Contacts of the helix formed by residues 435 - 456 (chain B) 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 THR 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ASP* 3.1 35.5 + - + +
110B ARG* 3.5 18.4 - - - +
429B LYS* 4.8 1.3 - - - -
432B GLY 4.8 3.4 - - - +
434B PHE* 1.3 79.0 - - - +
436B ASP* 1.3 63.7 + - - +
437B GLU* 2.7 20.3 + - - -
438B ALA* 3.1 18.9 + - + +
439B ILE* 3.0 26.7 + - - +
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Residues in contact with ASP 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 3.1 22.1 + - - +
429B LYS* 3.0 40.0 + - - +
435B THR* 1.3 73.1 - - - +
437B GLU* 1.3 57.3 + - + +
439B ILE* 3.0 6.6 + - - +
440B ASP* 2.6 47.0 + - - +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP* 3.4 21.5 - - - +
102B ARG* 3.6 25.6 + - - +
435B THR* 2.7 25.6 + - - -
436B ASP* 1.3 74.7 + - + +
438B ALA* 1.3 59.4 + - - +
440B ASP* 3.7 11.0 + - + +
441B ALA* 2.7 35.9 + - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 6.0 0.3 - - - +
101B ASP 3.4 25.1 - - - +
102B ARG* 3.7 20.8 - - + +
107B ILE* 4.7 9.2 - - + -
434B PHE* 5.1 2.7 - - + -
435B THR* 3.1 30.1 + - - +
437B GLU* 1.3 79.2 + - - +
439B ILE* 1.3 62.5 + - + +
441B ALA* 3.5 2.9 + - - +
442B TYR* 3.2 20.1 + - - +
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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
----------------------------------------------------------
421B LEU* 4.1 21.3 - - + +
425B ARG* 4.0 26.2 - - + +
428B LEU* 4.2 16.4 - - + -
429B LYS* 4.2 14.4 - - + -
434B PHE* 3.6 40.6 - - + -
435B THR 3.0 12.1 + - - +
436B ASP 3.0 7.5 + - - +
438B ALA* 1.3 76.7 - - - +
440B ASP* 1.3 63.0 + - - +
442B TYR* 3.5 6.3 + - - +
443B ILE* 3.1 40.3 + - + +
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG* 3.0 32.4 + - - -
436B ASP* 2.6 35.3 + - - +
437B GLU* 3.7 10.0 + - + -
439B ILE* 1.3 74.1 - - - +
441B ALA* 1.3 58.0 + - - +
443B ILE* 3.6 8.8 + - - +
444B ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 6.1 1.8 - - + +
56B GLY* 4.1 23.1 - - - +
102B ARG* 4.3 17.0 - - + +
437B GLU 2.7 22.6 + - - +
438B ALA* 3.6 4.7 - - - +
440B ASP* 1.3 71.8 - - - +
442B TYR* 1.3 65.2 + - - +
444B ALA* 3.1 16.1 + - - +
445B LEU* 3.1 19.7 + - + +
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Residues in contact with TYR 442 (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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24B THR* 3.7 33.3 - - + +
310B ALA* 2.8 30.0 + - + -
311B LEU* 3.6 22.4 + - + -
314B PRO* 3.3 19.6 - - - +
366B ASN* 5.3 3.3 - - + +
369B LEU* 3.5 33.7 - - + -
418B LEU* 4.5 5.8 - - + -
421B LEU* 4.4 10.3 - - + -
438B ALA 3.2 10.9 + - - +
439B ILE* 3.7 10.5 - - - +
441B ALA* 1.3 78.3 - - - +
443B ILE* 1.3 67.2 + - - +
445B LEU* 3.1 15.5 + - + +
446B ARG* 3.1 46.3 + - + +
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B LEU* 4.0 18.3 - - + +
421B LEU* 3.8 18.6 - - + -
422B ASP* 4.0 31.2 - - + +
425B ARG* 4.4 6.5 - - - +
439B ILE* 3.1 35.0 + - + +
440B ASP* 3.8 7.9 - - - +
441B ALA 3.3 0.2 - - - -
442B TYR* 1.3 81.3 - - - +
444B ALA* 1.3 57.9 + - - +
446B ARG* 3.5 1.2 + - - +
447B ARG* 2.9 67.1 + - + +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ASP 3.1 15.0 + - - +
441B ALA* 3.1 12.9 + - - +
443B ILE* 1.3 78.1 - - - +
445B LEU* 1.3 61.2 + - + +
447B ARG* 3.3 8.7 + - - +
448B GLU* 3.2 22.6 + - - +
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Residues in contact with LEU 445 (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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24B THR* 3.6 36.1 - - + -
25B LYS* 4.2 26.5 + - + +
55B GLY* 4.1 15.7 - - - -
56B GLY* 3.8 23.3 - - - +
441B ALA 3.1 13.5 + - - +
442B TYR* 3.1 7.5 + - + +
444B ALA* 1.3 75.7 - - + +
446B ARG* 1.3 69.9 + - + +
448B GLU* 2.9 41.7 - - - +
449B GLU* 3.2 11.5 + - - +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 3.1 47.7 + - - +
314B PRO* 3.3 37.0 + - + +
315B THR* 5.3 1.2 - - - +
364B ALA 4.6 2.4 + - - -
366B ASN 5.3 0.6 - - - +
414B LEU* 4.2 7.9 - - + +
418B LEU* 3.9 23.3 - - + -
442B TYR* 3.1 52.3 + - + +
445B LEU* 1.3 81.5 - - + +
447B ARG* 1.3 60.0 + - - +
449B GLU* 3.0 39.0 + - - +
450B ASP* 2.8 32.1 + - - +
465H TYR* 4.5 6.5 - - - -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLU* 3.7 21.3 + - - +
418B LEU* 3.7 16.4 - - + +
419B ASN* 3.5 39.6 - - - +
422B ASP* 5.7 4.2 + - - +
443B ILE* 2.9 45.1 + - + +
444B ALA* 3.4 10.1 - - - +
