Contacts of the helix formed by residues 366 - 385 (chain H) in PDB entry 1P8J
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 GLY 366 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295H ASN* 3.8 8.5 - - - -
329H TYR* 3.6 23.3 - - - -
342H SER* 2.7 23.8 + - - -
343H SER* 3.1 10.3 + - - -
365H THR* 1.3 74.4 - - - +
367H THR* 1.3 62.8 + - - -
368H SER 2.9 7.7 + - - -
369H ALA* 3.1 8.1 + - - +
370H SER 3.8 0.3 + - - -
805R AR7 4.2 3.6 - - - -
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Residues in contact with THR 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H ALA* 3.3 18.1 - - - +
293H SER* 3.8 17.5 - - - +
294H GLY* 3.2 37.7 + - - +
295H ASN* 2.7 23.5 + - - +
317H ILE 4.5 2.9 - - - +
318H SER* 5.3 0.2 - - - -
319H SER* 3.3 28.3 - - - +
329H TYR* 3.6 8.9 - - + -
330H SER* 5.4 2.9 - - - -
366H GLY* 1.3 71.6 - - - -
368H SER* 1.3 62.2 + - - +
369H ALA 3.1 0.2 - - - -
370H SER* 3.1 11.9 + - - -
371H ALA 3.2 11.3 + - - -
805R AR7 3.9 2.4 - - - +
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Residues in contact with SER 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H HIS* 2.9 12.4 - - - -
198H CYS* 3.5 6.8 - - - -
253H SER* 3.2 14.5 + - - -
292H ALA* 4.3 0.4 - - - -
364H HIS* 4.1 7.4 - - - -
365H THR 4.3 4.5 - - - -
366H GLY 2.9 1.4 - - - -
367H THR* 1.3 79.6 + - - +
369H ALA* 1.3 57.3 + - - +
372H PRO* 2.8 24.2 - - - +
805R AR7 1.4 56.7 + - - +
806R 0QE 2.3 8.2 - - - +
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Residues in contact with ALA 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201H GLU* 3.5 24.8 - - - +
342H SER* 3.7 4.5 - - - +
351H ILE* 3.7 24.2 - - + -
364H HIS* 3.7 10.5 - - + +
365H THR 4.0 5.8 + - - +
366H GLY 3.1 11.5 + - - +
367H THR 3.1 0.4 - - - -
368H SER* 1.3 78.3 - - - +
370H SER* 1.3 64.6 + - - +
371H ALA 3.5 0.2 - - - -
372H PRO* 3.3 8.2 - - - +
373H LEU* 3.2 24.7 - - - +
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Residues in contact with SER 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H ILE* 4.1 6.7 - - - -
318H SER 3.6 12.3 - - - -
319H SER* 2.7 28.0 + - - -
340H THR* 2.9 38.0 + - - +
341H TYR 4.4 1.3 - - - -
342H SER* 3.5 7.3 - - - -
366H GLY 3.8 0.2 + - - -
367H THR* 3.1 10.8 + - - -
369H ALA* 1.3 78.8 - - - +
371H ALA* 1.3 65.7 + - - +
373H LEU 3.3 0.9 + - - -
374H ALA* 3.0 21.1 + - - +
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Residues in contact with ALA 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251H SER* 3.9 8.7 - - - +
252H ALA 4.6 2.2 - - - +
253H SER* 3.7 11.2 - - - +
290H VAL* 3.3 14.9 - - + +
291H TRP* 3.9 6.7 - - - -
292H ALA* 3.7 30.5 - - + +
317H ILE* 4.4 5.5 - - - +
367H THR 3.2 3.2 + - - -
370H SER* 1.3 78.1 - - - +
372H PRO* 1.3 65.9 - - + +
374H ALA* 3.0 7.2 + - - +
375H ALA* 2.8 23.7 + - - +
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Residues in contact with PRO 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H ILE* 4.6 0.2 - - + -
198H CYS* 3.4 30.5 - - + +
201H GLU* 3.0 29.4 - - + +
202H VAL* 3.2 20.6 - - + +
251H SER* 3.6 13.7 - - - +
253H SER* 3.7 5.2 - - - +
368H SER 2.8 24.7 - - - +
