Contacts of the helix formed by residues 358 - 378 (chain B) in PDB entry 1J38
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 358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B SER* 3.6 15.9 - - - +
289B MET* 3.9 8.2 - - - +
299B MET* 4.5 0.3 - - - +
356B ARG* 3.0 29.4 + - + +
357B VAL* 1.3 79.5 - - - +
359B GLN* 1.3 64.0 + - - +
360B ASP* 3.6 7.7 + - - +
361B GLN* 3.2 30.2 + - + +
362B LEU* 3.2 12.6 + - - +
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Residues in contact with GLN 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL* 3.4 23.1 - - - +
284B ASP* 3.7 9.2 - - - +
285B VAL* 2.8 51.5 - - + +
286B SER* 3.0 24.5 + - - +
289B MET* 4.4 7.6 - - - -
358B THR* 1.3 72.0 - - - +
360B ASP* 1.3 62.1 + - - +
362B LEU* 3.3 18.0 + - + +
363B PHE* 3.4 42.8 + - + -
406B SER* 6.2 0.2 - - - -
411B LEU* 4.4 3.3 - - + +
433B LEU* 4.8 6.6 - - - +
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Residues in contact with ASP 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B GLN* 4.8 9.0 - - - +
268B SER* 5.5 4.2 + - - +
269B GLU* 4.9 13.2 - - - +
356B ARG* 5.3 4.9 + - - +
358B THR* 3.3 7.2 + - - +
359B GLN* 1.3 77.8 - - - +
361B GLN* 1.3 65.2 + - + +
363B PHE* 3.1 19.4 + - - +
364B THR* 2.8 35.5 + - - -
437B ASP* 5.2 5.0 - - - +
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Residues in contact with GLN 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.8 6.3 - - + -
353B GLN* 3.4 12.3 + - - +
354B CYS 4.1 3.5 - - - +
355B THR* 3.2 28.1 + - - -
356B ARG* 3.1 57.2 + - - +
358B THR* 3.2 16.7 + - - +
360B ASP* 1.3 84.5 + - + +
362B LEU* 1.3 51.6 + - - +
364B THR* 3.0 20.6 + - - +
365B VAL* 2.7 38.5 + - - +
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 6.1 1.1 - - + -
289B MET* 3.4 29.4 - - + -
299B MET* 3.6 27.3 - - + +
302B MET* 4.8 14.4 - - + -
358B THR 3.2 11.4 + - - +
359B GLN* 3.4 14.6 - - + +
360B ASP 3.3 0.4 - - - -
361B GLN* 1.3 76.1 - - - +
363B PHE* 1.3 59.7 - - + +
365B VAL* 3.5 3.5 + - + +
366B HIS* 2.7 57.4 + - + +
405B VAL* 4.9 15.9 - - + -
411B LEU* 5.2 7.4 - - + -
414B ILE* 5.6 0.9 - - + -
416B LEU* 4.5 14.8 - - + -
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Residues in contact with PHE 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B GLN* 3.4 45.1 + - + -
360B ASP* 3.1 19.6 + - - +
362B LEU* 1.3 78.7 - - + +
364B THR* 1.3 60.8 + - - +
366B HIS 3.3 0.9 + - - -
367B HIS* 2.8 26.9 + - - +
399B ASP* 5.2 0.3 - - - +
402B SER* 2.9 33.2 + - - +
405B VAL* 3.5 35.9 - - + -
406B SER* 3.6 23.8 - - - -
411B LEU* 5.8 0.2 - - + -
437B ASP* 5.6 7.4 - - - -
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Residues in contact with THR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA* 3.9 28.3 - - + -
353B GLN* 4.2 7.4 - - - +
360B ASP* 2.8 22.6 + - - -
361B GLN* 3.3 24.2 + - - +
363B PHE* 1.3 75.3 - - - +
365B VAL* 1.3 67.0 + - - +
367B HIS* 2.9 10.8 + - + +
368B GLU* 2.8 30.4 + - - +
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Residues in contact with VAL 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.9 37.0 - - + +
