Contacts of the helix formed by residues 366 - 385 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G ASN* 3.8 8.5 - - - -
329G TYR* 3.6 23.9 - - - -
342G SER* 2.7 24.4 + - - -
343G SER* 3.2 9.5 + - - -
365G THR* 1.3 75.0 - - - +
367G THR* 1.3 63.2 + - - -
368G SER 3.0 8.4 + - - -
369G ALA 3.1 8.0 + - - -
370G SER 3.8 0.2 + - - -
805Q AR7 4.2 3.4 - - - -
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Residues in contact with THR 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G ALA* 3.4 20.0 - - - +
293G SER* 3.9 17.5 - - - +
294G GLY* 3.3 35.5 + - - +
295G ASN* 2.8 22.1 + - - +
317G ILE 4.4 3.1 - - - +
318G SER* 5.4 0.2 - - - -
319G SER* 3.4 26.9 - - - +
329G TYR* 3.6 9.6 - - + -
330G SER* 5.4 3.4 - - - -
366G GLY* 1.3 70.8 - - - -
368G SER* 1.3 62.2 + - - +
369G ALA 3.1 0.7 - - - -
370G SER* 3.1 12.4 + - - -
371G ALA 3.2 11.8 + - - -
805Q AR7 3.9 2.4 - - - +
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Residues in contact with SER 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194G HIS* 2.9 12.7 - - - -
198G CYS* 3.5 6.4 - - - -
253G SER* 3.1 15.6 + - - -
292G ALA* 4.3 0.4 - - - -
364G HIS* 4.1 10.3 - - - -
365G THR 4.3 1.6 - - - -
366G GLY 3.0 0.6 - - - -
367G THR* 1.3 80.2 + - - +
369G ALA* 1.3 56.8 + - - +
372G PRO* 2.8 24.1 - - - +
805Q AR7 1.4 56.9 + - - +
806Q 0QE 2.3 8.6 - - - +
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Residues in contact with ALA 369 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G GLU* 2.6 33.7 - - - +
341G TYR 4.9 0.2 - - - -
342G SER* 3.6 10.3 - - - +
351G ILE* 3.6 18.2 - - + -
364G HIS* 3.7 14.1 - - + +
365G THR 4.0 6.7 + - - +
366G GLY 3.1 11.5 + - - +
367G THR 3.1 0.6 - - - -
368G SER* 1.3 78.3 - - - +
370G SER* 1.3 64.0 + - - +
371G ALA 3.5 0.2 - - - -
372G PRO* 3.3 5.0 - - - +
373G LEU* 3.2 14.2 - - - +
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Residues in contact with SER 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G ILE* 3.9 6.9 - - - +
318G SER 3.6 13.2 - - - -
319G SER* 2.6 27.8 + - - -
340G THR* 3.0 38.3 + - - +
341G TYR 4.4 0.9 - - - -
342G SER* 3.6 6.8 - - - -
366G GLY 3.8 0.2 + - - -
367G THR* 3.1 9.5 + - - -
369G ALA* 1.3 78.6 - - - +
371G ALA* 1.3 66.4 + - - +
373G LEU 3.3 0.9 + - - -
374G ALA* 3.0 21.8 + - - +
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Residues in contact with ALA 371 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251G SER* 3.9 8.5 - - - +
252G ALA 4.6 1.8 - - - +
253G SER* 3.7 13.0 - - - +
290G VAL* 3.4 15.4 - - + +
291G TRP* 3.9 6.5 - - - -
292G ALA* 3.7 30.7 - - + +
317G ILE* 4.4 5.3 - - - +
367G THR 3.2 2.8 + - - -
370G SER* 1.3 78.7 - - - +
372G PRO* 1.3 66.7 - - + +
374G ALA* 3.0 7.1 + - - +
375G ALA* 2.9 23.2 + - - +
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Residues in contact with PRO 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ILE* 4.7 0.2 - - + -
198G CYS* 3.4 31.0 - - + +
201G GLU* 3.5 19.1 - - + +
202G VAL* 3.2 20.0 - - + +
251G SER* 3.6 13.4 - - - +
253G SER* 3.8 5.2 - - - +
368G SER 2.8 29.6 - - - +
