Contacts of the helix formed by residues 309 - 331 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E HIS* 4.0 12.4 + - - +
309E THR* 4.1 14.4 - - - +
313E ARG* 4.0 19.3 - - + -
392E CYS* 3.7 22.4 - - - -
266H HIS* 4.5 4.3 - - - -
306H GLY 3.5 5.4 + - - -
307H MET 2.9 0.8 - - - -
308H LYS* 1.3 85.1 - - - +
310H LEU* 1.3 66.4 + - - +
311H HIS* 3.6 8.3 - - - -
312H LEU* 3.5 12.5 + - + -
313H ARG* 3.1 40.4 + - - +
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Residues in contact with LEU 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H ALA* 4.4 4.7 - - + -
126H LEU* 3.9 23.8 - - + -
241H THR* 4.6 9.0 - - + -
242H PRO* 4.7 0.9 - - + -
243H LEU* 3.6 19.5 - - + -
262H PHE* 3.7 17.5 - - + +
263H LEU* 3.8 24.9 - - + -
307H MET* 3.1 22.8 + - + +
308H LYS 3.6 0.4 - - - -
309H THR* 1.3 75.7 - - - +
311H HIS* 1.3 68.7 + - - +
313H ARG* 2.8 30.5 + - - +
314H VAL* 2.8 43.4 + - + +
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Residues in contact with HIS 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E GLN* 5.5 2.5 - - - -
428E VAL* 3.2 34.6 + - + +
430E ASP* 5.0 9.0 - - - -
58H GLY* 3.3 45.3 + - - +
61H ALA* 5.0 1.4 - - - +
62H ILE* 4.0 0.6 - - + +
243H LEU* 3.4 21.7 - - + +
307H MET 4.9 0.8 + - - -
308H LYS 3.5 24.7 - - - -
309H THR* 4.1 0.4 - - - -
310H LEU* 1.3 81.0 + - - +
312H LEU* 1.3 78.0 + - + +
314H VAL* 4.0 0.2 - - - +
315H GLN* 2.9 45.8 + - - +
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Residues in contact with LEU 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E LEU* 3.8 22.4 - - + +
313E ARG* 3.8 28.3 - - + +
316E GLN* 4.3 26.2 - - + +
428E VAL* 3.4 29.6 - - + -
309H THR* 3.7 14.1 - - - +
310H LEU 3.1 0.4 - - - -
311H HIS* 1.3 106.9 + - + +
313H ARG* 1.3 63.4 + - - +
315H GLN* 3.6 13.6 - - - +
316H GLN* 3.3 22.2 + - - +
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Residues in contact with ARG 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309E THR* 4.0 14.6 - - + -
312E LEU* 3.9 12.3 - - + -
262H PHE* 2.8 31.8 + - - +
263H LEU 3.5 8.1 + - - -
264H GLY 4.1 0.4 + - - -
265H GLY* 3.4 16.7 - - - -
266H HIS* 4.3 3.5 - - - -
306H GLY 2.7 24.4 + - - -
309H THR* 3.1 26.1 + - - +
310H LEU* 2.8 35.9 + - - +
312H LEU* 1.3 72.9 - - - +
314H VAL* 1.3 60.8 + - - +
316H GLN* 3.3 3.3 + - - +
317H GLN* 2.7 44.1 + - - +
390H GLY 4.3 5.9 + - - -
391H GLY 6.1 0.2 - - - -
392H CYS* 3.8 25.4 - - - +
428H VAL* 4.2 5.2 - - + -
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Residues in contact with VAL 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H THR* 4.2 14.8 - - + +
243H LEU* 3.5 22.4 - - + -
244H ASN* 4.0 17.9 - - - +
262H PHE* 5.4 9.2 - - + -
310H LEU* 2.8 49.2 + - + +
311H HIS 4.0 0.7 - - - +
313H ARG* 1.3 72.9 - - + +
315H GLN* 1.3 54.5 + - - +
317H GLN* 3.2 9.3 + - + +
318H ASN* 2.7 56.0 + - - +
359H GLY* 6.1 0.4 - - - -
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Residues in contact with GLN 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316E GLN* 5.4 4.9 + - - +
430E ASP* 5.6 4.0 + - - -
311H HIS* 2.9 34.5 + - - +
312H LEU* 3.6 16.0 - - - +
314H VAL* 1.3 77.6 - - - +
316H GLN* 1.3 63.4 + - - +
318H ASN* 3.3 9.5 + - - +
319H SER* 3.2 22.6 + - - -
