Contacts of the helix formed by residues 366 - 384 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D THR* 4.4 1.2 - - - +
23D ASP 3.2 15.6 + - - -
24D THR 2.7 26.6 + - - +
25D LYS 3.7 15.1 + - - +
26D GLY* 3.4 10.1 - - - -
104D PRO* 3.8 7.7 - - - +
311D LEU 3.7 5.3 + - - +
314D PRO* 4.4 2.0 - - - +
364D ALA 3.6 1.8 + - - -
365D ALA* 1.3 70.2 - - - +
367D PRO* 1.3 71.3 - - - +
368D TYR* 3.2 25.2 + - - +
369D LEU* 3.1 28.6 + - + +
370D CYS* 2.7 23.8 + - - +
442D TYR* 5.3 4.3 - - + +
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Residues in contact with PRO 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLY* 4.8 5.2 - - - +
232D ALA* 3.4 32.3 - - + +
235D ILE* 3.3 32.5 - - + -
236D GLN* 3.8 19.5 - - - +
239D LYS* 5.0 2.5 - - - +
268D MET* 5.3 2.9 - - + -
365D ALA* 3.1 11.7 - - + +
366D ASN* 1.3 87.2 - - - +
368D TYR* 1.3 56.3 + - + +
370D CYS* 4.4 1.6 - - + -
371D PHE* 2.7 51.1 + - + -
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Residues in contact with TYR 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 3.4 29.0 + - + -
88D ARG* 3.7 14.9 + - - -
104D PRO* 3.4 32.5 - - + +
105D ARG* 3.9 22.7 + - + +
108D ALA* 3.9 24.3 - - + +
229D THR* 4.0 6.5 - - + -
232D ALA* 3.2 30.2 + - + -
233D ASP* 2.6 36.5 + - - -
236D GLN* 4.2 9.5 - - + +
366D ASN* 3.4 12.8 - - - +
367D PRO* 1.3 75.9 - - + +
369D LEU* 1.3 65.7 + - - +
371D PHE* 3.8 2.6 - - - +
372D ALA* 3.0 25.4 + - - +
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Residues in contact with LEU 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D THR* 4.0 11.9 - - + +
104D PRO* 3.6 31.9 - - + +
107D ILE* 4.1 19.1 - - + -
311D LEU* 3.0 28.6 - - + +
366D ASN* 3.1 20.4 + - + +
368D TYR* 1.3 75.9 - - - +
370D CYS* 1.3 64.0 + - - +
372D ALA* 3.3 1.8 + - - +
373D ALA 3.0 20.1 + - - -
434D PHE* 4.3 15.3 - - + -
442D TYR* 3.5 37.7 - - + -
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Residues in contact with CYS 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D MET* 6.0 2.0 - - - -
270D CYS* 5.1 0.9 - - - -
308D ILE* 4.7 0.3 - - - +
311D LEU* 3.8 15.6 - - - +
312D ALA* 3.1 33.2 - - - -
361D PRO* 4.3 7.6 - - - -
365D ALA* 3.8 17.5 - - + -
366D ASN 2.7 22.0 + - - +
367D PRO* 3.5 3.4 - - + +
369D LEU* 1.3 75.6 - - - +
371D PHE* 1.3 73.3 + - + +
373D ALA* 3.3 3.3 + - - +
374D LEU* 3.1 34.4 + - - +
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Residues in contact with PHE 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 3.3 34.1 - + + -
128D PRO* 3.6 24.0 - - + -
228D MET* 3.5 37.5 - - + -
231D LYS* 4.1 10.3 - - + -
232D ALA* 3.6 30.1 - - + -
235D ILE* 4.2 11.4 - - + -
268D MET* 4.9 7.4 - - + -
270D CYS* 4.1 20.4 - - - -
367D PRO* 2.7 31.8 + - + +
368D TYR* 3.8 3.6 - - - +
370D CYS* 1.3 81.6 - - + +
372D ALA* 1.3 63.7 + - - +
374D LEU* 3.1 2.5 + - - -
375D LEU* 2.9 18.9 + - - +
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Residues in contact with ALA 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ILE* 4.7 5.8 - - + -
108D ALA* 4.7 2.0 - - - -
111D ALA* 4.2 13.7 - - + -
228D MET* 3.7 19.2 - - + +
368D TYR 3.0 18.3 + - - +
369D LEU* 3.5 4.3 - - - +
371D PHE* 1.3 75.6 - - - +
373D ALA* 1.3 55.3 + - - +
375D LEU* 2.9 4.3 + - - +
376D MET* 2.7 39.2 + - + +
434D PHE* 3.9 21.5 - - + -
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ILE* 3.9 24.1 - - + +
311D LEU* 3.6 21.1 - - + -
369D LEU 3.0 17.6 + - - +
370D CYS 3.6 4.5 - - - +
372D ALA* 1.3 75.3 - - - +
374D LEU* 1.3 63.2 + - - +
377D ALA* 3.1 26.5 + - - +
427D PHE* 3.7 3.5 - - + -
428D LEU* 3.9 22.6 - - + +
434D PHE* 4.7 0.6 - - - -
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Residues in contact with LEU 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.0 15.5 - - + -
270D CYS* 4.3 19.5 - - + -
272D MET* 3.8 24.7 - - + -
297D TYR* 3.7 9.8 + - - -
301D VAL* 4.3 15.3 - - + +
308D ILE* 3.3 35.7 - - + -
358D VAL* 4.7 4.3 - - + -
360D PHE* 4.6 8.5 - - + -
361D PRO* 4.4 6.7 - - + -
370D CYS* 3.1 32.5 + - - +
371D PHE 3.1 7.4 + - - +
373D ALA* 1.3 76.8 - - - +
375D LEU* 1.3 61.1 + - - +
377D ALA* 3.8 2.4 - - - +