369H ALA 3.3 5.4 - - - +
371H ALA* 1.3 88.0 - - + +
373H LEU* 1.3 62.2 + - - -
375H ALA* 3.1 1.5 + - + -
376H GLY* 2.9 19.9 + - - -
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Residues in contact with LEU 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H TYR* 4.0 34.5 - - + -
124H LEU* 4.7 1.1 - - + -
132H LEU* 4.2 12.6 - - + -
201H GLU* 4.0 23.1 - - + +
215H VAL* 3.7 24.8 - - + +
340H THR* 4.1 10.3 - - - +
341H TYR 3.5 23.8 - - - +
351H ILE* 4.4 9.4 - - + -
369H ALA 3.2 21.2 + - - +
370H SER 3.3 7.3 + - - +
371H ALA 3.2 0.6 - - - -
372H PRO* 1.3 77.9 - - - +
374H ALA* 1.3 62.6 + - - +
376H GLY* 3.3 2.3 + - - -
377H ILE* 3.1 27.7 + - - +
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Residues in contact with ALA 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H VAL* 4.0 3.6 - - + -
317H ILE* 3.7 24.9 - - + -
340H THR* 3.9 3.5 - - + +
370H SER 3.0 12.4 + - - +
371H ALA 3.0 10.4 + - - +
373H LEU* 1.3 75.2 - - - +
375H ALA* 1.3 59.7 + - - +
377H ILE* 3.2 2.8 + - - +
378H ILE* 2.8 39.1 + - + +
429H LEU* 3.7 28.3 - - + -
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Residues in contact with ALA 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149H VAL* 4.4 5.0 - - + +
202H VAL* 4.2 8.5 - - + -
249H ILE* 3.7 19.8 - - + +
251H SER* 4.0 19.1 - - - -
290H VAL* 4.2 12.3 - - + +
371H ALA 2.8 12.9 + - - +
372H PRO* 3.1 14.1 + - + +
374H ALA* 1.3 77.2 - - - +
376H GLY* 1.3 57.1 + - - +
378H ILE* 3.2 4.3 + - - +
379H ALA* 2.8 29.0 + - - +
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Residues in contact with GLY 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202H VAL* 4.2 14.1 - - - +
215H VAL* 3.5 20.4 - - - -
216H ALA* 3.9 4.6 - - - +
372H PRO 2.9 13.2 + - - -
373H LEU 3.7 3.6 - - - -
374H ALA 3.2 0.2 - - - -
375H ALA* 1.3 76.9 - - - +
377H ILE* 1.3 57.3 + - - +
379H ALA* 2.9 24.2 + - - +
380H LEU* 3.0 15.2 + - - +
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Residues in contact with ILE 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H LEU* 4.2 30.3 - - + -
134H VAL* 4.4 1.3 - - + -
215H VAL* 3.8 17.0 - - + -
340H THR* 5.2 0.2 - - + -
373H LEU 3.1 16.5 + - - +
374H ALA 3.2 6.9 + - - +
376H GLY* 1.3 74.8 - - - +
378H ILE* 1.3 61.8 + - - +
380H LEU* 3.3 7.4 + - - +
381H THR* 2.9 26.7 + - - +
429H LEU* 3.8 35.0 - - + -
431H ALA* 4.0 32.5 - - + +
434H MET* 4.2 20.0 - - + -
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Residues in contact with ILE 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H ILE* 3.6 16.2 - - + -
288H ILE* 4.0 12.1 - - + -
290H VAL* 3.6 28.3 - - + -
315H LEU* 3.9 26.5 - - + -
317H ILE* 6.0 1.3 - - + -
374H ALA* 2.8 23.1 + - + +
375H ALA* 3.6 5.4 - - - +
377H ILE* 1.3 75.2 - - + +
379H ALA* 1.3 60.6 + - - +
381H THR* 3.3 8.0 + - - -
382H LEU* 3.0 26.5 + - - +
393H MET* 3.7 31.6 - - + -
397H VAL* 5.1 2.2 - - + -
429H LEU* 5.4 3.6 - - + -
434H MET* 4.5 9.6 - - + -
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Residues in contact with ALA 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H GLY* 4.9 1.3 - - - -
147H ILE* 3.5 32.5 - - + +
