Contacts of the helix formed by residues 339 - 357 (chain A) in PDB entry 1P84
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 MET 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A TYR* 4.0 33.9 - - + -
311A LEU* 4.5 13.0 - - + +
336A ASN* 3.3 38.2 + - + +
338A THR* 1.3 89.4 - - - +
340A ILE* 1.3 63.7 + - - +
341A ASP* 3.1 6.7 - - - +
342A ASP* 3.0 35.1 + - - +
343A LEU* 3.3 10.1 + - - +
1C MET* 4.0 28.5 - - + -
5C LYS* 5.6 1.1 - - - +
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 4.1 16.6 - - + -
261A ILE* 5.2 7.4 - - + -
311A LEU 6.0 0.4 - - - -
334A THR* 4.3 11.0 - - + -
336A ASN 3.7 14.8 - - - +
337A VAL* 4.0 15.9 - - - +
338A THR 3.7 1.4 - - - -
339A MET* 1.3 77.6 - - - +
341A ASP* 1.3 63.5 + - - +
343A LEU* 3.2 12.4 + - + +
344A ILE* 3.1 27.3 + - + +
438A GLN 3.8 23.1 - - - +
439A ILE* 4.6 3.8 - - + -
441A GLY* 4.0 10.5 + - - +
442A LEU* 4.0 42.8 - - + +
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Residues in contact with ASP 341 (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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338A THR 4.3 7.6 - - - +
339A MET 4.2 5.9 - - - -
340A ILE* 1.3 78.9 + - - +
342A ASP* 1.3 59.4 + - - +
344A ILE* 3.6 5.3 + - - +
345A HIS* 2.9 30.7 + - - +
441A GLY 4.0 6.3 + - - +
443A LEU* 3.8 38.8 - - + +
448A ILE* 6.5 0.9 - - - -
4C ARG* 3.7 14.5 + - - +
5C LYS* 3.0 33.1 + - - -
19C ASP* 4.4 2.9 - - - +
13H TRP* 5.5 7.8 - - - +
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Residues in contact with ASP 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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311A LEU* 4.1 14.1 - - + -
339A MET* 3.0 32.6 + - + +
341A ASP* 1.3 76.8 - - - +
343A LEU* 1.3 61.6 + - - +
345A HIS* 4.1 5.4 - - - -
346A PHE* 2.8 44.3 + - + -
1C MET* 3.7 12.3 - - - +
2C ALA* 3.0 27.2 + - - +
4C ARG* 5.5 0.2 + - - -
5C LYS* 3.1 33.0 + - - -
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Residues in contact with LEU 343 (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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261A ILE* 6.2 0.9 - - + -
306A ILE* 4.9 8.1 - - + -
311A LEU* 3.5 43.6 - - + +
312A CYS* 3.9 12.3 - - + -
315A PHE* 6.0 2.7 - - + -
330A PHE* 4.7 9.6 - - + -
332A THR* 3.8 33.4 - - + +
334A THR* 4.2 14.1 - - + -
339A MET 3.3 5.3 + - - +
340A ILE* 3.2 17.4 + - + +
342A ASP* 1.3 80.5 - - - +
344A ILE* 1.3 68.3 + - + +
346A PHE* 4.1 1.8 - - - +
347A THR* 3.1 37.5 + - - +
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Residues in contact with ILE 344 (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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261A ILE* 4.2 30.7 - - + -
263A LEU* 4.3 8.5 - - + -
330A PHE* 4.2 18.2 - - + -
340A ILE* 3.1 21.3 + - + +
341A ASP* 4.0 5.2 - - - +
343A LEU* 1.3 85.4 - - + +
345A HIS* 1.3 55.8 + - - +
347A THR* 3.6 3.3 + - - -
348A LEU* 3.0 36.9 + - + +
442A LEU* 3.9 18.6 - - + -
448A ILE* 3.8 39.7 - - + -
451A ASP* 5.1 1.1 - - - +
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Residues in contact with HIS 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 ASP 2.9 21.7 + - - +
342A ASP* 3.2 6.0 + - - +
344A ILE* 1.3 75.3 - - - +
346A PHE* 1.3 81.9 + + - +
348A LEU* 3.5 1.6 + - - +
349A LYS* 3.0 62.6 + - + +
451A ASP* 2.9 30.8 + - - +
2C ALA* 4.2 27.3 - - + +
4C ARG* 4.9 9.8 + - - +
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Residues in contact with PHE 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 LEU* 3.9 15.3 - - + -
305A ASN* 3.7 47.9 - - + +
306A ILE* 4.8 2.7 - - + -
311A LEU* 3.7 19.1 - - + -
342A ASP* 2.8 28.7 + - + +
343A LEU 4.1 1.6 - - - +
345A HIS* 1.3 84.7 - + - +
347A THR* 1.3 67.5 + - - +
349A LYS* 3.0 9.5 + - + +
350A GLN* 3.0 25.6 + - - +
1C MET* 3.7 43.7 - - - -
2C ALA* 4.0 2.9 - - - -
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Residues in contact with THR 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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302A LEU* 3.8 26.5 - - + +
317A HIS* 4.4 4.5 - - + -
330A PHE* 3.8 32.7 - - + -
343A LEU* 3.1 30.7 + - - +
344A ILE 3.9 3.4 - - - -
346A PHE* 1.3 78.0 - - - +
348A LEU* 1.3 63.4 + - + +
350A GLN* 3.2 4.2 + - - +
351A TRP* 3.1 54.6 + - + +
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Residues in contact with LEU 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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263A LEU* 4.3 17.7 - - + -
330A PHE* 4.8 2.0 - - + -
344A ILE* 3.0 25.9 + - + +
345A HIS 4.2 0.9 - - - +
347A THR* 1.3 83.4 - - + +
349A LYS* 1.3 61.6 + - - +
351A TRP* 3.6 28.6 + - + +
352A ASN* 3.1 30.5 + - - +
