Contacts of the helix formed by residues 366 - 384 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 4.4 0.8 - - - +
23E ASP 3.2 15.0 + - - -
24E THR 2.7 26.8 + - - +
25E LYS 3.7 15.1 + - - +
26E GLY* 3.4 10.4 - - - -
104E PRO* 3.8 8.1 - - - +
311E LEU 3.7 5.8 + - - +
314E PRO* 4.4 2.0 - - - +
364E ALA 3.6 2.0 + - - -
365E ALA* 1.3 69.4 - - - +
367E PRO* 1.3 71.8 - - - +
368E TYR* 3.2 24.3 + - - +
369E LEU* 3.1 28.3 + - + +
370E CYS* 2.7 24.1 + - - +
442E TYR* 5.3 4.3 - - + +
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Residues in contact with PRO 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLY* 4.8 4.5 - - - +
232E ALA* 3.4 32.3 - - + +
235E ILE* 3.3 32.1 - - + -
236E GLN* 3.8 19.7 - - - +
239E LYS* 5.0 2.9 - - - +
268E MET* 5.3 3.6 - - + -
365E ALA* 3.1 12.0 - - + +
366E ASN* 1.3 85.8 - - - +
368E TYR* 1.3 56.6 + - + +
370E CYS* 4.4 1.6 - - + -
371E PHE* 2.7 51.4 + - + -
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Residues in contact with TYR 368 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E THR* 3.4 28.3 + - + -
88E ARG* 3.7 14.6 + - - -
104E PRO* 3.4 32.8 - - + +
105E ARG* 3.9 23.7 + - + +
108E ALA* 3.9 23.2 - - + +
229E THR* 4.0 6.1 - - + -
232E ALA* 3.2 29.8 + - + -
233E ASP* 2.6 35.8 + - - -
236E GLN* 4.2 9.2 - - + +
366E ASN* 3.2 13.4 + - - +
367E PRO* 1.3 75.4 - - + +
369E LEU* 1.3 65.5 + - - +
371E PHE* 3.8 2.4 - - - +
372E ALA* 3.0 26.0 + - - +
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Residues in contact with LEU 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E THR* 4.0 12.1 - - + +
104E PRO* 3.6 32.1 - - + +
107E ILE* 4.1 18.8 - - + -
311E LEU* 3.0 30.0 - - + +
366E ASN* 3.1 20.9 + - + +
368E TYR* 1.3 76.8 - - - +
370E CYS* 1.3 62.7 + - - +
372E ALA* 3.3 2.2 + - - +
373E ALA 3.0 19.9 + - - -
434E PHE* 4.3 15.0 - - + -
442E TYR* 3.5 37.7 - - + -
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Residues in contact with CYS 370 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E MET* 6.0 2.0 - - - -
270E CYS* 5.1 0.9 - - - -
308E ILE* 4.7 0.3 - - - +
311E LEU* 3.8 15.0 - - - +
312E ALA* 3.1 32.3 - - - -
361E PRO* 4.3 7.6 - - - -
365E ALA* 3.8 18.2 - - + -
366E ASN 2.7 21.1 + - - +
367E PRO* 3.5 3.8 - - + +
369E LEU* 1.3 75.0 - - - +
371E PHE* 1.3 72.4 + - + +
373E ALA* 3.3 3.1 + - - +
374E LEU* 3.1 34.8 + - - +
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Residues in contact with PHE 371 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 3.3 34.8 - + + -
128E PRO* 3.6 24.0 - - + -
228E MET* 3.5 36.8 - - + -
231E LYS* 4.1 10.3 - - + -
232E ALA* 3.6 31.2 - - + -
235E ILE* 4.2 11.2 - - + -
268E MET* 4.9 7.0 - - + -
270E CYS* 4.1 20.2 - - - -
367E PRO* 2.7 32.4 + - + +
368E TYR* 3.8 2.7 - - - +
370E CYS* 1.3 81.2 - - + +
372E ALA* 1.3 62.3 + - - +
374E LEU* 3.1 2.5 + - - -
375E LEU* 2.9 19.6 + - - +
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Residues in contact with ALA 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E ILE* 4.7 6.3 - - + -
108E ALA* 4.7 1.8 - - - -
111E ALA* 4.2 13.2 - - + -
228E MET* 3.7 19.4 - - + +
368E TYR 3.0 18.2 + - - +
369E LEU* 3.5 4.0 - - - +
371E PHE* 1.3 75.6 - - - +
373E ALA* 1.3 56.1 + - - +
375E LEU* 2.9 3.8 + - - +
376E MET* 2.7 38.3 + - + +
434E PHE* 3.9 21.8 - - + -
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Residues in contact with ALA 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E ILE* 3.9 23.6 - - + +
311E LEU* 3.6 21.5 - - + -
369E LEU 3.0 16.9 + - - +
370E CYS 3.6 5.2 - - - +
372E ALA* 1.3 75.1 - - - +
374E LEU* 1.3 63.2 + - - +
377E ALA* 3.1 26.0 + - - +
427E PHE* 3.7 3.7 - - + -
428E LEU* 3.9 22.4 - - + +
434E PHE* 4.7 0.4 - - - -
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Residues in contact with LEU 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 4.0 15.7 - - + -
270E CYS* 4.3 19.1 - - + -
272E MET* 3.8 23.8 - - + -
297E TYR* 3.7 9.3 + - - -
301E VAL* 4.3 15.5 - - + +
308E ILE* 3.3 36.6 - - + -
358E VAL* 4.7 3.8 - - + -
360E PHE* 4.6 8.3 - - + -
361E PRO* 4.4 6.5 - - + -
370E CYS* 3.1 32.5 + - - +
371E PHE 3.1 7.6 + - - +
373E ALA* 1.3 78.2 - - - +