149H VAL* 4.2 8.7 - - + -
216H ALA* 3.8 18.8 - - + -
219H ALA* 4.8 0.7 - - + -
249H ILE* 3.5 11.9 - - + +
375H ALA 2.8 13.4 + - - +
376H GLY* 2.9 12.7 + - - +
378H ILE* 1.3 75.7 - - - +
380H LEU* 1.3 64.2 + - - +
382H LEU* 3.2 1.8 + - - +
383H GLU* 3.1 18.2 + - - +
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Residues in contact with LEU 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H VAL* 4.8 1.8 - - + -
137H ALA* 3.8 23.6 - - + -
138H TRP* 4.2 5.2 - - - +
142H PHE* 3.5 10.7 - - + +
143H THR* 3.4 40.6 - - - -
144H GLY 3.5 0.4 - - - +
215H VAL* 3.8 31.0 - - + +
216H ALA* 3.9 5.8 - - - -
376H GLY 3.0 15.6 + - - +
377H ILE* 3.5 7.4 - - + +
379H ALA* 1.3 74.7 - - - +
381H THR* 1.3 64.0 + - - +
383H GLU* 3.2 9.1 + - - +
384H ALA* 3.1 17.2 + - - +
431H ALA* 4.5 12.3 - - + -
435H VAL* 3.8 18.7 - - + +
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Residues in contact with THR 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H ILE 2.9 14.2 + - - -
378H ILE* 3.5 9.0 - - - -
380H LEU* 1.3 79.1 - - - +
382H LEU* 1.3 60.9 + - - +
384H ALA* 3.2 6.0 + - - +
385H ASN 3.1 15.6 + - - -
388H LEU* 3.7 11.2 - - + +
393H MET* 3.9 8.1 - - - -
396H LEU* 3.5 31.4 - - + -
434H MET* 3.3 34.3 - - + +
435H VAL* 4.2 9.2 + - - +
438H ALA* 3.6 11.2 - - + +
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Residues in contact with LEU 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H ILE* 3.8 13.5 - - + -
248H HIS* 3.6 35.2 - - + -
249H ILE* 4.1 15.3 - - + -
282H ARG* 3.5 26.9 - - - +
288H ILE* 4.1 11.9 - - + -
378H ILE 3.0 8.9 + - - +
379H ALA 3.2 8.5 + - - +
381H THR* 1.3 75.4 - - - +
383H GLU* 1.3 63.7 + - - +
385H ASN 3.7 14.8 - - - +
386H LYS* 2.9 38.1 + - - +
388H LEU* 4.3 3.4 - - + -
393H MET* 3.8 23.1 - - + -
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Residues in contact with GLU 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H GLY 3.8 8.4 - - - +
142H PHE* 3.2 22.3 - - + +
143H THR 2.8 13.6 + - - -
144H GLY 2.7 25.9 + - - +
145H HIS* 3.2 39.9 + - - +
147H ILE* 3.9 15.8 - - + +
379H ALA 3.1 12.5 + - - +
380H LEU 3.2 7.8 + - - +
382H LEU* 1.3 76.9 - - - +
384H ALA* 1.3 61.3 + - - +
385H ASN* 3.2 1.2 + - - -
386H LYS* 4.3 9.8 + - - +
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Residues in contact with ALA 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H PHE* 3.4 33.0 - - + -
380H LEU 3.1 11.7 + - - +
381H THR 3.4 9.9 - - - +
383H GLU* 1.3 78.4 - - - +
385H ASN* 1.3 61.6 + - - +
435H VAL* 4.0 25.8 - - + +
438H ALA* 4.4 3.1 - - + -
439H GLN* 4.0 16.7 - - + +
901H NAG 5.3 2.5 - - - +
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Residues in contact with ASN 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H THR 3.1 3.0 + - - -
382H LEU* 2.9 10.3 + - - +
383H GLU 3.1 0.6 - - - -
384H ALA* 1.3 82.1 - - - +
386H LYS* 1.3 58.3 + - - +
387H ASN* 2.9 27.7 + - - +
388H LEU* 3.3 42.6 + - + +
438H ALA* 2.8 29.7 + - + +
439H GLN* 4.5 5.2 + - - -
441H TRP* 4.1 14.1 + - - -
901H NAG 3.8 14.9 - - - +
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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