Contacts of the helix formed by residues 366 - 384 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J THR* 4.4 1.0 - - - +
23J ASP 3.2 15.6 + - - -
24J THR 2.7 26.0 + - - +
25J LYS 3.7 14.9 + - - +
26J GLY* 3.4 9.8 - - - -
104J PRO* 3.8 7.9 - - - +
311J LEU 3.7 5.8 + - - +
314J PRO* 4.4 2.0 - - - +
364J ALA 3.6 2.2 + - - -
365J ALA* 1.3 69.0 - - - +
367J PRO* 1.3 70.6 - - - +
368J TYR* 3.2 25.2 + - - +
369J LEU* 3.1 29.0 + - + +
370J CYS* 2.7 24.3 + - - +
442J TYR* 5.3 4.3 - - + +
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Residues in contact with PRO 367 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J GLY* 4.8 3.6 - - - +
232J ALA* 3.4 30.5 - - + +
235J ILE* 3.3 32.3 - - + -
236J GLN* 3.8 20.4 - - - +
239J LYS* 5.0 2.9 - - - +
268J MET* 5.4 3.6 - - + -
365J ALA* 3.1 12.0 - - + +
366J ASN* 1.3 88.4 - - - +
368J TYR* 1.3 58.0 + - + +
370J CYS* 4.4 1.8 - - + -
371J PHE* 2.7 51.1 + - + -
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Residues in contact with TYR 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 3.4 28.9 + - + -
88J ARG* 3.7 14.4 + - - -
104J PRO* 3.4 33.0 - - + +
105J ARG* 3.9 22.0 + - + +
108J ALA* 3.9 23.6 - - + +
229J THR* 4.0 6.7 - - + -
232J ALA* 3.2 30.4 + - + -
233J ASP* 2.6 35.9 + - - -
236J GLN* 4.2 8.8 - - + +
366J ASN* 3.2 13.4 + - - +
367J PRO* 1.3 75.8 - - + +
369J LEU* 1.3 65.7 + - - +
371J PHE* 3.8 2.7 - - - +
372J ALA* 3.0 25.8 + - - +
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Residues in contact with LEU 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J THR* 4.0 11.9 - - + +
104J PRO* 3.6 32.3 - - + +
107J ILE* 4.1 18.4 - - + -
311J LEU* 3.0 29.3 - - + +
366J ASN* 3.1 21.6 + - + +
368J TYR* 1.3 75.6 - - - +
370J CYS* 1.3 64.3 + - - +
372J ALA* 3.5 1.8 - - - +
373J ALA 3.0 19.8 + - - -
434J PHE* 4.3 15.5 - - + -
442J TYR* 3.5 37.2 - - + -
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Residues in contact with CYS 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268J MET* 6.0 1.6 - - - -
270J CYS* 5.1 0.9 - - - -
308J ILE* 4.7 0.3 - - - +
311J LEU* 3.8 15.1 - - - +
312J ALA* 3.1 33.4 - - - -
361J PRO* 4.3 7.9 - - - -
365J ALA* 3.8 18.6 - - + -
366J ASN 2.7 22.2 + - - +
367J PRO* 3.5 3.4 - - + +
369J LEU* 1.3 73.9 - - - +
371J PHE* 1.3 73.0 + - + +
373J ALA* 3.3 3.1 + - - +
374J LEU* 3.1 34.6 + - - +
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Residues in contact with PHE 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 3.3 34.5 - + + -
128J PRO* 3.6 23.8 - - + -
228J MET* 3.5 36.3 - - + -
231J LYS* 4.1 10.5 - - + -
232J ALA* 3.6 30.3 - - + -
235J ILE* 4.2 11.2 - - + -
268J MET* 4.9 7.0 - - + -
270J CYS* 4.1 20.4 - - - -
367J PRO* 2.7 30.9 + - + +
368J TYR* 3.8 3.1 - - - +
370J CYS* 1.3 83.1 - - + +
372J ALA* 1.3 63.0 + - - +
374J LEU* 3.1 2.6 + - + -
375J LEU* 2.9 19.8 + - - +
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Residues in contact with ALA 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ILE* 4.7 6.3 - - + -
108J ALA* 4.7 2.0 - - - -
111J ALA* 4.2 13.7 - - + -
228J MET* 3.7 19.6 - - + +
368J TYR 3.0 18.4 + - - +
369J LEU* 3.5 4.3 - - - +
371J PHE* 1.3 74.5 - - - +
373J ALA* 1.3 56.1 + - - +
375J LEU* 2.9 4.5 + - - +
376J MET* 2.7 39.4 + - - +
434J PHE* 3.9 21.1 - - + -
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Residues in contact with ALA 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J ILE* 3.9 24.4 - - + +
311J LEU* 3.6 21.1 - - + -
369J LEU 3.0 16.7 + - - +
370J CYS 3.6 4.9 - - - +
372J ALA* 1.3 75.5 - - - +
374J LEU* 1.3 62.6 + - - +
377J ALA* 3.1 26.3 + - - +
427J PHE* 3.7 3.3 - - + -
428J LEU* 3.9 22.6 - - + +
434J PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 4.0 15.9 - - + -
270J CYS* 4.3 19.5 - - + -
272J MET* 3.8 24.7 - - + -
297J TYR* 3.7 9.4 + - - -
301J VAL* 4.3 15.1 - - + +
308J ILE* 3.3 36.8 - - + -
358J VAL* 4.8 4.5 - - + -
360J PHE* 4.6 8.5 - - + -
361J PRO* 4.4 6.5 - - + -
370J CYS* 3.1 32.0 + - - +
371J PHE 3.1 7.2 + - - +
373J ALA* 1.3 77.5 - - - +
375J LEU* 1.3 61.4 + - - +
377J ALA* 3.4 2.8 + - - +
378J GLY* 3.0 18.0 + - - -
