Contacts of the helix formed by residues 309 - 331 (chain J) in PDB entry 1I43
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 THR 309 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266J HIS* 4.4 4.7 - - - -
306J GLY 3.4 6.3 + - - -
307J MET 2.9 0.2 - - - -
308J LYS* 1.3 84.2 - - - +
310J LEU* 1.3 66.8 + - - +
311J HIS* 3.6 9.2 - - - -
312J LEU* 4.0 11.7 - - + -
313J ARG* 3.0 40.3 + - - +
266K HIS* 4.1 8.9 + - - +
309K THR* 4.0 14.7 + - - +
313K ARG* 3.9 24.9 - - + -
392K CYS* 3.7 20.2 - - - -
428K VAL* 5.3 0.2 - - + -
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Residues in contact with LEU 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J ALA* 4.4 5.2 - - + -
126J LEU* 3.9 24.2 - - + -
241J THR* 4.7 5.4 - - + -
242J PRO* 4.7 3.1 - - + -
243J LEU* 3.6 20.9 - - + -
262J PHE* 3.8 17.9 - - + +
263J LEU* 3.8 25.4 - - + +
307J MET* 3.1 23.2 + - + +
308J LYS 3.6 0.6 - - - -
309J THR* 1.3 75.3 - - - +
311J HIS* 1.3 58.7 + - - +
313J ARG* 2.9 28.8 + - - +
314J VAL* 2.7 52.8 + - + +
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Residues in contact with HIS 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J GLY* 3.4 38.1 + - - +
61J ALA* 5.1 1.0 - - - +
62J ILE* 3.9 7.7 - - + +
243J LEU* 3.4 21.4 - - + +
307J MET 5.1 0.8 + - - -
308J LYS 3.6 14.3 - - - -
309J THR* 4.1 0.7 - - - -
310J LEU* 1.3 79.7 + - - +
312J LEU* 1.3 80.0 + - + +
314J VAL* 3.9 0.2 - - - +
315J GLN* 2.9 46.2 + - - +
316K GLN* 5.3 2.2 - - - -
428K VAL* 3.2 46.3 + - + +
429K GLU 5.3 0.7 - - - -
430K ASP* 4.8 10.3 - - - +
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Residues in contact with LEU 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309J THR* 3.7 12.8 - - + +
310J LEU 3.1 0.8 - - - -
311J HIS* 1.3 109.2 - - + +
313J ARG* 1.3 65.4 + - - +
315J GLN* 3.5 13.3 - - - +
316J GLN* 3.2 16.5 + - - +
312K LEU* 3.7 26.4 - - + +
313K ARG* 3.8 29.6 - - + +
316K GLN* 4.2 26.9 - - + +
428K VAL* 3.4 27.4 - - + +
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Residues in contact with ARG 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J PHE* 2.8 26.8 + - - +
263J LEU 3.6 3.8 + - - -
264J GLY 4.4 0.2 - - - -
265J GLY* 3.2 18.0 - - - -
266J HIS* 4.4 5.2 - - - -
306J GLY 2.6 26.5 + - - -
309J THR* 3.0 25.0 + - - +
310J LEU* 2.9 35.7 + - - +
312J LEU* 1.3 78.2 - - - +
314J VAL* 1.3 68.0 + - - +
316J GLN* 3.2 5.0 + - - +
317J GLN* 2.8 37.1 + - - +
390J GLY 4.2 5.5 + - - -
391J GLY 6.2 0.2 - - - -
392J CYS* 4.1 15.0 - - - +
428J VAL* 4.2 7.9 - - + -
309K THR* 4.0 24.9 - - + -
312K LEU* 3.8 11.9 - - + -
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Residues in contact with VAL 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241J THR* 4.2 16.2 - - + +
243J LEU* 3.5 26.2 - - + -
244J ASN* 4.1 14.4 - - - +
262J PHE* 5.3 9.9 - - + -
310J LEU* 2.7 41.6 + - + +
311J HIS 3.9 2.7 - - - +
313J ARG* 1.3 71.5 - - + +
315J GLN* 1.3 65.4 + - - +
317J GLN* 2.9 11.7 + - + +
318J ASN* 2.8 44.6 + - - +
359J GLY* 6.1 0.4 - - - -
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Residues in contact with GLN 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311J HIS* 2.9 37.9 + - - +
312J LEU* 3.5 12.7 - - - +
313J ARG 3.3 0.2 - - - -
314J VAL* 1.3 76.3 - - - +
316J GLN* 1.3 61.2 + - - +
318J ASN* 3.2 16.2 + - - +