448A ILE* 3.5 42.0 - - + +
451A ASP* 3.9 19.3 - - + +
452A MET* 3.6 27.4 - - - +
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Residues in contact with LYS 349 (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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345A HIS* 3.0 45.7 + - + +
346A PHE* 3.0 11.4 + - + +
348A LEU* 1.3 75.3 - - - +
350A GLN* 1.3 68.9 + - - +
352A ASN* 3.1 28.6 + - - +
353A ARG* 3.5 8.8 + - - +
451A ASP* 3.3 30.1 + - - -
453A SER 2.9 28.3 + - - -
454A MET* 3.9 20.0 - - + +
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Residues in contact with GLN 350 (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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285A PHE* 3.7 28.8 - - + -
301A LYS* 4.0 15.4 - - - +
302A LEU* 3.8 33.8 + - + +
305A ASN* 3.8 15.2 - - - +
346A PHE 3.0 15.6 + - - +
347A THR* 3.4 10.8 - - - +
349A LYS* 1.3 78.9 - - + +
351A TRP* 1.3 62.0 + - - +
353A ARG* 2.9 63.3 + - - +
354A LEU 3.9 0.3 + - - -
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Residues in contact with TRP 351 (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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263A LEU* 3.9 24.0 - - + -
265A VAL* 5.3 3.1 - - + -
285A PHE* 3.6 28.3 - + - -
302A LEU* 5.9 0.2 - - - +
317A HIS* 2.9 32.9 + + - -
328A TRP* 3.6 28.0 - + - -
329A GLY* 3.8 17.0 - - - -
330A PHE* 3.4 36.8 - + + -
347A THR* 3.1 24.3 + - + +
348A LEU* 3.9 22.2 - - + +
349A LYS 3.3 0.2 - - - -
350A GLN* 1.3 76.3 - - + +
352A ASN* 1.3 62.9 + - - +
354A LEU* 3.3 18.8 + - - +
355A THR* 4.4 1.7 + - - -
426A LEU* 4.0 20.7 - - + +
452A MET* 4.4 19.1 - - + -
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Residues in contact with ASN 352 (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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348A LEU 3.1 16.0 + - - +
349A LYS* 3.1 41.3 + - - +
350A GLN 3.1 0.8 - - - -
351A TRP* 1.3 77.8 - - - +
353A ARG* 1.3 64.1 + - + +
355A THR* 3.1 20.5 + - - -
356A ILE* 3.7 6.0 + - - +
427A TRP* 3.9 18.4 - - + -
451A ASP 3.2 18.4 + - - +
452A MET* 3.4 21.6 + - - +
453A SER* 3.4 3.1 - - - +
454A MET* 3.7 19.9 - - - +
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Residues in contact with ARG 353 (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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284A ILE* 6.0 0.2 - - - +
285A PHE* 5.2 4.2 - - - -
301A LYS* 3.6 21.6 - - - +
349A LYS 3.7 8.7 - - - +
350A GLN* 2.9 49.3 + - - +
352A ASN* 1.3 73.2 - - + +
354A LEU* 1.3 57.9 + - + +
355A THR 2.8 10.8 + - - -
356A ILE* 4.2 4.9 - - + -
357A SER* 2.8 63.4 + - - +
358A VAL* 3.2 8.8 + - + +
359A THR* 4.2 4.0 - - - +
362A GLU* 2.9 42.0 + - - -
454A MET* 6.3 1.3 - - - -
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Residues in contact with LEU 354 (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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281A ALA* 3.9 25.8 - - + +
284A ILE* 3.8 27.1 - - + -
285A PHE* 3.6 37.2 - - + -
328A TRP* 4.4 1.6 - - + -
350A GLN 3.9 0.2 + - - -
351A TRP 3.5 9.9 - - - +
352A ASN 3.2 1.2 - - - -
353A ARG* 1.3 78.3 - - + +
355A THR* 1.3 56.1 + - - +
358A VAL* 3.9 18.3 - - + +
418A VAL* 3.8 11.0 - - + +
419A LYS* 3.3 28.2 + - - +
421A TRP* 4.4 3.1 - - + -
422A ALA* 3.6 15.0 - - + +
426A LEU* 4.1 17.7 - - + -
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Residues in contact with THR 355 (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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351A TRP 5.0 2.1 + - - -
352A ASN 3.1 10.8 + - - -
353A ARG 2.9 1.2 - - - -
354A LEU* 1.3 79.4 - - - +
356A ILE* 1.3 65.1 + - + +
419A LYS* 3.8 24.1 - - - +
422A ALA* 3.4 27.4 + - - +
423A GLY* 3.8 17.5 - - - -
426A LEU* 5.0 0.7 - - - +
427A TRP* 3.8 32.4 + - + +
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Residues in contact with ILE 356 (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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352A ASN 3.9 10.1 - - - +
353A ARG* 2.9 9.2 + - + +
355A THR* 1.3 96.1 - - + +
357A SER* 1.3 70.2 + - - +
358A VAL 4.0 0.9 - - - -
419A LYS* 3.6 18.6 + - - +
427A TRP* 4.4 16.2 - - + -
454A MET* 4.0 27.8 - - + -
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Residues in contact with SER 357 (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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353A ARG* 2.8 53.3 + - - +
356A ILE* 1.3 83.9 - - - +
358A VAL* 1.3 64.5 + - - +
359A THR* 3.4 6.9 + - - +
419A LYS* 4.8 2.0 - - - +
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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