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Residues in contact with LEU 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ALA* 3.7 26.5 - - + +
115J LEU* 4.4 1.8 - - + -
124J VAL* 3.8 34.8 - - + -
126J PHE* 4.4 2.7 - - + -
228J MET* 4.0 11.7 - - - -
274J LEU* 4.4 3.6 - - + -
297J TYR* 3.2 21.8 - - + +
371J PHE 2.9 11.3 + - - +
372J ALA 2.9 8.3 + - - +
374J LEU* 1.3 76.7 - - - +
376J MET* 1.3 65.8 + - - +
378J GLY* 3.0 2.3 + - - -
379J LEU* 2.9 59.9 + - + +
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Residues in contact with MET 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ALA* 4.0 16.6 - - + -
114J TYR* 4.3 19.5 - - + -
372J ALA* 2.7 26.7 + - + +
375J LEU* 1.3 77.1 - - - +
377J ALA* 1.3 60.5 + - - +
379J LEU* 3.5 4.8 + - - +
380J ASP* 3.1 27.4 + - - +
427J PHE* 3.6 23.2 - - - +
428J LEU* 3.7 25.8 - - + +
430J ALA* 3.4 20.6 - - + +
433J VAL* 3.4 41.3 - - + -
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Residues in contact with ALA 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300J GLY* 3.1 30.9 - - - +
301J VAL* 4.1 1.1 - - - -
304J HIS* 3.4 17.5 - - + -
308J ILE* 3.6 20.0 - - + -
373J ALA 3.1 20.0 + - - +
374J LEU 3.8 2.2 - - - +
376J MET* 1.3 76.5 - - - +
378J GLY* 1.3 63.3 + - - +
380J ASP 3.6 0.2 + - - -
381J GLY 3.2 7.4 + - - -
427J PHE* 3.4 21.3 - - + -
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Residues in contact with GLY 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297J TYR* 3.4 51.9 - - - -
301J VAL* 4.5 0.9 - - - +
374J LEU 3.0 9.0 + - - -
375J LEU 3.0 6.1 + - - -
377J ALA* 1.3 76.8 - - - +
379J LEU* 1.3 62.2 + - - +
381J GLY 3.2 8.8 + - - -
382J ILE* 3.2 12.6 + - - +
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Residues in contact with LEU 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J TYR* 3.6 38.8 - - + -
115J LEU* 3.2 33.7 - - + -
118J THR* 4.9 2.0 - - - +
120J ILE* 4.0 19.2 - - + +
274J LEU* 4.3 13.2 - - + -
375J LEU* 2.9 44.7 + - + +
376J MET* 3.9 7.2 - - - +
378J GLY* 1.3 77.9 - - - +
380J ASP* 1.3 56.5 + - - +
382J ILE* 3.0 8.2 + - + +
383J LYS* 2.9 36.0 + - - +
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Residues in contact with ASP 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J LYS* 4.8 1.7 + - - +
304J HIS* 3.0 33.1 + - - +
376J MET 3.1 18.8 + - - +
377J ALA 3.9 1.3 - - - +
378J GLY 3.3 0.2 - - - -
379J LEU* 1.3 77.3 - - - +
381J GLY* 1.3 61.6 + - - +
383J LYS* 3.8 23.4 + - - +
384J ASN* 3.2 33.1 + - - +
386J ILE* 3.8 12.5 - - - +
427J PHE* 4.0 16.9 - - + +
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Residues in contact with GLY 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296J TYR* 3.3 27.4 - - - +
300J GLY* 3.7 10.1 - - - -
377J ALA 3.2 9.5 + - - -
378J GLY 3.2 1.5 + - - -
379J LEU 3.1 0.6 - - - -
380J ASP* 1.3 77.6 + - - +
382J ILE* 1.3 57.1 + - - +
385J LYS 3.2 4.0 + - - -
386J ILE* 2.8 41.9 + - - -
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Residues in contact with ILE 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ILE* 3.7 36.3 - - + -
274J LEU* 4.4 6.5 - - + -
293J GLN* 3.7 42.4 - - + +
296J TYR* 3.6 23.1 - - + -
297J TYR* 4.0 15.0 - - + +
378J GLY 3.2 13.4 + - - +
379J LEU* 3.0 10.0 + - - +
381J GLY* 1.3 77.1 - - - +
383J LYS* 1.3 70.8 + - - +
385J LYS* 3.0 24.0 + - - +
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Residues in contact with LYS 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J TYR* 3.1 30.3 + - - +
118J THR* 4.8 11.2 - - + -
120J ILE* 4.2 14.4 - - + -
379J LEU* 2.9 23.5 + - - +
380J ASP* 3.8 27.8 + - - +
382J ILE* 1.3 77.4 - - - +
384J ASN* 1.3 71.5 + - - +
385J LYS* 3.3 11.3 + - - +
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Residues in contact with ASN 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303J LYS* 5.8 1.4 + - - -
380J ASP* 3.2 26.3 + - - +
381J GLY 3.8 0.4 - - - -
383J LYS* 1.3 95.3 - - - +
385J LYS* 1.3 68.8 + - - +
386J ILE* 3.0 18.1 + - + +
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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
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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