375E LEU* 1.3 62.7 + - - +
377E ALA* 3.4 2.6 + - - +
378E GLY* 3.0 18.0 + - - -
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Residues in contact with LEU 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ALA* 3.7 26.7 - - + +
115E LEU* 4.4 1.8 - - + -
124E VAL* 3.8 35.4 - - + -
126E PHE* 4.4 2.0 - - + -
228E MET* 4.0 11.9 - - - -
274E LEU* 4.4 3.4 - - + -
297E TYR* 3.2 21.5 - - + +
371E PHE 2.9 11.2 + - - +
372E ALA 2.9 7.5 + - - +
374E LEU* 1.3 77.5 - - - +
376E MET* 1.3 64.7 + - - +
378E GLY* 3.0 2.6 + - - -
379E LEU* 2.9 59.9 + - + +
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Residues in contact with MET 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E ALA* 4.0 17.3 - - + -
114E TYR* 4.3 19.7 - - + -
372E ALA* 2.7 26.6 + - + +
375E LEU* 1.3 77.3 - - - +
377E ALA* 1.3 60.5 + - - +
379E LEU* 3.5 5.1 + - - +
380E ASP* 3.1 27.2 + - - +
427E PHE* 3.6 23.7 - - - +
428E LEU* 3.7 25.8 - - + +
430E ALA* 3.4 21.1 - - + +
433E VAL* 3.4 39.9 - - + -
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Residues in contact with ALA 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E GLY* 3.1 29.7 - - - +
301E VAL* 4.1 1.3 - - - -
304E HIS* 3.4 16.5 - - + -
308E ILE* 3.6 21.1 - - + -
373E ALA 3.1 19.8 + - - +
374E LEU 3.8 2.0 - - - +
376E MET* 1.3 76.4 - - - +
378E GLY* 1.3 63.2 + - - +
380E ASP 3.6 0.2 + - - -
381E GLY 3.2 7.6 + - - -
427E PHE* 3.4 21.3 - - + -
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Residues in contact with GLY 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E TYR* 3.4 52.1 - - - -
301E VAL* 4.5 0.7 - - - -
374E LEU 3.0 8.6 + - - -
375E LEU 3.0 6.3 + - - -
377E ALA* 1.3 77.6 - - - +
379E LEU* 1.3 62.9 + - - +
381E GLY 3.2 8.7 + - - -
382E ILE* 3.2 13.0 + - - +
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Residues in contact with LEU 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.6 38.8 - - + -
115E LEU* 3.3 35.0 - - + -
118E THR* 4.9 1.6 - - - +
120E ILE* 4.0 20.4 - - + -
274E LEU* 4.3 12.3 - - + -
375E LEU* 2.9 43.9 + - + +
376E MET* 3.9 7.4 - - - +
378E GLY* 1.3 76.4 - - - +
380E ASP* 1.3 56.5 + - - +
382E ILE* 3.0 9.0 + - + +
383E LYS* 2.9 35.7 + - - +
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Residues in contact with ASP 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LYS* 4.8 2.1 + - - +
304E HIS* 3.0 32.6 + - - +
376E MET 3.1 17.7 + - - +
377E ALA 3.9 1.1 - - - +
378E GLY 3.3 0.2 - - - -
379E LEU* 1.3 76.4 - - - +
381E GLY* 1.3 61.7 + - - +
383E LYS* 3.8 22.7 + - - +
384E ASN* 3.2 32.8 + - - +
386E ILE* 3.8 12.6 - - - +
427E PHE* 4.0 17.3 - - + +
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Residues in contact with GLY 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E TYR* 3.3 27.9 - - - +
300E GLY* 3.7 10.3 - - - -
377E ALA 3.2 9.9 + - - -
378E GLY 3.2 1.5 + - - -
379E LEU 3.1 0.8 - - - -
380E ASP* 1.3 77.6 + - - +
382E ILE* 1.3 56.8 - - - +
385E LYS 3.2 3.6 + - - -
386E ILE* 2.8 40.7 + - - -
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Residues in contact with ILE 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ILE* 3.7 37.5 - - + -
274E LEU* 4.4 6.3 - - + -
293E GLN* 3.7 42.8 - - + +
296E TYR* 3.6 22.4 - - + -
297E TYR* 4.0 15.5 - - + +
378E GLY 3.2 14.3 + - - +
379E LEU* 3.0 9.6 + - + +
381E GLY* 1.3 76.0 - - - +
383E LYS* 1.3 70.0 + - - +
385E LYS* 3.0 24.1 + - - +
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Residues in contact with LYS 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E TYR* 3.1 30.0 + - - +
118E THR* 4.8 11.7 - - + -
120E ILE* 4.2 14.6 - - + -
379E LEU* 2.9 23.9 + - - +
380E ASP* 3.8 27.6 + - - +
382E ILE* 1.3 76.4 - - - +
384E ASN* 1.3 71.4 + - - +
385E LYS* 3.3 11.1 + - - +
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Residues in contact with ASN 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LYS* 5.8 1.8 + - - +
380E ASP* 3.2 26.7 + - - +
381E GLY 3.8 0.2 - - - -
383E LYS* 1.3 96.3 + - - +
385E LYS* 1.3 69.3 + - - +
386E ILE* 3.0 18.3 + - + +
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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