Contacts of the helix formed by residues 333 - 348 (chain B) in PDB entry 1JPW
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 TYR 333 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B VAL* 4.2 35.4 - - + -
292B LYS* 4.6 18.6 - - + +
295B ALA* 4.5 11.4 - - + -
331B TYR* 3.7 1.8 - - - +
332B THR* 1.3 77.1 + - - +
334B GLU* 1.3 66.9 + - - +
335B LYS* 3.4 44.0 + - + +
336B LEU* 2.9 45.1 + - + +
337B LEU* 2.9 12.7 + - - +
44E VAL* 3.9 13.8 - - + +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B THR 3.1 8.9 + - - +
333B TYR* 1.3 72.2 - - + +
335B LYS* 1.3 62.2 + - + +
337B LEU* 3.4 10.2 + - - +
338B TRP* 2.8 38.5 + - - +
374B SER* 3.1 31.6 + - - -
376B ARG* 2.6 48.6 + - - +
377B LEU* 4.4 7.5 - - + +
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Residues in contact with LYS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA* 4.7 2.6 - - + +
333B TYR* 3.2 33.3 + - + +
334B GLU* 1.3 86.0 - - + +
336B LEU* 1.3 65.4 + - - +
338B TRP* 3.6 5.7 - - + +
339B THR* 3.1 30.0 + - - +
376B ARG* 4.2 5.4 - - - +
40E ASP* 3.1 40.0 + - - +
41E LEU* 4.9 8.5 - - + -
43E ASP* 5.8 4.6 - - - +
44E VAL* 3.7 25.4 - - + +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B VAL* 3.9 17.5 - - + +
294B LEU* 3.3 35.2 - - + +
295B ALA* 3.6 15.9 - - - +
298B THR* 4.1 3.6 - - + -
327B ILE* 3.6 25.1 - - + -
331B TYR* 3.6 29.8 - - + -
333B TYR* 2.9 23.7 + - + +
335B LYS* 1.3 74.5 - - - +
337B LEU* 1.3 68.0 + - + +
338B TRP 2.9 0.3 + - - -
339B THR* 2.9 6.7 + - - -
340B THR* 2.8 37.5 + - - +
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 4.3 5.6 - - + +
328B MET* 3.7 33.2 - - - +
331B TYR* 3.7 21.8 - - + +
332B THR* 3.9 19.3 - - - +
333B TYR 2.9 13.9 + - - +
334B GLU* 3.7 5.8 - - - +
336B LEU* 1.3 78.2 - - + +
338B TRP* 1.3 56.3 + - - +
340B THR* 3.7 0.8 + - - -
341B SER* 3.0 30.0 + - - -
369B HIS* 3.5 43.3 - - + +
372B ASP* 4.5 2.2 - - - +
377B LEU* 3.6 25.3 - - + +
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Residues in contact with TRP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 2.8 26.1 + - - +
335B LYS* 3.6 6.3 - - + +
336B LEU 2.9 0.8 + - - -
337B LEU* 1.3 71.8 - - - +
339B THR* 1.3 86.3 + - + +
341B SER* 2.4 28.1 + - - -
342B ARG* 3.0 42.7 + - + +
376B ARG* 3.3 65.3 - - + +
377B LEU* 3.8 6.9 - - + +
380B ASN* 3.5 24.9 + - - -
40E ASP* 3.9 22.4 - - - -
41E LEU* 5.5 5.4 - - + -
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA* 3.7 14.8 + - - +
298B THR* 2.5 27.3 + - - -
299B ASP* 4.1 18.8 - - + +
302B GLN* 4.9 0.9 - - - +
335B LYS 3.1 14.3 + - - +
336B LEU* 2.9 20.6 + - - -
338B TRP* 1.3 92.8 - - + +
340B THR* 1.3 60.1 + - - +
342B ARG* 3.2 15.2 + - - +
343B VAL* 3.0 24.4 + - - +
41E LEU* 4.1 16.4 - - + -
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Residues in contact with THR 340 (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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298B THR* 3.5 17.5 - - - +
324B LEU* 3.6 41.1 - - + +
327B ILE* 3.7 17.1 - - + +
328B MET* 3.6 26.0 - - + -
336B LEU* 2.8 20.0 + - - +
337B LEU 4.3 0.2 - - - -
339B THR* 1.3 73.9 + - - +
341B SER* 1.3 62.4 + - - +
343B VAL* 2.8 26.6 + - - +
344B LEU* 2.9 12.3 + - + +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B MET* 4.0 17.7 - - - -
337B LEU 3.0 15.8 + - - -
338B TRP* 2.4 28.5 + - - -
340B THR* 1.3 74.7 - - - +
342B ARG* 1.3 51.9 + - - +
344B LEU* 3.2 7.9 + - - +
345B LYS* 2.7 37.4 + - - +
366B LEU* 5.1 3.6 - - - -
