Contacts of the helix formed by residues 340 - 356 (chain B) in PDB entry 2JGZ
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 PRO 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU* 3.5 31.4 - - + +
183B GLU* 6.2 1.1 - - + -
299B ARG* 4.5 3.4 - - - +
338B HIS 3.5 7.8 - - - +
339B PHE* 1.3 85.9 - - + +
341B PRO* 1.3 74.1 - - + +
342B SER* 4.3 1.1 - - - +
343B GLN* 2.8 39.3 + - + +
344B ILE* 3.1 10.1 + - - +
371B TYR* 4.4 5.2 - - - +
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Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 3.4 18.4 - - + +
299B ARG* 3.4 29.4 - - - +
300B PRO 3.4 22.7 - - - +
301B LEU 4.0 2.5 - - - -
302B PRO* 3.7 35.6 - - + +
305B PHE* 4.0 7.9 - - + -
339B PHE 3.7 2.0 - - - +
340B PRO* 1.3 82.4 - - + +
342B SER* 1.3 62.1 - - - +
344B ILE* 3.2 9.0 + - + +
345B ALA* 3.0 23.0 + - - +
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Residues in contact with SER 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 3.3 16.0 + - - -
182B GLU* 2.3 33.0 + - - -
305B PHE* 3.7 35.3 - - - +
341B PRO* 1.3 80.0 - - - +
343B GLN* 1.3 57.7 + - - +
345B ALA* 3.4 1.4 + - - +
346B ALA* 2.9 29.8 + - - +
371B TYR* 2.8 20.7 + - - -
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Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PHE* 3.6 14.7 - - + -
340B PRO* 2.8 32.5 + - + +
342B SER* 1.3 77.6 + - - +
344B ILE* 1.3 65.4 - - - +
345B ALA 3.2 0.2 - - - -
346B ALA* 4.6 0.9 - - - +
347B GLY* 3.1 19.4 + - - -
371B TYR* 3.6 30.8 + - + +
375B SER* 3.1 28.8 + - - -
376B LEU* 4.0 9.0 - - + +
378B PRO* 4.5 3.4 - - - +
379B VAL* 3.4 29.6 - - + +
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO* 4.3 10.5 - - + -
327B MET* 3.6 24.5 - - + -
330B THR* 3.8 25.6 - - + +
336B MET* 3.9 33.0 - - + +
339B PHE* 3.7 30.5 - - + +
340B PRO 3.1 12.9 + - - +
341B PRO* 3.4 11.0 - - + +
343B GLN* 1.3 74.9 - - - +
345B ALA* 1.3 57.5 + - - +
347B GLY* 3.4 1.2 + - - -
348B ALA* 3.0 28.8 + - - +
379B VAL* 4.1 7.4 - - + +
383B LEU* 4.8 0.7 - - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PRO 3.6 22.2 - - - +
305B PHE* 3.7 16.4 - - + -
306B LEU* 3.7 15.7 - - - +
309B ALA* 5.8 1.3 - - - -
327B MET* 4.1 13.2 - - - -
341B PRO 3.0 15.2 + - - +
342B SER 3.7 4.3 - - - +
344B ILE* 1.3 73.9 - - - +
346B ALA* 1.3 67.4 + - - +
347B GLY 3.1 0.9 - - - -
348B ALA* 3.4 1.3 + - - -
349B PHE* 3.1 24.4 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE 5.7 0.2 + - - -
309B ALA* 5.7 0.2 - - - -
342B SER 2.9 17.7 + - - +
345B ALA* 1.3 75.1 - - - +
347B GLY* 1.3 57.9 + - - +
349B PHE* 3.2 3.7 + - - +
350B CYS* 2.8 31.0 + - - +
361B TRP* 3.8 22.5 - - + -
369B LEU* 4.3 13.3 - - + +
371B TYR* 3.8 13.9 - - + -
376B LEU* 3.7 22.2 - - + -
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Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLN 3.1 20.2 + - - -
344B ILE 3.7 1.1 - - - -
346B ALA* 1.3 76.7 - - - +
348B ALA* 1.3 55.7 + - - +
350B CYS* 3.1 7.0 + - - +
351B LEU* 2.9 31.2 + - - +
376B LEU* 4.0 14.1 - - - +
379B VAL* 4.2 9.9 - - - -
380B MET* 3.6 6.2 - - - +
383B LEU* 3.7 6.7 - - - -
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA* 3.9 16.0 - - + +
326B LEU* 3.3 25.0 - - + +
327B MET* 4.0 14.8 - - + +
344B ILE 3.0 16.9 + - - +
345B ALA* 4.1 3.1 - - - +
347B GLY* 1.3 75.3 - - - +
349B PHE* 1.3 57.7 + - - +
352B ALA* 3.1 26.7 + - - +
383B LEU* 3.5 19.4 - - + +