445B LEU 3.1 0.4 - - - -
446B ARG* 1.3 78.6 - - - +
448B GLU* 1.3 57.4 + - - +
450B ASP* 3.5 11.3 + - - +
451B ASP* 3.0 35.6 + - - +
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Residues in contact with GLU 448 (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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25B LYS* 5.0 3.3 + - - +
444B ALA 3.2 8.7 + - - +
445B LEU* 2.9 43.6 - - - +
447B ARG* 1.3 74.7 - - - +
449B GLU* 1.3 68.0 - - + +
451B ASP* 3.3 25.4 - - - +
452B ARG* 3.3 14.6 + - - +
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Residues in contact with GLU 449 (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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25B LYS* 2.7 32.4 + - - +
314B PRO 4.0 1.2 - - - +
414B LEU* 5.4 0.2 - - - +
445B LEU 3.2 10.6 + - - +
446B ARG* 3.0 44.1 + - - +
448B GLU* 1.3 76.7 - - + +
450B ASP* 1.3 67.5 + - - +
452B ARG* 3.0 17.6 + - - +
453B VAL* 3.4 9.2 + - - +
464H LEU* 3.7 27.4 - - + +
465H TYR* 3.3 33.7 + - - +
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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
----------------------------------------------------------
316B THR* 3.6 24.3 - - - +
413B SER* 6.0 0.2 - - - -
414B LEU* 3.8 23.4 + - + +
415B GLU* 4.3 20.9 + - - +
418B LEU* 5.4 2.2 - - + -
446B ARG 2.8 16.0 + - - +
447B ARG* 3.8 12.7 - - - +
449B GLU* 1.3 74.8 - - - +
451B ASP* 1.3 58.3 + - - +
453B VAL* 3.2 3.1 + - - +
454B ARG* 2.8 66.5 + - - +
465H TYR* 4.6 0.6 + - - -
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Residues in contact with ASP 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ARG* 3.0 26.5 + - - +
448B GLU* 3.3 17.5 - - - +
449B GLU 3.1 0.2 - - - -
450B ASP* 1.3 77.4 - - - +
452B ARG* 1.3 54.7 + - + +
454B ARG* 2.8 29.0 + - - +
455B MET* 2.7 54.3 + - - +
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Residues in contact with ARG 452 (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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142B ALA* 4.6 6.7 + - - +
448B GLU 3.5 14.1 - - - +
449B GLU* 3.0 10.7 + - - +
451B ASP* 1.3 76.9 - - + +
453B VAL* 1.3 63.1 + - - +
455B MET* 3.8 3.2 - - - +
456B THR* 2.9 38.9 + - - -
261H PHE* 6.0 7.5 - - - -
460H VAL* 4.0 21.9 - - + +
463H GLU* 2.6 40.0 + - - -
464H LEU* 3.5 29.9 - - + +
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR* 3.5 29.8 - - + +
320B LYS* 4.4 7.2 - - - +
449B GLU 3.4 5.1 + - - +
450B ASP 3.2 5.7 + - - +
452B ARG* 1.3 76.3 - - - +
454B ARG* 1.3 64.0 + - + +
455B MET 3.3 0.5 + - - -
456B THR* 3.6 16.0 - - - +
320H LYS* 4.0 5.9 + - - -
458H HIS* 4.2 21.5 + - + +
460H VAL* 4.1 13.0 - - + -
461H GLU* 4.0 23.3 - - + +
464H LEU* 3.9 23.6 - - + -
465H TYR* 4.8 0.4 - - + -
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Residues in contact with ARG 454 (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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415B GLU* 4.2 18.9 + - - -
450B ASP* 2.8 43.9 + - - +
451B ASP* 2.8 30.8 + - - +
453B VAL* 1.3 80.2 - - + +
455B MET* 1.3 68.4 + - - +
319H TYR 4.9 7.7 + - - +
320H LYS* 3.4 26.8 - - - +
323H VAL* 5.5 4.9 - - - +
412H GLY 5.1 9.5 + - - -
413H SER* 6.6 0.4 - - - -
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Residues in contact with MET 455 (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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451B ASP* 2.7 40.7 + - - +
452B ARG* 4.1 2.9 - - - +
454B ARG* 1.3 89.0 - - - +
456B THR* 1.3 59.5 + - - +
457B PRO* 3.7 5.4 - - - +
258H LYS* 5.3 1.4 - - - +
261H PHE* 3.8 31.7 - - + -
320H LYS* 3.3 24.4 - - - +
323H VAL* 4.2 38.6 - - + -
324H PRO* 5.9 1.6 - - + +
326H TYR* 5.1 9.6 - - + +
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Residues in contact with THR 456 (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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142B ALA* 4.8 7.9 - - + +
147B SER* 4.7 7.2 - - - +
452B ARG* 2.9 28.8 + - - -
453B VAL 3.6 0.7 - - - +
454B ARG 3.7 0.2 - - - -
455B MET* 1.3 76.3 - - - +
457B PRO* 1.3 79.7 - - + +
261H PHE* 4.5 20.0 - - + -
320H LYS* 3.2 11.9 - - - -
458H HIS* 2.8 39.8 - - - +
460H VAL* 3.7 17.1 - - + +
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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
------------------------------------------------------------
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