Contacts of the helix formed by residues 316 - 331 (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 ASP 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B SER 5.4 0.2 + - - -
314B GLU* 3.2 17.8 + - + +
315B VAL* 1.3 75.9 - - - +
317B VAL* 1.3 63.4 + - - +
318B GLU* 3.1 22.3 + - - +
319B GLN* 3.2 29.1 + - + +
320B HIS* 3.1 24.5 + - - +
357B ASP* 4.2 6.8 - - - +
358B ASN* 3.4 17.7 + - - +
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Residues in contact with VAL 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B VAL* 4.3 12.8 + - + -
316B ASP* 1.3 73.9 + - - +
318B GLU* 1.3 57.4 + - - +
320B HIS* 4.2 8.0 - - + +
321B THR* 2.6 39.3 + - - +
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Residues in contact with GLU 318 (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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316B ASP* 3.1 14.1 + - - +
317B VAL* 1.3 79.1 - - - +
319B GLN* 1.3 58.3 + - - +
321B THR* 3.0 8.8 + - - -
322B LEU* 2.9 23.2 + - - +
356B LEU* 3.6 26.1 - - + +
357B ASP* 5.0 8.5 - - - +
412B ILE* 3.4 19.6 - - + +
415B LEU* 4.0 20.8 - - - +
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Residues in contact with GLN 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASP* 3.2 28.3 + - + +
318B GLU* 1.3 77.0 - - - +
320B HIS* 1.3 63.9 + - - +
322B LEU* 3.4 3.0 + - - +
323B ALA* 3.0 28.2 + - - +
349B PHE* 3.3 38.5 + - + -
352B ALA* 3.4 10.7 - - + +
353B LEU* 2.9 50.4 + - - +
356B LEU* 3.8 14.6 - - + -
358B ASN* 3.4 19.6 - - - +
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Residues in contact with HIS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 6.2 1.1 - - + -
306B LEU* 4.1 28.0 - - + +
307B ARG* 4.6 21.9 + - - -
310B SER* 2.8 40.4 + - - +
315B VAL* 6.5 1.1 - - + -
316B ASP 3.1 16.8 + - - +
317B VAL* 4.2 7.6 - - + +
319B GLN* 1.3 80.3 - - - +
321B THR* 1.3 61.7 + - - +
323B ALA* 3.4 3.7 + - - +
324B LYS* 2.9 39.9 + - + +
349B PHE* 5.4 0.2 - - - -
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Residues in contact with THR 321 (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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317B VAL* 2.6 25.6 + - - +
318B GLU* 3.0 11.4 + - - -
320B HIS* 1.3 81.5 - - - +
322B LEU* 1.3 60.9 + - - +
324B LYS* 3.4 10.5 + - + +
325B TYR* 3.2 21.8 + - - +
404B TYR* 4.5 5.5 - - + -
409B HIS* 4.0 23.8 - - + +
410B ALA* 5.3 3.9 - - + +
412B ILE* 3.7 28.0 - - + +
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Residues in contact with LEU 322 (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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318B GLU 2.9 12.5 + - - +
319B GLN 3.8 6.3 - - - +
320B HIS 3.3 0.2 - - - -
321B THR* 1.3 73.7 - - - +
323B ALA* 1.3 65.7 + - - +
325B TYR* 3.2 13.0 + - + +
326B LEU* 3.1 36.9 + - + +
352B ALA* 3.9 19.1 - - + -
355B ILE* 4.0 21.3 - - + -
356B LEU* 3.7 35.9 - - + -
412B ILE* 3.5 23.9 - - + +
415B LEU* 5.6 2.9 - - + -
417B GLN* 3.3 27.1 - - - +
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Residues in contact with ALA 323 (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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306B LEU* 3.7 28.0 - - + -
319B GLN 3.0 17.2 + - - +
320B HIS* 3.7 4.5 - - - +
322B LEU* 1.3 76.7 - - - +
324B LYS* 1.3 64.4 + - - +
325B TYR 3.0 0.7 + - - -
326B LEU* 3.1 3.3 + - - +
327B MET* 2.9 24.9 + - - +
348B ALA* 3.9 24.9 - - - +
349B PHE* 4.1 12.8 - - + -
352B ALA* 4.1 1.5 - - + +
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Residues in contact with LYS 324 (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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220B GLN* 3.7 32.8 - - - +
224B TYR* 4.1 2.6 + - + +
303B LEU* 4.9 14.4 - - + -
306B LEU* 3.7 18.2 - - + +
307B ARG* 5.5 4.3 - - - +