300B PHE* 3.9 30.7 - - + -
303B GLY* 5.0 4.7 - - - -
353B GLN* 3.6 23.3 - - - +
355B THR* 4.6 1.1 - - + -
361B GLN 2.7 22.9 + - - +
362B LEU* 3.7 7.9 - - + +
363B PHE 3.3 0.2 - - - -
364B THR* 1.3 72.9 - - - +
366B HIS* 1.3 61.8 + - + +
368B GLU* 3.2 2.3 + - - +
369B LEU* 2.8 49.9 + - + +
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Residues in contact with HIS 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 4.6 4.0 - - + +
303B GLY* 3.4 35.6 + - - -
306B PHE* 4.3 10.8 - + + -
307B PHE* 4.5 4.1 - - + -
362B LEU* 2.7 46.6 + - + +
363B PHE 3.3 0.6 + - - -
364B THR 3.2 0.2 - - - -
365B VAL* 1.3 75.0 - - + +
367B HIS* 1.3 68.0 + - - +
369B LEU* 3.0 8.8 + - - +
370B GLY 2.7 19.8 + - - -
398B GLY* 3.4 13.2 - - - +
401B LEU* 4.5 15.9 - - + +
402B SER* 3.1 24.5 - - - +
405B VAL* 3.9 29.7 - - + +
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Residues in contact with HIS 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B PHE 2.8 14.9 + - - +
364B THR* 2.9 14.6 + - + +
366B HIS* 1.3 75.0 - - - +
368B GLU* 1.3 66.7 + - - +
370B GLY* 2.7 27.2 + - - -
371B HIS* 3.1 13.5 + + - -
394B HIS 5.4 0.3 - - - +
395B GLU* 2.8 36.0 + - + +
398B GLY* 3.8 13.1 + - - -
399B ASP* 2.7 26.5 + - - +
402B SER* 4.2 0.4 + - - -
507B TYR* 5.0 6.7 - + - -
702B ZN 2.3 33.0 - - - -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA* 3.4 24.1 - - + +
339B SER* 3.1 13.8 - - - +
340B ALA* 3.0 25.5 + - - +
351B ILE* 3.2 24.9 - - + -
353B GLN* 3.7 18.6 - - - +
364B THR* 2.8 23.7 + - - +
365B VAL 3.5 4.7 - - - +
367B HIS* 1.3 86.3 - - - +
369B LEU* 1.3 57.7 + - - +
371B HIS* 2.7 33.8 + - - +
372B ILE* 3.1 11.6 + - - +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PHE* 3.6 21.3 - - + +
303B GLY* 4.8 12.6 - - - -
304B ASP* 5.1 0.7 - - - +
307B PHE* 3.4 25.0 - - + -
315B LEU* 3.4 45.3 - - + -
319B PHE* 4.5 0.7 - - + -
351B ILE* 3.7 5.4 - - + -
365B VAL* 2.8 51.2 + - + +
366B HIS* 3.0 9.8 + - - +
368B GLU* 1.3 72.2 - - - +
370B GLY* 1.3 57.0 + - - +
372B ILE* 3.0 12.6 + - + +
373B GLN* 2.7 30.8 + - - +
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Residues in contact with GLY 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PHE* 3.9 5.1 - - - -
366B HIS 2.7 6.3 + - - -
367B HIS 2.7 12.5 + - - -
369B LEU* 1.3 79.0 - - - +
371B HIS* 1.3 60.6 + - - -
373B GLN* 3.2 3.5 + - - +
374B TYR* 3.2 18.7 + - - +
394B HIS 4.8 1.8 - - - -
397B VAL* 3.7 17.6 - - - +
398B GLY* 3.4 25.1 - - - -
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Residues in contact with HIS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 3.3 20.0 - - + -
367B HIS* 3.1 13.8 + + - -
368B GLU* 2.7 34.7 + - - +
370B GLY* 1.3 70.8 - - - +
372B ILE* 1.3 61.6 + - - +
374B TYR* 3.0 6.2 + - - +
375B PHE* 3.0 29.0 + + + -
394B HIS* 2.6 56.2 + + + -
395B GLU* 3.2 15.9 - - - -
702B ZN 2.1 36.2 - - - -
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 3.7 23.6 - - + -
319B PHE* 4.0 9.0 - - + -