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Residues in contact with GLN 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311E HIS* 5.0 2.8 + - - -
312E LEU* 4.1 22.1 - - + +
315E GLN* 5.4 4.9 + - - +
312H LEU 3.3 8.8 + - - +
313H ARG 3.3 7.7 + - - +
315H GLN* 1.3 76.5 - - - +
317H GLN* 1.3 66.5 + - - +
319H SER* 3.0 17.5 + - - -
320H THR* 3.0 26.7 + - - +
427H GLY 4.9 0.2 - - - +
428H VAL* 3.3 38.4 + - + +
429H GLU 3.4 13.7 + - - -
430H ASP* 4.5 7.1 + - - +
431H PHE* 4.6 4.0 - - - +
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Residues in contact with GLN 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262H PHE* 3.7 23.7 - - + -
313H ARG* 2.7 38.6 + - - +
314H VAL* 3.7 5.8 + - + +
316H GLN* 1.3 74.9 - - - +
318H ASN* 1.3 61.9 + - - +
320H THR* 4.2 3.8 - - - -
321H ALA* 3.1 27.9 + - - +
360H GLY* 3.6 16.6 - - - +
390H GLY* 3.4 17.9 + - - +
391H GLY 3.8 14.4 + - - +
392H CYS* 5.7 0.2 - - - -
426H PHE* 2.6 30.7 + - - +
427H GLY 3.3 17.5 + - - +
428H VAL* 4.2 8.7 - - + +
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Residues in contact with ASN 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H ASN* 2.9 32.5 + - - +
314H VAL* 2.7 30.9 + - - +
315H GLN* 3.4 9.1 - - - +
316H GLN 3.2 0.2 - - - -
317H GLN* 1.3 72.8 - - - +
319H SER* 1.3 64.6 + - - +
322H LEU* 3.2 21.7 + - - +
339H TYR* 3.6 5.0 + - - -
356H THR 5.1 0.6 + - - -
357H GLY* 3.8 8.3 - - - -
358H PHE 4.2 5.8 - - - +
359H GLY* 3.0 34.7 + - - -
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Residues in contact with SER 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H GLN 3.2 10.3 + - - -
316H GLN* 3.0 11.0 + - - -
318H ASN* 1.3 74.9 - - - +
320H THR* 1.3 69.4 + - - +
322H LEU* 2.9 18.4 + - - +
323H ARG* 2.9 37.3 + - - +
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Residues in contact with THR 320 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H GLN* 3.0 29.6 + - - +
317H GLN* 4.2 4.7 - - - -
319H SER* 1.3 76.8 - - - +
321H ALA* 1.3 53.4 + - - +
323H ARG* 3.9 3.8 + - - +
324H MET* 2.8 40.9 + - + +
426H PHE* 3.6 30.7 - - + -
427H GLY 5.3 2.3 + - - -
429H GLU 4.6 2.9 + - - -
431H PHE* 3.8 34.0 - - + +
434H LEU* 3.9 16.6 - - + +
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Residues in contact with ALA 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H GLN 3.1 18.6 + - - +
318H ASN 3.8 0.2 - - - +
319H SER 3.1 0.8 - - - -
320H THR* 1.3 78.1 - - - +
322H LEU* 1.3 57.3 + - - +
324H MET* 3.7 0.7 - - - +
325H ALA* 2.8 30.8 + - - +
339H TYR* 3.5 4.9 - - - +
359H GLY 3.2 21.5 - - - +
360H GLY* 3.7 11.9 - - - +
362H VAL* 3.6 18.8 - - + +
426H PHE* 3.8 13.4 - - + -
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Residues in contact with LEU 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318H ASN 3.2 11.5 + - - +
319H SER* 2.9 10.6 + - - +
321H ALA* 1.3 78.2 - - - +
323H ARG* 1.3 68.2 + - + +
325H ALA* 2.9 18.4 + - - +
326H GLU* 3.1 24.6 + - - +
339H TYR* 3.6 29.5 + - + +
341H GLY* 4.1 20.6 - - - +
342H LEU* 4.7 5.4 - - + +
358H PHE* 4.9 11.7 - - + -
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Residues in contact with ARG 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H SER* 2.9 36.6 + - - +
320H THR* 3.9 2.3 + - - +
322H LEU* 1.3 82.7 - - + +
324H MET* 1.3 64.2 + - - +
326H GLU* 3.3 12.9 + - - +
327H ILE* 3.1 28.9 + - + +