320B HIS* 2.9 29.3 + - + +
321B THR* 3.5 12.8 - - + +
323B ALA* 1.3 75.3 - - - +
325B TYR* 1.3 56.9 + - - +
327B MET* 3.7 5.8 - - + +
328B GLU* 3.2 28.8 + - - +
403B LYS* 6.0 0.2 - - - +
404B TYR* 3.7 22.3 + - + +
409B HIS* 4.3 17.8 + - - +
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Residues in contact with TYR 325 (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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321B THR 3.2 10.3 + - - +
322B LEU* 3.6 22.0 - - + +
323B ALA 3.0 0.8 - - - -
324B LYS* 1.3 77.3 - - - +
326B LEU* 1.3 73.4 + - + +
328B GLU* 3.0 11.8 + - - +
329B LEU* 3.3 30.5 + - + +
387B VAL* 5.3 4.5 - - + +
390B VAL* 3.8 8.8 - - - +
391B ASN* 4.7 2.1 + - - -
400B VAL* 4.2 5.6 - - + -
401B LYS* 3.4 49.3 - - - +
404B TYR* 3.5 42.0 - + + -
412B ILE* 4.2 5.4 - - + -
413B SER* 3.5 24.9 + - - -
417B GLN* 4.1 14.9 + - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 3.1 38.6 + - + +
323B ALA 3.7 2.7 - - - +
325B TYR* 1.3 82.7 - - + +
327B MET* 1.3 61.9 + - - +
329B LEU* 3.3 15.7 + - + +
330B THR* 3.3 5.7 - - - +
348B ALA* 3.3 29.4 - - + +
351B LEU* 4.3 20.6 - - + -
352B ALA* 4.1 12.8 - - - +
355B ILE* 4.9 6.5 - - + -
383B LEU* 3.2 30.3 - - + +
387B VAL* 3.7 30.1 - - + -
417B GLN* 5.0 1.6 - - - +
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Residues in contact with MET 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B TYR* 3.3 26.4 + - + +
302B PRO* 3.6 17.7 - - + +
303B LEU* 3.6 30.5 - - + +
306B LEU* 3.6 42.2 - - + -
323B ALA 2.9 14.5 + - - +
324B LYS* 3.7 4.9 - - + +
326B LEU* 1.3 78.4 - - - +
328B GLU* 1.3 59.3 + - - +
330B THR* 2.8 29.2 + - - -
331B MET 3.9 1.2 + - - -
344B ILE* 3.6 20.0 - - + -
345B ALA* 4.1 12.8 - - - -
348B ALA* 4.0 8.9 - - + +
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Residues in contact with GLU 328 (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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210B VAL* 4.9 2.1 - - - +
213B GLN* 4.4 2.9 - - - +
220B GLN* 3.1 27.5 + - - +
224B TYR* 3.1 13.2 + - - +
324B LYS* 3.2 11.2 + - - +
325B TYR 3.0 7.4 + - - +
327B MET* 1.3 75.7 - - - +
329B LEU* 1.3 63.8 + - - +
331B MET* 3.4 40.2 + - + +
332B LEU* 3.8 4.9 - - - +
400B VAL* 4.0 17.8 - - + +
403B LYS* 2.9 29.7 + - - +
404B TYR* 2.7 35.2 + - + -
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Residues in contact with LEU 329 (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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325B TYR* 3.3 42.6 + - + +
326B LEU* 3.6 12.1 - - + +
327B MET 3.3 0.2 - - - -
328B GLU* 1.3 73.8 - - - +
330B THR* 1.3 61.2 + - + +
332B LEU* 2.9 34.1 + - + +
333B ASP 4.0 1.7 + - - -
383B LEU* 5.3 1.3 - - + +
386B ASN* 4.3 42.0 + - + +
387B VAL* 4.4 12.6 - - + +
390B VAL* 4.2 21.1 - - + -
397B HIS 5.9 0.9 - - - +
400B VAL* 3.8 22.0 - - + -
401B LYS 4.7 2.0 - - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 4.7 0.2 + - - -
224B TYR* 5.3 1.6 - - - -
302B PRO* 5.9 0.3 - - - +
326B LEU 3.3 5.6 - - - +
327B MET* 2.8 19.4 + - - +
329B LEU* 1.3 75.2 - - + +
331B MET* 1.3 65.1 + - - +
333B ASP* 3.0 21.2 + - - +
336B MET* 3.7 36.8 - - + +
344B ILE* 3.8 23.6 - - + +
383B LEU* 3.3 34.5 - - + -
386B ASN* 5.0 2.0 - - - +
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Residues in contact with MET 331 (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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202B ARG* 2.4 32.6 + - - -
206B ILE* 4.2 15.6 - - + +
210B VAL* 3.9 26.7 - - + -
223B MET* 3.8 25.1 - - + -
224B TYR* 3.6 39.5 - - + -
227B VAL* 4.0 26.5 - - + +
328B GLU* 3.4 35.4 + - + +
329B LEU 3.0 1.2 + - - -
330B THR* 1.3 82.8 + - - +
332B LEU* 1.3 53.4 + - + +
400B VAL* 4.7 1.8 - - + -
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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