Contacts of the helix formed by residues 458 - 466 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147F SER* 4.7 1.0 + - - -
320F LYS* 4.4 2.9 - - - +
453F VAL* 4.2 19.8 + - + +
456F THR* 2.8 50.2 - - - +
457F PRO 3.1 17.8 + - - -
458F HIS* 3.2 27.2 + - + +
320L LYS* 5.3 1.0 + - - -
456L THR 3.4 1.0 + - - -
457L PRO* 1.3 73.2 - - - +
459L PRO* 1.3 80.4 - - + +
460L VAL* 2.9 40.0 - - + +
461L GLU* 2.8 41.4 + - + +
462L PHE* 3.4 6.6 - - - -
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Residues in contact with PRO 459 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F PHE* 4.5 3.8 - - - +
141F GLY 4.3 4.3 - - - +
147F SER* 3.8 15.9 - - - +
148F HIS* 3.5 39.0 - - - +
149F VAL* 4.2 3.6 - - + +
459F PRO* 3.5 35.0 - - + -
147L SER* 4.1 6.7 - - - +
457L PRO 4.1 4.0 - - - +
458L HIS* 1.3 91.3 - - + +
460L VAL* 1.3 51.9 + - + +
462L PHE* 2.7 43.4 + - + +
463L GLU* 3.5 2.9 + - - +
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Residues in contact with VAL 460 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ALA* 4.1 13.2 - - + -
147F SER* 5.5 0.2 - - - -
452F ARG* 4.0 34.3 - - + +
453F VAL* 4.0 11.4 - - + +
456F THR* 3.7 22.4 - - + +
458L HIS* 2.9 29.8 - - + +
459L PRO* 1.3 75.7 - - + +
461L GLU* 1.3 57.0 + - - +
463L GLU* 3.1 9.3 + - + +
464L LEU* 2.8 47.8 + - + +
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Residues in contact with GLU 461 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F MET* 3.9 4.2 - - + +
316F THR* 2.7 27.3 + - - +
317F ASN* 2.8 46.5 + - + +
320F LYS* 3.0 31.2 + - - +
453F VAL* 4.1 6.9 - - + +
457L PRO* 3.6 0.7 - - - +
458L HIS* 2.8 35.6 + - + +
460L VAL* 1.3 77.5 - - - +
462L PHE* 1.3 54.0 + - + +
464L LEU* 4.4 0.4 - - - -
465L TYR* 2.5 54.0 + - + +
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Residues in contact with PHE 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ILE* 4.4 5.6 - - + -
140F PHE* 3.6 26.8 - - + -
149F VAL* 3.5 38.4 - - + -
151F ILE* 4.4 6.7 - - + -
256F MET* 3.4 31.0 - - + -
259F PRO* 3.2 36.8 - - + -
457L PRO* 4.0 13.9 - - + -
458L HIS 3.4 13.0 - - - -
459L PRO 2.7 17.6 + - - +
461L GLU* 1.3 75.7 - - + +
463L GLU* 1.3 68.5 + - - +
466L TYR* 2.9 42.0 + + + +
467L SER 4.7 0.2 + - - -
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Residues in contact with GLU 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F PHE* 3.4 26.8 - - + -
141F GLY* 4.7 3.8 - - - -
142F ALA* 4.0 23.6 + - - +
452F ARG* 2.6 41.6 + - - +
459L PRO 3.5 2.2 + - - +
460L VAL* 3.3 14.8 - - - +
462L PHE* 1.3 81.7 - - - +
464L LEU* 1.3 61.4 + - + +
466L TYR 5.0 0.2 + - - -
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Residues in contact with LEU 464 (chain L).
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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449F GLU* 3.6 44.7 - - + +
452F ARG* 3.6 33.2 - - + +
453F VAL* 3.8 11.0 - - + -
460L VAL* 2.8 31.3 + - + +
463L GLU* 1.3 82.5 - - + +
465L TYR* 1.3 86.1 + - + +
467L SER 5.6 0.2 - - - -
468L VAL* 5.2 2.3 - - - +
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Residues in contact with TYR 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F MET* 3.8 17.9 - - + +
257F PRO* 5.6 0.4 - - + -
314F PRO 4.1 1.3 + - - -
315F THR* 3.4 44.0 - - + -
316F THR* 3.3 38.7 + - - +
317F ASN* 4.2 4.9 - - + -
414F LEU* 4.5 1.7 - - - +
446F ARG* 4.6 3.8 - - - -
449F GLU* 3.4 42.8 + - - +
461L GLU* 2.5 41.8 + - + +
464L LEU* 1.3 97.7 - - + +
466L TYR* 1.3 65.3 + - - +
467L SER 3.2 2.7 - - - -
468L VAL* 2.9 35.8 + - + +
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Residues in contact with TYR 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E LYS 4.6 1.6 - - - -
170E GLY 4.4 7.0 - - - -
171E HIS* 3.3 32.7 - + - -
135F PHE* 3.8 11.9 - + - -
138F ILE* 3.6 38.2 - - + +
140F PHE* 4.5 7.2 - + + -
243F HIS* 4.8 0.2 + - - -
252F THR* 2.6 42.1 + - - +
253F ALA 3.9 1.6 + - - -
254F THR* 2.8 55.6 + - + -
255F PHE 4.1 1.9 + - - -
256F MET* 3.9 15.5 - - - -
461L GLU 3.8 2.0 + - - -
462L PHE* 2.9 31.4 + + + +
465L TYR* 1.3 77.2 - - - +
467L SER* 1.3 62.5 + - - +
468L VAL 3.1 4.5 + - - +
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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