369G ALA 3.3 14.6 - - - +
371G ALA* 1.3 90.1 - - + +
373G LEU* 1.3 59.2 + - - +
375G ALA* 3.1 1.2 + - + -
376G GLY* 2.9 20.1 + - - -
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Residues in contact with LEU 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G TYR* 4.1 35.9 - - + -
124G LEU* 5.2 0.7 - - + -
132G LEU* 5.0 8.1 - - + -
201G GLU* 3.6 26.2 - - + +
215G VAL* 3.6 26.2 - - + +
340G THR* 4.0 13.0 - - + +
341G TYR 3.5 24.9 - - - +
351G ILE* 4.4 5.4 - - + -
369G ALA 3.2 15.3 - - - +
370G SER 3.3 7.8 + - - +
371G ALA 3.2 0.4 - - - -
372G PRO* 1.3 77.8 - - - +
374G ALA* 1.3 62.1 + - - +
376G GLY* 3.3 2.3 + - - -
377G ILE* 3.1 28.5 + - + +
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Residues in contact with ALA 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G VAL* 4.0 4.0 - - + -
317G ILE* 3.7 27.6 - - + -
340G THR* 4.1 3.8 - - + +
370G SER 3.0 12.7 + - - +
371G ALA 3.0 8.9 + - - +
373G LEU* 1.3 75.8 - - - +
375G ALA* 1.3 59.9 + - - +
377G ILE* 3.2 2.8 + - - +
378G ILE* 2.8 38.7 + - + +
429G LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G VAL* 4.3 3.9 - - + +
202G VAL* 4.2 9.0 - - + -
249G ILE* 3.8 22.9 - - + +
251G SER* 4.0 20.6 - - - -
290G VAL* 4.2 13.6 - - + +
371G ALA 2.9 12.9 + - - +
372G PRO* 3.1 9.4 + - + +
374G ALA* 1.3 75.8 - - - +
376G GLY* 1.3 59.1 + - - +
378G ILE* 3.2 4.2 + - - +
379G ALA* 2.8 27.9 + - - +
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Residues in contact with GLY 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202G VAL* 4.2 13.9 - - - +
215G VAL* 3.6 19.3 - - - -
216G ALA* 3.8 5.3 - - - +
372G PRO 2.9 13.2 + - - -
373G LEU 3.3 3.3 + - - -
374G ALA 3.2 0.2 - - - -
375G ALA* 1.3 76.8 - - - +
377G ILE* 1.3 57.2 + - - +
379G ALA* 2.9 23.3 + - - +
380G LEU* 3.0 16.3 + - - +
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Residues in contact with ILE 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU* 4.1 28.7 - - + -
134G VAL* 4.5 2.9 - - + -
215G VAL* 3.5 18.6 - - + +
340G THR* 4.9 1.1 - - + -
373G LEU* 3.1 14.9 + - + +
374G ALA 3.2 6.9 + - - +
376G GLY* 1.3 75.1 - - - +
378G ILE* 1.3 61.5 + - + +
380G LEU* 3.4 7.6 + - - +
381G THR* 2.9 26.2 + - - +
429G LEU* 3.8 35.4 - - + -
431G ALA* 4.0 31.9 - - + +
434G MET* 4.2 18.6 - - + -
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Residues in contact with ILE 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249G ILE* 3.6 16.8 - - + -
288G ILE* 4.1 10.3 - - + -
290G VAL* 3.7 24.7 - - + -
315G LEU* 4.0 28.9 - - + -
317G ILE* 6.0 1.1 - - + -
374G ALA* 2.8 25.2 + - + +
375G ALA* 3.6 6.1 - - - +
377G ILE* 1.3 77.2 - - + +
379G ALA* 1.3 61.7 + - - +
381G THR* 3.4 7.3 + - - -
382G LEU* 3.0 25.6 + - - +
393G MET* 3.6 30.9 - - + +
397G VAL* 5.0 2.5 - - + -
429G LEU* 5.4 3.1 - - + -
434G MET* 4.5 10.1 - - + -
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Residues in contact with ALA 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G GLY* 4.7 2.6 - - - -
147G ILE* 3.5 32.5 - - + +
149G VAL* 4.2 9.0 - - + -
216G ALA* 3.8 18.6 - - + -