340B ALA* 3.8 12.1 - - + -
349B VAL* 3.6 38.4 - - + -
350B ARG 3.9 10.8 - - - +
351B ILE* 3.6 31.9 - - + -
368B GLU 3.1 11.8 + - - +
369B LEU* 3.0 12.3 + - + +
371B HIS* 1.3 73.8 - - - +
373B GLN* 1.3 65.8 + - - +
375B PHE* 3.3 11.6 + - + +
376B LEU* 3.0 26.7 + - + +
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B PHE* 3.7 40.2 - - + -
312B LEU* 3.8 8.3 - - + +
313B THR* 3.1 52.0 - - - +
315B LEU* 5.4 3.5 - - - +
369B LEU 2.7 10.6 + - - +
370B GLY 3.2 8.7 + - - +
372B ILE* 1.3 73.3 - - - +
374B TYR* 1.3 53.4 + - - +
376B LEU* 3.5 6.9 - - - +
377B GLN* 2.7 61.7 + - + +
397B VAL* 4.5 1.1 - - + -
556B LEU* 3.9 21.1 - - + -
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Residues in contact with TYR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B GLY 3.2 7.4 + - - +
371B HIS 3.0 10.4 + - - +
373B GLN* 1.3 80.5 - - - +
375B PHE* 1.3 64.1 + - - +
377B GLN* 3.2 3.1 + - - -
378B TYR* 3.1 51.1 + + - -
388B GLY* 3.9 12.8 - - - -
389B ALA* 3.4 21.8 + - - +
393B PHE* 3.6 21.8 - - + +
394B HIS* 3.6 51.6 - + + +
397B VAL* 4.0 8.5 - - + -
555B MET* 4.9 3.9 + - - +
556B LEU* 3.4 52.8 - - + +
559B GLY* 4.9 2.7 + - - -
567B ALA* 5.5 0.3 - - - +
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Residues in contact with PHE 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B ALA* 3.5 29.2 - - + -
341B TRP 3.2 30.7 - - - -
342B ASP* 3.2 41.9 - - + +
349B VAL* 3.9 12.8 - - + -
371B HIS* 3.0 19.3 + + + -
372B ILE* 3.7 16.4 - - + +
374B TYR* 1.3 76.4 - - - +
376B LEU* 1.3 63.6 + - - +
378B TYR* 3.3 20.3 - - - -
379B GLN* 3.2 25.2 + - + +
386B ARG* 5.1 0.7 + - - -
394B HIS* 3.3 28.5 - + - -
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR* 3.6 39.3 - - + +
314B LYS 3.8 12.8 - - - +
315B LEU* 4.7 1.8 - - + -
316B PRO* 4.0 23.3 - - + -
347B ASP* 4.4 6.7 - - - +
349B VAL* 4.0 19.1 - - + -
372B ILE* 3.0 26.3 + - + +
373B GLN* 3.5 13.5 - - - +
375B PHE* 1.3 80.3 - - - +
377B GLN* 1.3 64.9 + - - +
378B TYR 3.1 0.9 + - - -
379B GLN* 3.5 36.0 + - - +
380B HIS* 5.0 1.2 - - - -
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Residues in contact with GLN 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.8 13.5 - - - +
313B THR* 3.4 12.1 + - - -
373B GLN* 2.7 46.3 + - - +
374B TYR 3.2 4.0 + - - +
376B LEU* 1.3 74.5 - - - +
378B TYR* 1.3 57.4 + - - +
380B HIS* 3.1 18.2 + - - -
553B HIS* 3.1 38.9 + - - +
556B LEU* 3.5 36.1 - - + -
557B SER* 3.5 20.0 - - - +
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Residues in contact with TYR 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ASP* 3.8 7.2 - - - -
374B TYR* 3.1 44.0 + + - -
375B PHE* 3.3 26.9 - - - -
377B GLN* 1.3 78.5 - - - +
379B GLN* 1.3 66.4 + - - +
380B HIS* 3.3 8.5 - - - -
381B GLN* 3.0 24.8 + - + +
386B ARG* 3.4 32.4 + - + +
387B THR* 3.1 29.2 - - - -
394B HIS* 2.9 23.9 + - - -
556B LEU 3.6 8.3 - - - +
557B SER 3.9 9.4 - - - +
559B GLY* 3.5 19.7 - - - -
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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