319J SER* 3.3 17.0 + - - -
316K GLN* 5.2 6.1 + - - +
430K ASP* 5.3 5.9 + - - -
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Residues in contact with GLN 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312J LEU 3.2 9.2 + - - +
313J ARG 3.2 7.7 + - - +
315J GLN* 1.3 79.6 - - - +
317J GLN* 1.3 63.1 + - - +
319J SER* 3.4 7.8 + - - -
320J THR* 3.1 37.6 + - - +
427J GLY 5.1 0.2 - - - +
428J VAL* 3.5 26.9 + - + +
429J GLU 3.3 24.5 + - - -
430J ASP* 4.5 7.7 + - - +
431J PHE* 4.5 4.4 - - - +
311K HIS* 5.3 2.0 + - - -
312K LEU* 4.2 22.0 - - + +
315K GLN* 5.4 5.0 + - - +
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Residues in contact with GLN 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262J PHE* 3.5 34.4 - - + -
313J ARG* 2.8 38.5 + - - +
314J VAL* 2.9 7.9 + - + +
316J GLN* 1.3 72.8 - - - +
318J ASN* 1.3 66.3 + - - +
320J THR* 4.1 3.5 - - - -
321J ALA* 3.0 27.5 + - - +
360J GLY* 3.6 16.3 - - - +
390J GLY* 3.8 10.2 + - - +
391J GLY 4.1 9.8 + - - -
426J PHE* 2.7 30.7 + - - +
427J GLY 3.4 19.3 + - - +
428J VAL* 4.3 7.0 - - + -
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Residues in contact with ASN 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J ASN* 2.9 31.9 + - - +
314J VAL* 2.8 26.5 + - - +
315J GLN* 3.4 12.5 - - - +
317J GLN* 1.3 74.9 - - - +
319J SER* 1.3 57.1 + - - +
322J LEU* 3.1 29.3 + - - +
339J TYR* 3.6 5.4 + - - -
356J THR 5.0 0.4 + - - -
357J GLY* 3.4 11.4 - - - -
358J PHE 3.9 7.9 - - - +
359J GLY* 3.0 32.7 + - - -
360J GLY 4.2 0.2 + - - -
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Residues in contact with SER 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315J GLN 3.3 12.6 + - - -
316J GLN* 3.8 9.2 - - - -
317J GLN 3.2 0.4 - - - -
318J ASN* 1.3 74.9 - - - +
320J THR* 1.3 67.2 + - - +
321J ALA 3.0 1.6 - - - -
322J LEU* 2.9 8.2 + - - +
323J ARG* 2.8 49.3 + - - +
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Residues in contact with THR 320 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316J GLN* 3.1 32.2 + - - +
317J GLN* 4.1 4.5 - - - -
319J SER* 1.3 78.1 - - - +
321J ALA* 1.3 56.7 + - - +
323J ARG* 4.8 3.1 + - - +
324J MET* 3.0 39.3 + - + +
426J PHE* 3.8 19.7 - - + -
427J GLY 5.5 2.3 + - - +
429J GLU 4.7 1.9 + - - -
431J PHE* 3.9 32.1 - - + +
434J LEU* 3.7 27.4 - - + -
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Residues in contact with ALA 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317J GLN 3.0 20.5 + - - +
318J ASN 3.7 0.4 - - - +
319J SER 3.0 0.6 - - - -
320J THR* 1.3 75.3 - - - +
322J LEU* 1.3 59.3 + - - +
324J MET 3.7 0.3 - - - -
325J ALA* 2.9 31.2 + - - +
339J TYR* 3.6 4.9 - - - +
359J GLY 3.3 22.2 - - - +
360J GLY* 3.6 11.7 - - - +
362J VAL* 3.7 18.5 - - + +
426J PHE* 4.0 12.7 - - + -
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Residues in contact with LEU 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318J ASN 3.1 15.1 + - - +
319J SER* 2.9 7.2 + - - +
321J ALA* 1.3 79.0 - - - +
323J ARG* 1.3 66.2 + - + +
325J ALA* 3.1 17.2 + - - +
326J GLU* 3.2 26.4 + - - +
339J TYR* 3.8 27.5 + - + +
341J GLY* 4.1 22.2 - - - +
342J LEU* 4.7 3.8 - - + +
358J PHE* 4.9 10.8 - - + -
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Residues in contact with ARG 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319J SER* 2.8 39.8 + - - +