377B LEU* 4.0 7.4 - - - +
380B ASN* 3.6 26.9 + - - +
381B CYS* 4.8 6.5 - - - -
384B THR* 3.9 2.4 + - - -
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Residues in contact with ARG 342 (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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299B ASP* 4.0 14.3 + - - -
302B GLN* 3.4 40.9 + - + +
338B TRP* 3.0 61.2 + - - +
339B THR* 3.4 13.0 - - - +
340B THR 3.1 0.2 - - - -
341B SER* 1.3 77.8 + - - +
343B VAL* 1.3 59.2 + - - +
345B LYS* 3.7 19.2 - - - +
346B VAL* 3.1 31.9 + - - +
380B ASN* 4.0 20.6 - - - +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B THR* 2.9 37.0 - - - +
301B LEU* 4.1 18.2 - - + +
302B GLN* 3.9 14.8 - - + +
305B ALA* 5.8 1.9 - - + +
315B ILE* 5.6 3.1 - - + -
324B LEU* 3.3 29.8 - - + -
339B THR 3.0 15.9 - - - +
340B THR* 2.8 10.8 + - - +
342B ARG* 1.3 76.9 - - - +
344B LEU* 1.3 61.3 + - - +
346B VAL* 3.7 3.1 + - - +
347B LEU* 3.2 36.1 + - + +
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PRO* 4.5 3.4 - - + +
324B LEU* 3.6 32.3 - - + -
325B VAL* 4.3 20.0 - - + +
328B MET* 3.8 28.7 - - + -
340B THR 2.9 13.3 + - - +
341B SER* 3.7 7.2 - - - +
343B VAL* 1.3 76.9 - - - +
345B LYS* 1.3 59.0 + - - +
347B LEU* 3.2 5.7 + - + +
348B SER* 2.8 32.9 + - - -
357B ILE* 4.2 29.7 - - + +
362B GLY* 6.0 0.4 - - - -
365B ALA* 6.4 0.4 - - + -
366B LEU* 4.2 17.5 - - + -
384B THR* 4.0 12.0 - - + +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLN* 5.3 3.0 + - - -
306B TYR* 6.0 1.2 - - - -
341B SER 2.7 19.4 + - - +
342B ARG* 3.7 25.7 - - - +
343B VAL 3.4 0.2 - - - -
344B LEU* 1.3 72.9 - - - +
346B VAL* 1.3 63.2 + - - +
348B SER* 2.4 21.3 + - - -
349B VAL* 4.0 8.5 - - - +
380B ASN* 3.3 28.9 - - - +
383B TRP* 4.4 18.8 - - + -
384B THR* 2.9 23.1 + - - +
387B ASN* 4.2 1.5 + - - +
23E ASP* 4.0 10.9 - - - +
24E GLU 3.4 20.6 + - - +
25E GLY* 3.5 21.6 - - - -
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Residues in contact with VAL 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLN* 4.1 21.3 - - + +
305B ALA* 4.0 7.2 - - + +
306B TYR* 3.9 29.2 - - + +
312B LYS* 3.3 28.8 - - - +
342B ARG 3.1 19.4 + - - +
343B VAL* 3.9 4.7 - - - +
344B LEU 3.2 0.4 - - - -
345B LYS* 1.3 79.7 - - - +
347B LEU* 1.3 63.2 + - - +
348B SER 3.1 1.3 + - - -
349B VAL* 3.1 25.3 - - - +
24E GLU* 3.9 27.4 - - - +
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Residues in contact with LEU 347 (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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305B ALA* 4.5 5.2 - - + -
312B LYS* 3.7 34.1 - - + +
315B ILE* 4.1 26.7 - - + -
321B PRO* 4.8 6.3 - - + -
324B LEU* 3.9 24.9 - - + -
343B VAL* 3.2 22.0 + - + +
344B LEU* 3.2 6.9 + - + +
346B VAL* 1.3 80.5 - - + +
348B SER* 1.3 60.7 + - - +
349B VAL 3.3 1.0 + - - -
350B CYS* 3.4 5.7 + - - +
353B ASN* 3.0 58.2 - - - +
357B ILE* 3.9 7.4 - - + -
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU 2.8 11.8 + - - -
345B LYS* 2.4 32.1 + - - -
346B VAL 3.1 0.2 - - - -
347B LEU* 1.3 77.7 - - - +
349B VAL* 1.3 58.0 + - - +
350B CYS 3.3 0.2 - - - -
354B LYS* 3.1 31.8 - - - +
357B ILE* 4.0 6.7 - - - -
384B THR* 3.9 7.3 - - - +
387B ASN* 3.5 23.2 + - - +
388B LEU* 3.6 26.2 - - - -
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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
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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