Contacts of the helix formed by residues 434 - 452 (chain B) in PDB entry 5FN2
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 ALA 434 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B LEU* 4.7 1.3 - - + -
421B THR* 2.7 47.5 + - + +
424B LEU* 4.6 15.3 - - + -
432B LEU 3.5 0.6 - - - -
433B PRO* 1.3 80.4 - - - +
435B LEU* 1.3 60.4 + - - +
436B PRO* 3.3 1.1 - - - -
437B ILE* 3.1 36.0 - - + +
438B SER* 3.2 7.8 + - - -
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Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASP* 5.5 0.2 - - - +
261B VAL* 6.1 0.2 - - + -
381B LEU* 4.1 11.7 - - + -
382B GLY* 4.3 11.7 - - - +
385B ASP* 3.1 41.7 - - + +
389B TYR* 3.0 25.6 - - - +
418B LEU* 6.2 3.6 - - + -
421B THR* 3.9 14.1 - - + +
432B LEU* 3.6 52.5 - - + +
434B ALA* 1.3 76.4 - - - +
436B PRO* 1.4 64.0 - - + +
438B SER* 2.4 23.6 + - - -
439B ILE* 2.9 15.6 + - - +
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Residues in contact with PRO 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 3.4 28.5 - - - +
255B VAL* 5.3 0.4 - - - -
257B ASP* 5.2 1.6 - - + -
258B LEU* 3.6 32.5 - - + +
261B VAL* 5.3 1.1 - - + -
385B ASP* 4.2 4.3 - - - +
432B LEU 4.3 3.1 - - - +
433B PRO 3.2 25.1 - - - +
435B LEU* 1.4 95.3 - - + +
437B ILE* 1.3 51.7 - - - +
439B ILE* 3.2 14.5 + - + +
440B THR* 2.7 36.5 + - - +
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Residues in contact with ILE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B GLY* 4.5 9.4 - - - +
420B LEU* 4.9 16.2 - - + -
433B PRO 5.3 0.7 - - - +
434B ALA* 3.1 34.9 + - + +
435B LEU 3.2 0.4 - - - -
436B PRO* 1.3 80.7 - - - +
438B SER* 1.3 63.2 + - - +
440B THR* 3.2 9.1 + - + +
441B PHE* 2.9 58.0 + - + -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 3.1 23.5 + - - -
413B ALA 4.3 3.8 - - - +
414B ILE* 4.0 12.9 - - - +
417B GLY* 3.3 39.5 - - - -
418B LEU* 3.8 3.4 - - - -
421B THR* 4.6 0.4 - - - -
434B ALA 3.2 5.3 + - - -
435B LEU* 2.4 25.9 + - - -
437B ILE* 1.3 80.6 - - - +
439B ILE* 1.3 60.2 + - - +
441B PHE* 3.2 5.6 + - - +
442B GLY* 2.9 25.6 + - - -
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Residues in contact with ILE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 3.1 35.4 - - + +
253B ILE* 6.0 1.1 - - + -
254B SER* 3.6 31.6 - - - +
385B ASP* 3.2 29.2 - - + +
388B PHE* 4.7 15.7 - - + -
389B TYR* 3.7 24.0 - - + +
392B LEU* 3.7 9.1 - - + +
414B ILE* 5.5 0.7 - - - -
435B LEU 2.9 11.8 + - - +
436B PRO* 3.4 5.8 - - + +
438B SER* 1.3 82.3 + - - +
440B THR* 1.3 56.8 - - - +
442B GLY* 3.2 2.6 + - - -
443B LEU* 2.9 31.2 + - + +
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Residues in contact with THR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 4.5 6.4 + - - -
436B PRO* 2.7 22.4 + - - +
437B ILE* 3.2 12.7 + - + -
439B ILE* 1.3 75.7 - - - +
441B PHE* 1.3 63.5 + - + +
443B LEU* 3.2 17.0 + - + +
444B VAL* 2.9 40.3 + - + +
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Residues in contact with PHE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ALA* 3.8 14.6 - - + +
416B ILE* 3.9 21.8 - - + -
417B GLY* 5.4 1.3 - - - -
420B LEU* 4.7 16.2 - - + -
437B ILE* 2.9 46.1 + - + +
438B SER* 3.4 11.0 - - - +
440B THR* 1.3 79.8 - - + +
442B GLY* 1.3 58.4 + - - +
444B VAL* 3.2 9.4 + - + +
445B PHE* 2.9 42.7 + + - -
40C PHE* 4.3 24.7 - + - -
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.1 19.2 - - - +
410B CYS* 4.1 10.0 - - - -
413B ALA* 3.5 17.4 - - - +
414B ILE* 4.6 2.9 - - - -
438B SER 2.9 14.5 + - - -
439B ILE 3.6 3.4 - - - -
441B PHE* 1.3 76.9 - - - +
443B LEU* 1.3 55.8 + - - +
445B PHE* 3.2 3.3 + - - +
446B TYR* 2.9 29.1 + - - +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 3.8 20.4 - - + +
