Contacts of the helix formed by residues 458 - 466 (chain F) 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 HIS 458 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320F LYS* 5.3 1.0 + - - -
456F THR 3.4 0.6 + - - -
457F PRO* 1.3 72.3 - - - +
459F PRO* 1.3 79.4 - - + +
460F VAL* 2.9 39.8 - - + +
461F GLU* 2.8 39.7 + - + +
462F PHE* 3.4 7.2 - - - -
147L SER* 4.7 0.6 + - - -
320L LYS* 4.5 3.6 - - - +
453L VAL* 4.2 19.9 + - + +
456L THR* 2.8 51.9 - - + +
457L PRO 3.1 16.9 + - - -
458L HIS* 3.2 26.8 + - + +
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Residues in contact with PRO 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F SER* 4.1 7.6 - - - +
457F PRO 4.1 3.6 - - - +
458F HIS* 1.3 92.9 - - + +
460F VAL* 1.3 52.7 + - - +
462F PHE* 2.7 41.5 + - + +
463F GLU* 3.5 4.0 + - - +
140L PHE* 4.5 4.0 - - - +
141L GLY 4.3 4.3 - - - +
147L SER* 3.8 15.7 - - - +
148L HIS* 3.5 39.7 - - - +
149L VAL* 4.2 3.6 - - + +
459L PRO* 3.5 35.0 - - + -
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Residues in contact with VAL 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458F HIS* 2.9 31.1 - - + +
459F PRO* 1.3 76.2 - - + +
461F GLU* 1.3 57.3 + - - +
463F GLU* 3.1 9.3 + - + +
464F LEU* 2.8 48.3 + - + +
142L ALA* 4.1 13.9 - - + -
452L ARG* 4.0 34.3 - - + +
453L VAL* 4.1 11.0 - - + +
456L THR* 3.7 22.0 - - + +
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Residues in contact with GLU 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457F PRO* 3.6 4.2 - - - +
458F HIS* 2.8 40.6 + - + +
460F VAL* 1.3 76.8 - - - +
462F PHE* 1.3 53.3 + - + +
465F TYR* 2.5 54.6 + - + +
256L MET* 3.9 4.4 - - + +
316L THR* 2.7 27.8 + - - +
317L ASN* 2.8 45.0 + - + +
320L LYS* 3.0 25.5 + - - +
453L VAL* 4.0 6.8 - - + +
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Residues in contact with PHE 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457F PRO* 4.0 14.1 - - + -
458F HIS 3.4 13.9 - - - -
459F PRO 2.7 17.4 + - - +
461F GLU* 1.3 75.1 - - + +
463F GLU* 1.3 69.0 + - - +
466F TYR* 2.9 41.6 + + + +
467F SER 4.7 0.2 + - - -
135L PHE* 6.3 0.2 - + - -
138L ILE* 4.4 5.4 - - + -
140L PHE* 3.6 28.1 - - + -
149L VAL* 3.5 38.1 - - + -
151L ILE* 4.5 8.1 - - + -
256L MET* 3.4 31.6 - - + -
259L PRO* 3.2 36.1 - - + -
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Residues in contact with GLU 463 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F PRO 3.5 1.6 + - - -
460F VAL* 3.1 15.5 + - - +
462F PHE* 1.3 82.3 - - - +
464F LEU* 1.3 61.9 + - + +
466F TYR 5.0 0.2 + - - -
467F SER 5.9 0.3 + - - -
140L PHE* 3.4 24.7 - - + -
141L GLY* 4.7 3.5 - - - -
142L ALA* 4.0 24.4 + - - +
452L ARG* 2.6 41.5 + - - +
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Residues in contact with LEU 464 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460F VAL* 2.8 30.7 + - + +
463F GLU* 1.3 83.7 - - + +
465F TYR* 1.3 85.3 + - + +
467F SER 5.6 0.2 - - - -
468F VAL* 5.2 1.9 - - - +
449L GLU* 3.6 45.0 - - + +
452L ARG* 3.5 33.9 - - + +
453L VAL* 3.8 10.5 - - + -
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Residues in contact with TYR 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461F GLU* 2.5 41.2 + - + +
464F LEU* 1.3 98.5 - - + +
466F TYR* 1.3 66.2 + - - +
467F SER 3.2 2.9 - - - -
468F VAL* 2.9 37.1 + - + +
256L MET* 3.8 16.4 - - + +
257L PRO* 5.7 0.7 - - + -
314L PRO 4.1 1.4 + - - -
315L THR* 3.4 42.6 - - + -
316L THR* 3.3 40.0 + - - +
317L ASN* 4.2 4.9 - - + -
414L LEU* 4.5 1.7 - - - +
446L ARG* 4.5 2.9 - - - -
449L GLU* 3.4 44.3 + - - +
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Residues in contact with TYR 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461F GLU 3.8 2.0 + - - -
462F PHE* 2.9 30.6 + + + +
464F LEU 3.9 0.2 - - - -
465F TYR* 1.3 77.1 - - - +
467F SER* 1.3 62.5 + - - +
468F VAL 3.1 4.6 + - - +
169G LYS 4.6 1.1 - - - -
170G GLY 4.4 7.4 - - - -
171G HIS* 3.2 32.2 - + - -
135L PHE* 3.9 11.4 - + - -
138L ILE* 3.6 41.8 - - + +
140L PHE* 4.5 6.5 - + + -
243L HIS* 4.8 0.2 + - - -
252L THR* 2.6 38.7 + - - +
253L ALA 3.9 1.4 + - - -
254L THR* 2.9 55.1 + - + -
255L PHE 4.2 1.9 + - - -
256L MET* 3.9 14.5 - - - -
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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