378D GLY* 3.0 17.8 + - - -
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.7 27.6 - - + +
115D LEU* 4.4 2.2 - - + -
124D VAL* 3.8 33.0 - - + -
126D PHE* 4.6 1.8 - - + -
228D MET* 4.0 11.4 - - + -
274D LEU* 4.4 4.3 - - + -
297D TYR* 3.2 22.1 + - + +
371D PHE 2.9 12.2 + - - +
372D ALA 2.9 7.6 + - - +
374D LEU* 1.3 77.0 - - - +
376D MET* 1.3 65.2 + - - +
378D GLY* 3.0 2.9 + - - -
379D LEU* 2.9 59.5 + - + +
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Residues in contact with MET 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 4.0 17.0 - - + -
114D TYR* 4.3 19.5 - - + -
372D ALA* 2.7 26.4 + - + +
373D ALA 4.2 0.2 - - - +
375D LEU* 1.3 76.4 - - - +
377D ALA* 1.3 61.0 + - - +
379D LEU* 3.5 4.6 + - - +
380D ASP* 3.1 26.9 + - - +
427D PHE* 3.6 24.0 - - - +
428D LEU* 3.7 26.2 - - + +
430D ALA* 3.4 21.1 - - + +
433D VAL* 3.4 39.7 - - + -
434D PHE* 5.1 0.2 - - + -
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Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D GLY* 3.1 31.3 - - - +
301D VAL* 4.1 1.3 - - - -
304D HIS* 3.4 16.2 - - + -
308D ILE* 3.6 20.9 - - + -
373D ALA 3.1 19.5 + - - +
374D LEU 3.8 2.2 - - - +
376D MET* 1.3 76.5 - - - +
378D GLY* 1.3 63.2 + - - +
381D GLY 3.2 7.4 + - - -
427D PHE* 3.4 21.2 - - + -
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Residues in contact with GLY 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D TYR* 3.4 51.6 - - - -
301D VAL* 4.5 0.7 - - - -
374D LEU 3.0 8.4 + - - -
375D LEU 3.0 6.3 + - - -
377D ALA* 1.3 76.2 - - - +
379D LEU* 1.3 64.6 + - - +
381D GLY 3.2 8.8 + - - -
382D ILE* 3.2 12.8 + - - +
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Residues in contact with LEU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.6 37.7 - - + +
115D LEU* 3.3 33.9 - - + -
118D THR* 4.9 2.2 - - - +
120D ILE* 4.0 19.7 - - + -
274D LEU* 4.3 12.6 - - + -
375D LEU* 2.9 46.6 + - + +
376D MET* 3.9 7.6 - - - +
378D GLY* 1.3 76.8 - - - +
380D ASP* 1.3 57.6 + - - +
382D ILE* 3.0 9.2 + - + +
383D LYS* 2.9 34.7 + - - +
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Residues in contact with ASP 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LYS* 4.8 2.1 + - - +
304D HIS* 3.0 32.9 + - - +
376D MET 3.1 18.8 + - - +
377D ALA 3.9 1.1 - - - +
379D LEU* 1.3 76.5 - - - +
381D GLY* 1.3 61.0 + - - +
383D LYS* 3.8 22.8 + - - +
384D ASN* 3.2 32.9 + - - +
386D ILE* 3.8 12.3 - - - +
427D PHE* 4.0 16.4 - - + +
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Residues in contact with GLY 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D TYR* 3.3 27.7 - - - +
300D GLY* 3.7 9.4 - - - -
377D ALA 3.2 9.7 + - - -
378D GLY 3.2 1.7 + - - -
379D LEU 3.1 0.4 - - - -
380D ASP* 1.3 78.2 + - - +
382D ILE* 1.3 57.0 + - - +
385D LYS 3.2 4.0 + - - -
386D ILE* 2.8 41.9 + - - -
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Residues in contact with ILE 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE* 3.7 36.8 - - + -
274D LEU* 4.4 6.7 - - + -
293D GLN* 3.7 42.2 - - + +
296D TYR* 3.6 23.3 - - + -
297D TYR* 4.0 15.3 - - + +
378D GLY 3.2 14.5 + - - +
379D LEU* 3.0 9.6 + - - +
381D GLY* 1.3 76.0 - - - +
383D LYS* 1.3 70.9 + - - +
385D LYS* 3.0 24.8 + - - +
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Residues in contact with LYS 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.1 30.5 + - - +
118D THR* 4.8 11.2 - - + -
120D ILE* 4.2 15.0 - - + -
379D LEU* 2.9 23.9 + - - +
380D ASP* 3.8 26.6 + - - +
382D ILE* 1.3 76.2 - - - +
384D ASN* 1.3 72.2 + - - +
385D LYS* 3.3 10.9 + - - +
430D ALA* 5.7 0.2 - - - -
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Residues in contact with ASN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D LYS* 5.8 2.0 + - - +
380D ASP* 3.2 26.4 + - - +
381D GLY 3.8 0.4 - - - -
383D LYS* 1.3 96.1 + - - +
385D LYS* 1.3 70.1 + - - +
386D ILE* 3.0 17.4 + - + +
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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
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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