Contacts of the helix formed by residues 333 - 349 (chain A) in PDB entry 1JPP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A VAL* 4.0 39.5 - - + -
292A LYS* 4.3 30.1 + - + +
295A ALA* 4.8 5.4 - - + -
331A TYR* 4.6 1.2 - - - +
332A THR* 1.3 78.8 + - - +
334A GLU* 1.3 67.1 + - - +
335A LYS* 3.5 35.9 - - + +
336A LEU* 3.3 34.0 + - + +
337A LEU* 3.1 21.7 + - - +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A THR 3.0 6.9 + - - +
333A TYR* 1.3 75.0 - - - +
335A LYS* 1.3 62.2 + - - +
336A LEU 3.1 0.3 + - - -
337A LEU* 3.2 8.0 + - - +
338A TRP* 2.9 29.4 + - - +
374A SER* 3.0 34.6 + - - +
376A ARG* 3.0 36.8 + - - +
377A LEU* 4.6 9.4 - - + +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 4.7 12.4 - - + +
333A TYR* 3.5 32.8 - - + +
334A GLU* 1.3 88.2 + - - +
336A LEU* 1.3 59.2 + - - +
338A TRP* 4.0 16.1 - - + +
339A THR* 3.3 27.2 + - + +
376A ARG* 4.5 10.1 - - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A VAL* 4.2 15.9 - - + +
294A LEU* 3.6 37.7 - - + +
295A ALA* 3.7 15.5 - - - +
298A THR* 4.6 2.7 - - + +
327A ILE* 4.0 24.5 - - + -
331A TYR* 4.0 25.4 - - + -
333A TYR* 3.3 24.9 + - + +
334A GLU 3.1 0.4 - - - -
335A LYS* 1.3 75.8 - - - +
337A LEU* 1.3 66.8 + - + +
338A TRP 3.1 1.6 - - - -
339A THR* 3.3 4.3 + - - -
340A THR* 2.9 42.0 + - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 4.3 8.3 - - + +
328A MET* 3.4 54.3 - - + +
331A TYR* 3.8 17.9 - - + +
332A THR* 3.7 16.8 - - - +
333A TYR 3.1 17.4 + - - +
334A GLU* 3.8 5.8 - - - +
336A LEU* 1.3 81.6 - - + +
338A TRP* 1.3 60.0 + - - +
340A THR* 4.2 0.9 - - - -
341A SER* 3.6 13.7 + - - -
369A HIS* 3.7 27.1 - - + +
372A ASP* 5.6 1.1 - - - +
377A LEU* 3.2 29.4 - - + +
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Residues in contact with TRP 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 5.6 2.5 - - - -
334A GLU* 2.9 25.5 + - - +
335A LYS* 4.0 13.7 - - + +
336A LEU 3.1 0.2 - - - -
337A LEU* 1.3 76.7 - - - +
339A THR* 1.3 86.9 + - + +
341A SER* 2.6 22.6 + - - -
342A ARG* 3.2 41.9 + - - +
376A ARG* 3.3 66.4 - - + +
377A LEU* 3.9 9.2 - - + +
380A ASN* 3.4 24.7 - - - +
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 4.1 11.0 + - + +
298A THR* 2.8 27.1 + - - +
299A ASP* 4.5 20.0 - - + +
302A GLN* 5.5 0.5 - - - +
335A LYS* 3.3 22.7 + - + +
336A LEU* 3.3 10.8 + - - -
338A TRP* 1.3 93.4 - - + +
340A THR* 1.3 67.1 + - - +
341A SER 3.1 2.5 - - - -
342A ARG* 3.0 22.7 + - + +
343A VAL* 3.1 15.8 + - - +
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Residues in contact with THR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A THR* 4.0 12.0 - - - +
324A LEU* 3.7 45.8 - - + +
327A ILE* 4.0 10.5 - - + +
328A MET* 4.2 21.5 - - + -
336A LEU* 2.9 32.5 + - - +
339A THR* 1.3 77.9 + - - +
341A SER* 1.3 60.8 + - - +
343A VAL* 3.6 7.0 + - - +
344A LEU* 3.3 22.4 + - + +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A MET* 4.3 13.2 - - - -
337A LEU 3.6 11.9 + - - -
338A TRP* 2.6 23.3 + - - -
340A THR* 1.3 75.8 - - - +
342A ARG* 1.3 60.6 + - - +
343A VAL 3.0 1.6 - - - -
344A LEU* 3.7 10.1 - - - +
345A LYS* 2.8 32.3 + - - +
366A LEU* 5.2 2.7 - - - -
377A LEU* 4.2 7.0 - - - +
380A ASN* 3.6 27.8 + - - +