431H PHE* 3.1 58.5 - - + +
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Residues in contact with MET 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H THR* 2.8 26.1 + - + +
321H ALA 3.8 0.7 - - - +
323H ARG* 1.3 71.5 - - - +
325H ALA* 1.3 59.8 + - - +
327H ILE* 4.3 13.0 - - + -
328H LEU* 2.8 52.2 + - + +
426H PHE* 3.3 32.8 - - + -
431H PHE* 3.5 24.2 - - + -
434H LEU* 5.6 0.2 - - + -
435H LYS* 3.7 30.1 - - + +
438H ILE* 3.6 29.4 - - + -
439H LEU* 6.1 1.3 - - + -
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Residues in contact with ALA 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H ALA 2.8 15.1 + - - +
322H LEU 3.0 11.7 - - - +
324H MET* 1.3 76.9 - - - +
326H GLU* 1.3 51.6 + - - +
328H LEU* 3.0 7.0 + - - +
329H GLU* 2.7 34.5 + - - +
337H VAL* 3.9 10.3 - - + +
339H TYR* 4.1 17.7 - - + -
342H LEU* 3.9 26.2 - - + -
362H VAL* 4.5 8.3 - - + +
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Residues in contact with GLU 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H LEU* 3.1 23.3 + - + +
323H ARG* 3.7 13.7 - - - +
325H ALA* 1.3 77.5 - - - +
327H ILE* 1.3 66.4 + - + +
329H GLU* 2.8 18.2 + - - +
330H ALA* 2.9 15.7 + - - +
342H LEU* 3.7 22.5 - - + +
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Residues in contact with ILE 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H ARG* 3.1 11.5 + - + +
324H MET* 3.7 20.2 - - + +
326H GLU* 1.3 78.8 - - + +
328H LEU* 1.3 63.8 + - + +
330H ALA* 3.6 6.0 + - - +
331H HIS* 3.2 21.4 + - + +
431H PHE* 3.8 19.1 - - + -
435H LYS* 3.7 32.1 - - + +
439H LEU* 4.5 25.4 - - + -
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Residues in contact with LEU 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H MET* 2.8 39.4 + - + +
325H ALA 3.3 3.6 - - - +
327H ILE* 1.3 77.0 - - + +
329H GLU* 1.3 65.8 + - - +
331H HIS* 3.0 13.3 + - + +
334H VAL* 3.1 31.8 - - + +
337H VAL* 3.7 12.1 - - + -
362H VAL* 4.5 9.9 - - + -
364H PHE* 3.6 41.5 - - + -
426H PHE* 4.9 6.1 - - + -
438H ILE* 4.0 13.0 - - + -
439H LEU* 6.2 0.4 - - + -
442H LEU* 3.9 28.7 - - + -
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Residues in contact with GLU 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H ALA 2.7 15.5 + - - +
326H GLU* 2.8 13.9 + - - +
328H LEU* 1.3 74.5 - - - +
330H ALA* 1.3 60.4 + - - +
331H HIS 3.5 5.0 + - - +
334H VAL* 4.5 5.9 - - - +
336H HIS* 5.8 0.9 - - - -
337H VAL* 3.6 25.9 + - + +
342H LEU* 3.9 21.3 - - + +
343H GLN 5.4 0.5 + - - -
344H SER* 2.7 32.3 + - - -
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Residues in contact with ALA 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H GLU 2.9 13.5 + - - +
327H ILE* 4.0 5.8 - - - +
329H GLU* 1.3 77.3 - - - +
331H HIS* 1.3 65.3 + - - +
332H PRO* 3.5 5.0 - - - +
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Residues in contact with HIS 331 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H ILE* 3.2 13.1 + - + +
328H LEU* 3.0 16.4 + - + +
329H GLU 3.9 1.9 - - - +
330H ALA* 1.3 78.5 - - - +
332H PRO* 1.3 81.6 - - + +
333H LYS* 2.9 51.4 + - + +
334H VAL* 3.2 30.7 + - + +
439H LEU* 4.0 19.9 + - + +
442H LEU* 3.8 33.3 - - + +
443H ASP* 5.4 4.3 + - - -
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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