320J THR* 5.4 1.2 + - - +
322J LEU* 1.3 76.9 - - + +
324J MET* 1.3 61.5 + - - +
325J ALA 3.2 0.7 + - - -
326J GLU* 3.2 15.1 + - - +
327J ILE* 3.1 28.8 + - + +
431J PHE* 2.9 60.9 - - + +
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Residues in contact with MET 324 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J THR* 3.0 26.3 + - + +
321J ALA 3.8 1.1 - - - +
323J ARG* 1.3 73.7 - - - +
325J ALA* 1.3 60.6 + - - +
327J ILE* 4.2 14.8 - - + -
328J LEU* 2.9 50.7 + - + +
426J PHE* 3.5 30.5 - - + -
431J PHE* 3.4 28.0 - - + -
435J LYS* 3.7 28.0 - - + +
438J ILE* 3.3 28.5 - - + -
439J LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 325 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321J ALA 2.9 14.1 + - - +
322J LEU 3.1 11.6 + - - +
324J MET* 1.3 74.0 - - - +
326J GLU* 1.3 55.2 + - - +
328J LEU* 3.0 10.7 + - - +
329J GLU* 2.7 33.6 + - - +
337J VAL* 4.0 11.1 - - + +
339J TYR* 4.2 17.5 - - + -
342J LEU* 3.9 26.2 - - + -
362J VAL* 4.5 5.6 - - + +
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Residues in contact with GLU 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322J LEU* 3.2 25.1 + - + +
323J ARG* 3.6 13.3 - - - +
325J ALA* 1.3 77.9 - - - +
327J ILE* 1.3 65.2 + - + +
329J GLU* 2.9 20.8 + - - +
330J ALA* 2.9 15.6 + - - +
342J LEU* 3.8 19.0 - - + +
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Residues in contact with ILE 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J ARG* 3.1 11.8 + - + +
324J MET* 3.7 20.6 - - + +
326J GLU* 1.3 77.6 - - + +
328J LEU* 1.3 63.6 + - + +
330J ALA* 3.4 7.5 + - - +
331J HIS* 3.1 20.5 + - + +
431J PHE* 3.8 19.3 - - + -
435J LYS* 3.8 30.1 - - + +
439J LEU* 4.5 24.5 - - + -
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Residues in contact with LEU 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324J MET* 2.9 39.6 + - + +
325J ALA* 3.3 3.8 - - - +
327J ILE* 1.3 74.3 - - + +
329J GLU* 1.3 66.6 + - - +
331J HIS* 3.0 13.3 + - + +
334J VAL* 3.0 39.6 - - + +
337J VAL* 3.8 12.3 - - + -
362J VAL* 4.5 11.9 - - + -
364J PHE* 3.7 38.8 - - + -
426J PHE* 4.9 7.0 - - + -
438J ILE* 4.0 13.5 - - + -
439J LEU* 6.4 0.2 - - + -
442J LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325J ALA 2.7 15.9 + - - +
326J GLU* 3.2 12.5 - - - +
328J LEU* 1.3 74.1 - - - +
330J ALA* 1.3 62.5 + - - +
331J HIS 3.4 5.9 + - - +
334J VAL* 4.4 6.0 - - - +
336J HIS* 6.1 0.3 - - - -
337J VAL* 3.7 23.2 + - + +
342J LEU* 3.9 20.6 - - + +
343J GLN 5.3 0.7 + - - -
344J SER* 2.8 32.7 + - - -
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Residues in contact with ALA 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326J GLU 2.9 14.4 + - - +
327J ILE* 3.8 6.5 - - - +
329J GLU* 1.3 76.7 - - + +
331J HIS* 1.3 64.6 + - - +
332J PRO* 3.5 4.9 - - - +
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Residues in contact with HIS 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327J ILE* 3.1 12.5 + - + +
328J LEU* 3.0 17.9 + - - +
329J GLU 3.7 3.5 - - - +
330J ALA* 1.3 79.4 - - - +
332J PRO* 1.3 77.7 - - + +
333J LYS* 3.0 45.1 + - + +
334J VAL* 3.4 26.7 + - + +
439J LEU* 3.9 21.8 - - + +
442J LEU* 3.8 42.1 + - + +
443J ASP* 4.3 8.2 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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