381A CYS* 5.1 4.9 - - - -
384A THR* 4.5 3.9 + - - -
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ASP* 4.5 9.9 + - - -
302A GLN* 3.4 44.4 + - + +
338A TRP* 3.3 46.3 - - + +
339A THR* 3.0 17.0 + - - +
341A SER* 1.3 83.7 + - - +
343A VAL* 1.3 55.7 + - - +
345A LYS* 3.8 9.2 - - - +
346A VAL* 3.1 29.5 + - - +
380A ASN* 3.9 22.9 - - - +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.3 32.1 - - - +
301A LEU* 4.2 13.7 - - + -
302A GLN* 4.0 19.3 - - + +
315A ILE* 5.7 5.8 - - + -
324A LEU* 3.5 29.2 - - + -
339A THR 3.1 13.9 + - - +
340A THR* 3.7 8.5 - - - +
341A SER 3.0 0.4 - - - -
342A ARG* 1.3 75.2 - - - +
344A LEU* 1.3 69.0 + - - +
345A LYS 3.1 0.5 + - - -
346A VAL* 3.2 16.0 + - - +
347A LEU* 3.3 23.3 + - + +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO* 5.0 4.5 - - + +
324A LEU* 4.1 28.9 - - + -
325A VAL* 4.8 14.4 - - + -
328A MET* 4.6 15.0 - - + -
340A THR 3.3 14.4 + - - +
341A SER* 3.2 10.5 + - - +
343A VAL* 1.3 80.0 - - - +
345A LYS* 1.3 63.8 + - - +
347A LEU* 3.2 9.1 + - + +
348A SER* 3.1 22.0 + - - -
357A ILE* 4.3 34.3 - - + +
362A GLY* 6.3 0.4 - - - -
366A LEU* 4.4 30.5 - - + -
384A THR* 4.3 10.4 - - + +
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Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A SER 2.8 17.9 + - - +
342A ARG* 3.8 10.1 - - - +
343A VAL 3.1 0.2 - - - -
344A LEU* 1.3 76.9 - - - +
346A VAL* 1.3 66.6 + - + +
348A SER* 2.5 28.6 + - - +
349A VAL* 3.8 7.2 + - + +
380A ASN* 4.1 23.6 + - - +
383A TRP* 4.4 38.6 - - + -
384A THR* 3.7 20.1 + - - +
387A ASN* 5.9 2.0 - - - +
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A GLN* 4.3 18.8 - - + +
305A ALA* 3.8 22.0 - - + +
306A TYR* 4.3 24.2 - - + -
307A GLY 5.2 0.2 - - - +
312A LYS* 3.1 39.7 + - + +
342A ARG 3.1 18.6 - - - +
343A VAL* 3.2 7.5 + - - +
345A LYS* 1.3 80.8 - - + +
347A LEU* 1.3 61.1 + - + +
348A SER 3.7 0.2 + - - -
349A VAL* 3.8 12.5 + - - +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ALA* 5.1 4.5 - - + -
312A LYS* 3.8 28.7 - - + +
315A ILE* 4.7 24.0 - - + -
321A PRO* 4.9 11.9 - - + -
324A LEU* 4.7 9.4 - - + -
343A VAL* 3.6 27.8 - - + +
344A LEU* 3.2 12.9 + - + +
345A LYS 3.1 0.8 - - - -
346A VAL* 1.3 73.0 - - - +
348A SER* 1.3 61.5 + - - +
349A VAL 3.1 7.2 + - - -
350A CYS* 3.4 21.7 - - - +
353A ASN* 2.9 41.9 - - - +
357A ILE* 4.6 8.5 - - + -
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Residues in contact with SER 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LEU 3.1 10.9 + - - -
345A LYS* 2.5 26.1 + - - +
347A LEU* 1.3 76.2 - - - +
349A VAL* 1.3 56.6 + - - +
354A LYS* 2.8 39.9 - - - -
357A ILE* 4.7 2.9 - - - +
384A THR* 4.0 8.8 - - - +
387A ASN* 3.4 26.1 + - - +
388A LEU* 3.8 24.9 - - - -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LYS* 4.5 8.3 - - - +
345A LYS* 4.3 6.5 - - + +
346A VAL* 3.9 16.2 - - - +
347A LEU 3.1 1.2 - - - -
348A SER* 1.3 76.7 + - - +
350A CYS* 1.3 72.3 + - - +
351A SER* 3.8 2.8 + - - -
354A LYS* 4.2 1.6 - - - -
387A ASN* 4.1 16.6 - - - +
1028C SER* 4.0 25.1 + - - +
1029C LEU* 6.1 2.6 - - + +
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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