219G ALA* 4.9 0.7 - - + -
249G ILE* 3.6 11.4 - - + +
375G ALA 2.8 13.3 + - - +
376G GLY* 2.9 10.5 + - - +
378G ILE* 1.3 75.3 - - - +
380G LEU* 1.3 65.1 + - - +
382G LEU 3.2 1.4 + - - -
383G GLU* 3.0 18.9 + - - +
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Residues in contact with LEU 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G VAL* 4.8 1.6 - - + +
137G ALA* 3.8 24.2 - - + -
138G TRP* 4.2 5.8 - - + +
142G PHE* 3.5 17.1 - - + +
143G THR* 3.4 33.7 - - - -
144G GLY 3.6 0.7 - - - +
215G VAL* 3.7 33.0 - - + +
216G ALA* 3.8 6.1 - - + -
376G GLY 3.0 16.2 + - - +
377G ILE* 3.6 6.1 - - - +
379G ALA* 1.3 76.4 - - - +
381G THR* 1.3 61.7 + - - +
383G GLU* 3.2 8.9 + - - +
384G ALA* 3.1 21.0 + - - +
431G ALA* 4.4 12.1 - - + -
435G VAL* 3.8 15.3 - - + +
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Residues in contact with THR 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G ILE 2.9 16.2 + - - -
378G ILE 3.6 8.1 - - - -
380G LEU* 1.3 77.6 - - - +
382G LEU* 1.3 61.7 + - - +
384G ALA* 3.2 6.0 + - - +
385G ASN 3.2 15.8 + - - -
388G LEU* 3.7 10.2 - - + +
393G MET* 3.9 12.3 - - - -
396G LEU* 3.6 31.6 - - + -
434G MET* 3.4 31.5 - - + +
435G VAL* 4.1 8.3 + - - +
438G ALA* 3.6 11.6 - - + +
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Residues in contact with LEU 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G ILE* 3.8 13.0 - - + -
248G HIS* 3.7 35.0 - - + -
249G ILE* 4.1 14.6 - - + -
282G ARG* 3.6 27.8 - - - +
288G ILE* 4.1 10.8 - - + -
378G ILE 3.0 9.3 + - - +
379G ALA 3.2 8.5 + - - +
381G THR* 1.3 73.0 - - - +
383G GLU* 1.3 68.1 + - - +
385G ASN 2.9 16.7 - - - +
386G LYS* 2.9 36.0 + - + +
388G LEU* 4.4 3.1 - - + -
393G MET* 3.8 22.7 - - + -
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Residues in contact with GLU 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G GLY 3.8 8.4 - - - +
142G PHE* 3.2 21.3 - - + +
143G THR 2.8 13.3 + - - -
144G GLY 2.8 21.9 + - - +
145G HIS* 3.2 42.4 + - - +
147G ILE* 3.9 14.8 - - + +
379G ALA 3.0 12.8 + - - +
380G LEU 3.2 7.8 + - - +
382G LEU* 1.3 77.2 - - - +
384G ALA* 1.3 62.1 + - - +
385G ASN* 3.2 1.7 + - - -
386G LYS* 4.4 8.7 + - - +
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Residues in contact with ALA 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G PHE* 3.4 32.4 - - + -
380G LEU 3.1 11.9 + - - +
381G THR 3.4 10.8 - - - +
382G LEU 3.1 0.2 - - - -
383G GLU* 1.3 78.3 - - - +
385G ASN* 1.3 61.0 + - - +
435G VAL* 4.0 24.7 - - + +
438G ALA* 4.3 2.9 - - + -
439G GLN* 3.6 19.7 - - + +
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Residues in contact with ASN 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381G THR 3.2 3.2 + - - -
382G LEU* 2.9 10.2 + - - +
383G GLU 3.1 0.6 - - - -
384G ALA* 1.3 82.5 - - - +
386G LYS* 1.3 57.8 + - - +
387G ASN* 3.0 30.1 + - - +
388G LEU* 3.3 43.0 + - + +
438G ALA* 2.8 31.2 + - + +
439G GLN* 4.6 4.6 + - - -
441G TRP 4.1 15.4 + - - +
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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