250B LEU* 3.4 46.2 - - + -
251B ALA* 3.9 25.1 - - + -
254B SER* 5.4 0.9 - - - +
392B LEU* 3.9 2.4 - - + +
439B ILE* 2.9 18.6 + - + +
440B THR* 3.3 18.2 - - + +
442B GLY* 1.3 75.1 - - - +
444B VAL* 1.3 63.9 + - + +
446B TYR* 3.2 13.5 + - - +
447B PHE* 3.1 41.3 + - + -
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Residues in contact with VAL 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B THR* 2.9 28.1 + - + +
441B PHE* 3.3 13.5 - - + +
443B LEU* 1.3 79.8 - - + +
445B PHE* 1.3 76.7 + - + +
446B TYR 3.4 0.2 + - - -
447B PHE* 4.9 2.8 - - - +
448B ALA* 3.3 25.1 + - + +
47C LEU* 6.2 4.3 - - + -
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ALA* 4.1 20.2 - - + +
410B CYS* 4.9 1.3 - - - -
413B ALA* 3.6 19.7 - - + -
441B PHE* 2.9 39.7 + + - +
442B GLY 3.2 4.0 + - - +
444B VAL* 1.3 88.5 - - + +
446B TYR* 1.3 53.8 + - - +
448B ALA* 4.4 0.8 - - - +
449B THR* 2.3 47.5 + - - +
40C PHE* 3.4 36.6 - + - -
43C LEU* 3.7 35.0 - - + -
44C VAL* 3.7 16.4 - - + -
47C LEU* 5.4 9.4 - - + -
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B TRP* 3.1 51.5 + + + -
392B LEU* 4.5 3.1 - - + -
396B ALA* 3.7 31.4 - - + -
399B THR* 3.1 27.2 + - - +
400B ALA* 5.0 0.2 - - + -
406B THR* 3.4 22.0 - - + +
410B CYS* 3.5 14.3 - - - -
442B GLY 2.9 14.7 + - - +
443B LEU* 3.2 10.7 + - - +
445B PHE* 1.3 77.9 - - - +
447B PHE* 1.3 100.1 + + - +
450B ASP* 2.9 37.1 + - + +
451B TYR* 6.4 1.1 - + - -
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Residues in contact with PHE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TRP* 5.8 6.3 - + - -
247B TRP* 3.7 36.6 - + + -
248B LEU* 6.5 1.1 - - + -
443B LEU* 3.1 45.7 + - + +
444B VAL* 4.9 1.8 - - - +
446B TYR* 1.3 106.6 - + - +
448B ALA* 1.3 59.3 + - - +
450B ASP* 3.2 3.7 + - - +
451B TYR* 2.9 46.6 + + + +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B VAL* 3.3 20.2 + - + +
445B PHE* 4.4 0.9 - - - +
446B TYR 3.3 0.4 - - - -
447B PHE* 1.3 81.1 - - - +
449B THR* 1.3 53.8 + - - +
452B LEU* 2.4 64.5 + - + +
453B VAL 4.1 0.4 - - - -
47C LEU* 3.6 19.7 - - + -
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Residues in contact with THR 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASN* 5.3 0.4 - - + -
406B THR* 3.6 35.2 - - + +
409B ALA* 3.8 15.9 - - + +
445B PHE* 2.3 34.0 + - - +
446B TYR 3.4 3.8 - - - -
448B ALA* 1.3 75.6 - - - +
450B ASP* 1.3 58.9 + - - +
453B VAL* 3.3 32.1 + - + +
454B GLN* 2.6 37.6 + - + +
47C LEU* 5.7 0.5 - - - +
132C PHE* 4.4 6.6 - - + -
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Residues in contact with ASP 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B THR 3.3 21.1 - - - +
400B ALA* 3.2 26.2 - - - +
401B SER* 3.8 6.9 + - - -
406B THR* 3.9 8.6 + - + +
446B TYR* 2.9 23.4 + - + +
447B PHE* 3.2 10.7 + - - +
449B THR* 1.3 76.2 - - - +
451B TYR* 1.3 73.8 + - + +
454B GLN* 2.7 37.7 - - - +
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Residues in contact with TYR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TRP* 4.6 18.2 - + - -
446B TYR* 6.4 0.7 - + - -
447B PHE* 2.9 35.6 + + + +
450B ASP* 1.3 92.4 - - + +
452B LEU* 1.3 75.5 + - + +
455B PRO* 3.2 17.6 - - - +
54C PHE* 4.3 11.2 - + + -
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ALA* 2.4 53.5 + - + +
450B ASP 3.6 0.4 - - - -
451B TYR* 1.3 84.0 - - + +
453B VAL* 1.3 63.9 + - - +
455B PRO* 3.3 9.0 - - - +
456B PHE* 4.2 4.5 - - - +
47C LEU* 4.5 1.3 - - + -
50C SER* 3.1 29.8 - - - +
51C VAL* 4.0 25.4 - - + +
53C TRP* 4.8 2.3 - - - -
54C PHE* 4.1 37.0 - - + +
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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