Contacts of the helix formed by residues 366 - 384 (chain G) in PDB entry 1FPY
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 ASN 366 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 4.4 0.6 - - - +
23G ASP 3.2 15.8 + - - -
24G THR 2.7 26.4 + - - +
25G LYS 3.7 14.4 + - - +
26G GLY* 3.4 10.3 - - - -
104G PRO* 3.8 8.3 - - - +
311G LEU 3.7 6.1 + - - +
314G PRO* 4.4 2.0 - - - +
364G ALA 3.6 2.0 + - - -
365G ALA* 1.3 69.6 - - - +
367G PRO* 1.3 72.3 - - - +
368G TYR* 3.2 25.0 + - - +
369G LEU* 3.1 28.2 + - + +
370G CYS* 2.7 24.0 + - - +
442G TYR* 5.3 4.7 - - + +
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Residues in contact with PRO 367 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G GLY* 4.8 4.0 - - - +
232G ALA* 3.4 31.0 - - + +
235G ILE* 3.3 32.1 - - + -
236G GLN* 3.8 21.1 - - - +
239G LYS* 5.0 2.5 - - - +
268G MET* 5.3 4.0 - - + -
365G ALA* 3.1 11.3 - - + +
366G ASN* 1.3 88.5 - - - +
368G TYR* 1.3 57.8 + - + +
370G CYS* 3.5 2.0 - - + +
371G PHE* 2.7 50.2 + - + -
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Residues in contact with TYR 368 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G THR* 3.4 29.7 + - + -
88G ARG* 3.7 14.6 + - - -
104G PRO* 3.4 32.3 - - + +
105G ARG* 3.9 23.1 + - + -
108G ALA* 3.9 24.1 - - + +
229G THR* 4.0 6.5 - - + -
232G ALA* 3.2 29.5 + - + -
233G ASP* 2.6 34.8 + - - -
236G GLN* 4.2 9.5 - - + +
366G ASN* 3.4 13.0 - - - +
367G PRO* 1.3 78.3 - - + +
369G LEU* 1.3 65.4 + - - +
371G PHE* 3.8 2.6 - - - +
372G ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 369 (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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24G THR* 4.0 11.9 - - + +
104G PRO* 3.6 32.1 - - + +
107G ILE* 4.1 19.1 - - + -
311G LEU* 3.0 28.5 - - + +
366G ASN* 3.1 21.3 + - + +
368G TYR* 1.3 76.1 - - - +
370G CYS* 1.3 64.7 + - - +
372G ALA* 3.3 2.4 + - - +
373G ALA 3.0 19.2 + - - -
434G PHE* 4.3 15.0 - - + -
442G TYR* 3.5 37.2 - - + -
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Residues in contact with CYS 370 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G MET* 6.0 1.3 - - - -
270G CYS* 5.1 1.3 - - - -
308G ILE* 4.7 0.5 - - - +
311G LEU* 3.8 15.6 - - - +
312G ALA* 3.1 33.0 - - - -
361G PRO* 4.3 7.6 - - - -
365G ALA* 3.8 17.7 - - + -
366G ASN 2.7 22.0 + - - +
367G PRO* 3.5 3.1 - - + +
369G LEU* 1.3 73.6 - - - +
371G PHE* 1.3 73.0 + - + +
373G ALA* 3.3 3.1 + - - +
374G LEU* 3.1 35.1 + - - +
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Residues in contact with PHE 371 (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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126G PHE* 3.3 35.6 - + + -
128G PRO* 3.6 23.3 - - + -
228G MET* 3.5 36.6 - - + -
231G LYS* 4.1 10.5 - - + -
232G ALA* 3.6 29.8 - - + -
235G ILE* 4.2 11.9 - - + -
268G MET* 4.9 7.2 - - + -
270G CYS* 4.1 19.7 - - - -
367G PRO* 2.7 31.3 + - + +
368G TYR* 3.8 3.1 - - - +
370G CYS* 1.3 82.9 - - + +
372G ALA* 1.3 63.4 + - - +
374G LEU* 3.1 2.5 + - - -
375G LEU* 2.9 18.7 + - - +
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Residues in contact with ALA 372 (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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107G ILE* 4.7 6.1 - - + -
108G ALA* 4.7 2.0 - - - -
111G ALA* 4.2 13.7 - - + -
228G MET* 3.7 19.2 - - + +
368G TYR 3.0 17.7 + - - +
369G LEU 3.5 4.0 - - - +
371G PHE* 1.3 74.2 - - - +
373G ALA* 1.3 56.1 + - - +
375G LEU* 2.9 4.8 + - - +
376G MET* 2.7 38.7 + - + +
434G PHE* 3.9 20.9 - - + -
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Residues in contact with ALA 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G ILE* 3.9 25.0 - - + +
311G LEU* 3.6 21.3 - - + -
369G LEU 3.0 16.2 + - - +
370G CYS 3.3 5.4 + - - +
372G ALA* 1.3 75.7 - - - +
374G LEU* 1.3 62.5 + - - +
377G ALA* 3.1 26.2 + - - +
427G PHE* 3.7 3.6 - - + -
428G LEU* 3.9 22.4 - - + +
434G PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 374 (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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126G PHE* 4.0 15.7 - - + -
270G CYS* 4.3 19.1 - - + -
272G MET* 3.8 24.0 - - + -
297G TYR* 3.7 9.1 + - - -
301G VAL* 4.3 14.9 - - + +
308G ILE* 3.3 36.6 - - + -
358G VAL* 4.8 3.8 - - + -
360G PHE* 4.6 8.7 - - + -
361G PRO* 4.4 6.7 - - + -
370G CYS* 3.1 32.2 + - - +
371G PHE 3.3 7.4 - - - +
373G ALA* 1.3 77.3 - - - +
375G LEU* 1.3 61.7 + - - +
377G ALA* 3.4 2.6 + - - +
378G GLY* 3.0 18.7 + - - -
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Residues in contact with LEU 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ALA* 3.7 26.9 - - + +
