residues in contact with PHE 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G TYR* 3.7 53.6 - + - -
113G PHE* 3.7 28.0 - + + -
300G PRO* 4.0 25.6 - - + -
301G PHE* 4.7 9.0 - + - -
370G LEU 2.8 14.8 + - - +
371G ALA 3.4 8.5 - - - +
373G ASP* 1.3 71.0 - - - +
375G VAL* 1.3 61.4 + - - +
377G LEU* 3.5 11.1 - - + +
378G THR* 2.8 34.4 + - - -
400G TRP* 3.9 26.0 - + + -
504G LOP 3.8 30.3 - - + -
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Residues in contact with VAL 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371G ALA 3.0 17.1 + - - +
372G ALA* 3.3 10.1 - - - +
374G PHE* 1.3 77.0 - - - +
376G ILE* 1.3 66.1 + - + +
378G THR* 3.0 9.3 + - - -
379G TRP* 2.8 23.7 + - + +
504G LOP 4.1 30.1 - - + -
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Residues in contact with ILE 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372G ALA* 2.8 36.1 + - + +
373G ASP* 3.3 14.1 - - - +
375G VAL* 1.3 75.0 - - + +
377G LEU* 1.3 65.0 + - - +
379G TRP* 2.9 19.4 + - + +
380G VAL* 2.8 25.4 + - + +
392G ILE* 4.0 26.2 - - + -
396G ALA* 4.9 7.2 - - + -
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Residues in contact with LEU 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G PRO* 3.6 16.1 - - + +
303G ALA* 3.4 33.7 - - + +
304G ILE* 3.5 36.3 - - + +
373G ASP* 2.5 37.0 + - - +
374G PHE* 3.5 9.9 - - + +
376G ILE* 1.3 73.1 - - - +
378G THR* 1.3 62.4 + - - +
380G VAL* 2.7 24.6 - - + +
381G GLY 3.2 5.0 + - - -
393G SER* 4.9 1.1 - - - +
396G ALA* 3.9 22.9 - - + +
397G SER* 4.4 4.0 - - - +
400G TRP* 4.3 16.4 - - + -
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Residues in contact with THR 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296G TRP* 4.0 19.5 - - + +
299G LEU* 3.6 37.2 - - + +
300G PRO* 3.4 23.6 - - + +
374G PHE* 2.8 21.9 + - - -
375G VAL* 3.0 10.9 + - - -
377G LEU* 1.3 77.2 - - - +
379G TRP* 1.3 66.5 + - - +
381G GLY 3.0 12.3 + - - -
504G LOP 5.1 8.0 - - + +
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Residues in contact with TRP 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375G VAL* 2.8 18.3 + - + +
376G ILE* 3.2 21.3 - - + +
378G THR* 1.3 74.2 - - - +
380G VAL* 1.3 92.6 + - + +
382G ALA* 3.4 10.3 - - + +
383G GLN* 3.2 31.2 + - + +
389G TYR* 3.6 26.9 - + - -
392G ILE* 4.3 12.8 - - + -
114H MET* 3.2 65.8 + - + +
115H GLY 3.8 12.1 + - - -
116H THR* 3.8 15.6 + - + -
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Residues in contact with VAL 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303G ALA* 4.1 9.6 - - + -
306G ARG* 2.8 14.9 + - - +
376G ILE* 2.8 13.7 + - + +
377G LEU* 2.7 33.4 - - + +
379G TRP* 1.3 96.5 - - + +
381G GLY* 1.3 52.0 + - - +
382G ALA 2.9 5.6 - - - -
383G GLN* 2.6 32.1 + - + +
389G TYR* 4.8 8.0 - - + +
392G ILE* 3.8 26.9 - - + -
393G SER* 4.6 18.4 - - - +
396G ALA* 5.6 0.4 - - + -
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Residues in contact with GLY 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293G VAL* 4.3 4.5 - - - +
299G LEU* 4.0 12.8 - - - +
302G TYR* 3.1 37.8 - - - -
303G ALA* 4.2 9.2 - - - -
306G ARG* 3.6 10.7 + - - -
377G LEU 3.2 7.6 + - - -
378G THR 3.0 9.4 + - - -
380G VAL* 1.3 77.5 - - - +
382G ALA* 1.3 58.1 + - - +
383G GLN 3.5 1.4 + - - +
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Residues in contact with ALA 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G VAL* 4.5 18.5 - - + +
299G LEU* 4.2 16.8 - - + +
378G THR 3.7 1.8 + - - -
379G TRP* 3.4 14.6 + - - +
380G VAL 2.9 0.6 - - - -
381G GLY* 1.3 77.9 - - - +
383G GLN* 1.3 68.7 + - - +
115H GLY* 4.5 7.2 - - - +
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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