Contacts of the helix formed by residues 316 - 336 (chain B) in PDB entry 5JJA
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 GLU 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B SER* 3.8 28.6 + - - +
282B THR* 5.5 0.4 + - - -
314B VAL 3.8 4.4 + - - +
315B ILE* 1.3 80.1 - - - +
317B PRO* 1.3 80.3 - - + +
318B SER* 4.4 7.6 - - - +
319B GLU* 3.0 20.1 + - + +
320B PHE* 2.9 19.2 + - - +
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Residues in contact with PRO 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU* 1.3 93.6 - - + +
318B SER* 1.3 62.9 + - - +
320B PHE* 3.0 13.3 + - + +
321B VAL* 3.1 19.7 + - + +
354B TYR* 3.8 17.0 - - + +
358B LEU* 4.0 24.2 - - + -
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLU* 4.5 5.9 - - - +
317B PRO* 1.3 79.0 - - - +
319B GLU* 1.3 67.7 + - - +
321B VAL* 3.2 24.9 - - - +
322B LYS* 3.7 15.4 - - - +
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Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B SER* 3.4 31.4 + - - +
280B THR* 3.9 17.4 - - - +
282B THR* 3.8 25.5 + - + +
283B GLU* 4.3 8.1 + - - +
315B ILE* 4.2 5.2 - - + -
316B GLU* 3.0 23.1 + - + +
318B SER* 1.3 79.2 + - - +
320B PHE* 1.3 68.5 + - - +
321B VAL 3.2 0.2 - - - -
322B LYS* 3.2 46.7 + - - +
323B ILE* 3.6 11.3 + - - +
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.9 24.7 - - + -
315B ILE* 3.8 16.5 - - + +
316B GLU 2.9 12.9 + - - +
317B PRO* 3.3 12.6 - - + +
319B GLU* 1.3 76.9 - - - +
321B VAL* 1.3 61.8 + - + +
323B ILE* 3.2 6.7 + - + +
324B MET* 2.9 54.3 + - + +
327B LEU* 5.2 0.9 - - + -
328B PHE* 3.5 35.4 - + - -
355B ILE* 5.4 2.0 - - + -
358B LEU* 3.7 51.6 - - + -
359B ILE* 4.3 0.9 - - + -
362B ASN* 3.8 11.2 - - - -
366B ILE* 3.9 7.6 - - + -
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Residues in contact with VAL 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B PRO* 3.1 12.2 + - + +
318B SER* 3.2 24.9 - - - +
320B PHE* 1.3 77.3 - - + +
322B LYS* 1.3 65.6 + - + +
323B ILE 3.4 0.9 + - - -
324B MET* 3.6 27.8 - - + +
325B GLU* 5.2 1.2 + - - +
362B ASN* 3.6 33.4 - - - +
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU* 4.0 29.2 + - + +
318B SER* 3.7 16.6 - - - +
319B GLU* 3.2 38.1 + - - +
320B PHE 3.2 0.8 - - - -
321B VAL* 1.3 81.4 - - + +
323B ILE* 1.3 67.5 + - + +
324B MET 3.7 0.2 - - - -
326B PRO* 4.9 5.7 - - - +
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Residues in contact with ILE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 4.8 2.9 - - + -
283B GLU* 3.9 30.7 - - + +
286B VAL* 3.9 25.4 - - + -
287B MET* 3.8 25.4 - - + -
290B LEU* 5.1 0.2 - - - +
315B ILE* 4.2 17.5 - - + -
319B GLU 3.6 12.3 - - - +
320B PHE* 3.2 11.4 + - + +
322B LYS* 1.3 82.7 - - + +
324B MET* 1.3 69.4 + - - +
325B GLU 3.3 3.0 + - - -
326B PRO* 3.4 9.1 - - - +
327B LEU* 3.1 45.9 + - + +
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Residues in contact with MET 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 2.9 46.5 + - + +
321B VAL* 3.6 30.7 - - + +
322B LYS 3.7 0.6 - - - -
323B ILE* 1.3 81.7 - - - +
325B GLU* 1.3 73.5 + - + +
327B LEU* 4.2 3.6 - - - -
328B PHE* 3.0 36.0 + - + +
362B ASN* 3.6 30.5 - - - +
365B LYS* 4.1 28.0 - - + -
366B ILE* 4.0 11.3 - - + +
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL 5.2 0.9 + - - +
322B LYS 5.4 0.4 + - - -
324B MET* 1.3 88.2 - - + +
326B PRO* 1.3 75.3 - - + +
328B PHE 4.0 0.3 - - - -
329B ARG* 3.1 50.5 + - - +
365B LYS* 3.9 30.5 - - + +
366B ILE* 6.4 0.4 - - + -
369B ILE* 4.2 19.0 - - + +
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Residues in contact with PRO 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B MET* 4.0 30.3 - - + -
290B LEU* 3.8 20.0 - - + +
322B LYS 4.9 4.3 - - - +
323B ILE* 3.4 17.0 - - - +
325B GLU* 1.3 94.5 - - + +
327B LEU* 1.3 59.8 + - - +
329B ARG* 3.5 22.5 + - - +
330B GLN* 3.3 18.5 + - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 4.7 3.1 - - + -
290B LEU* 3.8 14.1 - - + +
308B LEU* 3.9 39.6 - - + +
312B LEU* 3.8 34.1 - - + -