115G LEU* 4.4 2.0 - - + -
124G VAL* 3.8 32.3 - - + -
126G PHE* 4.4 2.0 - - + -
228G MET* 4.0 12.6 - - - -
274G LEU* 4.4 3.8 - - + -
297G TYR* 3.2 22.4 + - + +
371G PHE 2.9 10.9 + - - +
372G ALA 2.9 7.7 + - - +
374G LEU* 1.3 77.1 - - - +
376G MET* 1.3 66.4 + - - +
378G GLY* 3.0 2.9 + - - -
379G LEU* 2.9 59.9 + - + +
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Residues in contact with MET 376 (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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111G ALA* 4.0 17.5 - - + -
114G TYR* 4.3 20.0 - - + -
372G ALA* 2.7 26.6 + - + +
375G LEU* 1.3 77.7 - - - +
377G ALA* 1.3 62.2 + - - +
379G LEU* 3.9 4.3 - - - +
380G ASP* 3.1 27.5 + - - +
427G PHE* 3.6 23.6 - - - +
428G LEU* 3.7 25.8 - - + +
430G ALA* 3.4 20.6 - - + +
433G VAL* 3.4 40.8 - - + -
434G PHE* 5.1 0.2 - - + -
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Residues in contact with ALA 377 (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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300G GLY* 3.1 30.9 - - - +
301G VAL* 4.1 1.1 - - - -
304G HIS* 3.4 16.0 - - + -
308G ILE* 3.6 20.6 - - + -
373G ALA 3.1 19.5 + - - +
374G LEU 3.8 2.5 - - - +
376G MET* 1.3 76.5 - - - +
378G GLY* 1.3 61.9 + - - +
381G GLY 3.2 7.8 + - - -
427G PHE* 3.4 21.5 - - + -
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Residues in contact with GLY 378 (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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297G TYR* 3.4 51.8 - - - -
301G VAL* 4.5 0.6 - - - +
374G LEU 3.0 9.0 + - - -
375G LEU 3.0 6.0 + - - -
377G ALA* 1.3 76.0 - - - +
379G LEU* 1.3 62.6 + - - +
381G GLY 3.2 8.7 + - - -
382G ILE* 3.2 13.0 + - - +
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Residues in contact with LEU 379 (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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114G TYR* 3.6 39.3 - - + +
115G LEU* 3.2 33.2 - - + -
118G THR* 4.9 2.5 - - - +
120G ILE* 4.0 19.7 - - + +
274G LEU* 4.3 13.5 - - + -
375G LEU* 2.9 45.7 + - + +
376G MET* 3.9 7.4 - - - +
377G ALA 3.4 0.2 - - - -
378G GLY* 1.3 77.4 - - - +
380G ASP* 1.3 58.3 + - - +
382G ILE* 3.0 7.7 + - + +
383G LYS* 2.9 35.9 + - - +
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Residues in contact with ASP 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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303G LYS* 4.8 2.1 + - - +
304G HIS* 3.0 33.1 + - - +
376G MET 3.1 18.6 + - - +
377G ALA 3.9 0.7 - - - +
379G LEU* 1.3 76.2 - - - +
381G GLY* 1.3 61.7 + - - +
383G LYS* 3.8 23.9 + - - +
384G ASN* 3.2 33.0 + - - +
386G ILE* 3.8 12.6 - - - +
427G PHE* 4.0 16.2 - - + +
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Residues in contact with GLY 381 (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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296G TYR* 3.3 28.1 - - - +
300G GLY* 3.7 10.3 - - - -
377G ALA 3.2 9.1 + - - -
378G GLY 3.2 1.9 + - - -
379G LEU 3.1 0.8 - - - -
380G ASP* 1.3 78.2 + - - +
382G ILE* 1.3 56.7 + - - +
385G LYS 3.2 3.8 + - - -
386G ILE* 2.8 41.6 + - - -
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Residues in contact with ILE 382 (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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120G ILE* 3.7 36.6 - - + -
274G LEU* 4.4 6.1 - - + -
282G PHE* 5.5 0.2 - - + -
293G GLN* 3.7 42.2 - - + +
296G TYR* 3.6 23.0 - - + -
297G TYR* 4.0 15.9 - - + +
378G GLY 3.2 13.4 + - - +
379G LEU* 3.0 9.6 + - - +
381G GLY* 1.3 75.8 - - - +
383G LYS* 1.3 71.0 + - - +
384G ASN 3.3 0.2 - - - -
385G LYS* 3.0 23.8 + - - +
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Residues in contact with LYS 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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114G TYR* 3.1 31.3 + - - +
118G THR* 4.8 11.7 - - + -
120G ILE* 4.2 14.4 - - + -
379G LEU* 2.9 23.7 + - - +
380G ASP* 3.8 28.3 + - - +
382G ILE* 1.3 76.4 - - - +
384G ASN* 1.3 71.7 + - - +
385G LYS* 3.3 11.3 + - - +
430G ALA* 5.7 0.2 - - - -
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Residues in contact with ASN 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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303G LYS* 5.8 1.6 + - - -
380G ASP* 3.2 27.2 + - - +
381G GLY 3.8 0.2 - - - -
383G LYS* 1.3 96.1 - - - +
385G LYS* 1.3 68.9 + - - +
386G ILE* 3.0 17.7 + - + +
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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