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Residues in contact with PHE 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B LEU* 4.1 13.5 - - + -
309B ALA* 3.8 35.4 - - + -
310B SER* 3.1 35.7 - - - -
312B ILE 4.8 5.2 - - - -
313B GLY 5.5 0.7 - - - -
314B GLU 6.0 2.0 - - - -
319B GLN* 3.3 33.7 + - + -
320B HIS* 5.4 0.4 - - - -
323B ALA* 4.1 10.5 - - + +
345B ALA 3.1 17.4 + - - +
346B ALA* 3.6 4.0 - - - +
348B ALA* 1.3 78.6 - - - +
350B CYS* 1.3 58.2 + - - +
352B ALA* 3.9 1.1 - - - -
353B LEU* 3.2 35.4 + - + +
361B TRP* 4.5 9.4 - + - -
365B LEU* 4.1 18.4 - - + -
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Residues in contact with CYS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 2.8 17.0 + - - +
347B GLY 3.1 5.1 + - - +
349B PHE* 1.3 77.6 - - - +
351B LEU* 1.3 62.9 + - - +
353B LEU* 3.3 8.7 - - - +
354B LYS* 3.3 22.5 + - - +
361B TRP* 3.7 32.3 - - + -
373B GLU* 4.4 17.9 - - - -
376B LEU* 3.8 13.5 - - + -
380B MET* 3.5 24.5 - - - -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 4.3 15.5 - - + -
347B GLY 2.9 16.4 + - - +
348B ALA 4.3 2.9 - - - +
350B CYS* 1.3 74.4 - - - +
352B ALA* 1.3 60.5 + - - +
354B LYS* 3.3 8.9 + - + +
355B ILE* 3.0 48.4 + - + +
380B MET* 3.7 28.5 - - + +
383B LEU* 3.5 34.1 - - + -
384B ALA* 4.0 9.6 - - + +
387B VAL* 5.5 0.7 - - + -
421B ALA* 6.1 2.7 - - + -
422B LEU* 5.3 4.0 - - + -
424B GLN* 4.1 21.1 - - - +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLN* 3.4 33.4 - - + +
322B LEU* 3.9 24.0 - - + -
323B ALA 4.1 6.7 - - - +
326B LEU* 4.1 2.2 - - + +
348B ALA 3.1 20.5 + - - +
349B PHE* 3.9 5.6 - - - +
350B CYS 3.3 0.2 - - - -
351B LEU* 1.3 75.7 - - - +
353B LEU* 1.3 66.5 + - - +
355B ILE 3.3 0.2 + - - -
356B LEU* 3.1 25.6 + - - +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLN* 2.9 39.6 + - - +
349B PHE* 3.2 21.1 + - + +
350B CYS* 3.3 11.7 - - - +
352B ALA* 1.3 78.4 - - - +
354B LYS* 1.3 63.3 + - + +
356B LEU 3.4 3.6 - - - +
358B ASN* 3.2 34.9 + - + +
359B GLY 3.9 21.4 + - - +
360B GLU 3.9 23.1 - - - +
361B TRP* 4.2 16.6 - - + +
365B LEU* 4.1 19.1 - - + -
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Residues in contact with LYS 354 (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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350B CYS* 3.3 11.2 + - - +
351B LEU* 3.3 15.3 + - + +
352B ALA 3.2 0.8 - - - -
353B LEU* 1.3 80.9 - - + +
355B ILE* 1.3 62.9 + - + +
356B LEU 3.2 9.4 - - - +
357B ASP 4.8 0.5 - - - +
359B GLY 5.4 2.7 - - - +
373B GLU* 3.9 21.9 + - - +
377B LEU* 6.2 2.2 - - - +
380B MET* 3.5 30.7 - - + +
421B ALA* 5.7 11.2 - - + +
424B GLN* 5.8 5.1 + - - +
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.0 22.0 - - + -
326B LEU* 4.9 9.9 - - + -
351B LEU* 3.0 46.3 + - + +
352B ALA 4.1 1.8 - - - +
354B LYS* 1.3 76.1 - - + +
356B LEU* 1.3 65.6 + - + +
387B VAL* 5.8 0.9 - - + -
415B LEU* 6.4 0.7 - - + -
416B PRO 4.8 4.9 - - - +
417B GLN* 4.0 29.2 - - + +
419B ASN* 4.2 16.8 - - - +
421B ALA* 5.4 3.8 - - + -
422B LEU* 4.1 27.4 - - + -
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU* 3.6 28.3 - - + +
319B GLN* 3.8 32.3 - - + -
322B LEU* 3.7 29.2 - - + -
352B ALA 3.1 10.1 + - - +
353B LEU 3.4 0.2 - - - +
354B LYS 3.2 12.8 - - - +
355B ILE* 1.3 87.6 - - + +
357B ASP* 1.3 76.5 + - - +
358B ASN* 3.2 11.8 + - - +
412B ILE* 5.9 0.4 - - + -
415B LEU* 4.4 23.3 - - + -
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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