320B PHE* 5.2 0.7 - - + -
323B ILE* 3.1 34.4 + - + +
324B MET* 3.7 4.5 - - - +
325B GLU 3.2 0.2 - - - -
326B PRO* 1.3 77.8 - - - +
328B PHE* 1.3 87.8 + - + +
330B GLN* 3.1 7.1 + - - +
331B LEU* 2.9 27.9 + - + -
349B TYR* 5.0 2.7 - - + -
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 5.5 2.2 - - + -
320B PHE* 3.5 33.0 - + - -
324B MET* 3.0 30.2 + - + +
325B GLU 4.3 0.9 - - - +
327B LEU* 1.3 85.9 - - + +
329B ARG* 1.3 60.9 + - - +
331B LEU* 3.7 31.4 - - + -
332B ALA* 2.9 31.2 + - - +
349B TYR* 5.4 0.7 - + - -
350B TRP* 5.9 0.9 - + - -
355B ILE* 4.7 8.1 - - + -
359B ILE* 3.5 36.6 - - + -
366B ILE* 3.8 25.6 - - + -
369B ILE* 3.6 17.1 - - + +
370B MET* 3.6 16.0 - - + +
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Residues in contact with ARG 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 GLU* 3.1 41.5 + - - +
326B PRO* 3.7 32.8 - - - +
327B LEU 3.3 0.2 - - - -
328B PHE* 1.3 77.7 - - - +
330B GLN* 1.3 59.4 + - - +
332B ALA* 3.7 4.1 + - - +
333B LYS* 3.4 35.6 + - - +
369B ILE* 3.6 27.1 - - + +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.9 23.5 + - + +
293B TRP* 3.3 63.1 + - + +
294B PRO 4.9 3.5 + - - +
295B LYS* 5.3 4.0 - - - +
301B GLU* 3.8 2.8 - - - +
308B LEU* 5.9 1.3 - - + -
326B PRO 3.3 7.2 + - - +
327B LEU 3.1 9.0 + - - +
329B ARG* 1.3 74.2 - - - +
331B LEU* 1.3 65.6 + - - +
333B LYS* 3.2 30.0 + - - +
334B CYS* 3.1 24.6 + - - -
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Residues in contact with LEU 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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293B TRP* 6.4 0.2 - - - -
305B LEU* 3.7 21.5 - - + -
308B LEU* 5.4 3.1 - - + +
327B LEU* 2.9 17.8 + - + +
328B PHE* 3.3 37.7 + - + +
330B GLN* 1.3 78.2 - - - +
332B ALA* 1.3 57.3 + - - +
334B CYS* 3.2 5.5 + - - +
335B VAL* 2.9 27.9 + - + +
346B ALA* 3.9 19.5 - - + +
349B TYR* 3.7 46.7 - - + -
350B TRP* 5.6 3.6 - - + +
370B MET* 3.9 14.6 - - + -
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Residues in contact with ALA 332 (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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328B PHE 2.9 17.2 + - - +
329B ARG* 3.9 6.7 - - - +
330B GLN 3.2 0.2 - - - -
331B LEU* 1.3 73.9 - - - +
333B LYS* 1.3 64.6 + - + +
335B VAL* 3.4 5.7 + - - +
336B SER* 3.3 22.0 + - - -
369B ILE* 3.8 22.2 - - + +
370B MET* 4.0 19.0 - - + +
372B PRO* 6.2 0.2 - - + -
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Residues in contact with LYS 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B HIS* 3.4 18.6 - - + -
301B GLU* 6.0 0.2 - - - +
329B ARG* 3.4 25.4 + - - +
330B GLN* 3.2 34.7 + - - +
332B ALA* 1.3 78.0 - - + +
334B CYS* 1.3 61.0 + - - +
336B SER* 2.9 22.6 + - - -
337B SER 3.3 6.4 + - - -
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Residues in contact with CYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TRP* 3.8 20.4 - - - -
297B HIS* 5.1 0.7 - - - -
301B GLU* 3.3 25.6 - - - -
305B LEU* 4.1 13.5 - - + -
330B GLN* 3.1 24.4 + - - +
331B LEU* 3.5 9.2 - - - +
333B LYS* 1.3 74.4 - - - +
335B VAL* 1.3 65.0 + - - +
337B SER* 2.9 21.7 + - - +
342B VAL* 4.0 11.2 - - + -
343B ALA* 3.4 9.5 + - - -
346B ALA* 3.7 17.7 - - + -
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Residues in contact with VAL 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 2.9 19.8 + - + +
332B ALA* 3.4 9.2 + - - +
334B CYS* 1.3 75.8 - - - +
336B SER* 1.3 59.0 + - - +
337B SER 3.5 0.9 + - - +
343B ALA* 3.6 18.4 - - - +
346B ALA* 3.8 21.8 - - + +
347B LEU* 3.8 34.0 - - + +
350B TRP* 5.4 2.0 - - - +
370B MET* 4.1 19.3 - - + -
371B PHE* 6.3 2.7 - - + -
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B HIS* 4.3 6.8 + - - -
332B ALA 3.3 12.4 + - - -
333B LYS* 2.9 18.6 + - - -
334B CYS 3.1 0.2 - - - -
335B VAL* 1.3 76.8 - - - +
337B SER* 1.3 63.3 + - - +
338B PRO* 3.6 2.9 - - - +
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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