Contacts of the helix formed by residues 425 - 430 (chain G) 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 ARG 425 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421G LEU 3.2 16.7 + - - +
422G ASP* 2.7 44.9 + - - +
423G LEU 2.5 13.7 + - - +
424G ASP* 1.3 72.4 - - - +
426G GLU* 1.3 73.7 + - - +
427G PHE 3.4 0.7 - - - -
428G LEU* 3.1 21.0 + - - +
429G LYS* 3.4 26.6 + - + +
436G ASP* 3.1 36.6 + - - +
439G ILE* 4.0 20.0 - - + +
440G ASP* 3.0 37.4 + - - -
443G ILE* 4.4 4.4 - - - +
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Residues in contact with GLU 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU 4.9 5.2 - - - +
424G ASP* 3.1 6.6 - - - +
425G ARG* 1.3 84.7 - - + +
427G PHE* 1.3 64.1 + - - +
428G LEU 3.0 1.7 + - - -
429G LYS* 3.0 48.9 + - - +
430G ALA* 3.5 8.1 + - - +
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Residues in contact with PHE 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304G HIS* 3.5 39.9 - + + +
307G ALA* 4.2 9.6 - - + -
308G ILE* 4.5 6.1 - - + -
373G ALA* 3.7 4.0 - - + -
376G MET* 3.6 16.1 - - - +
377G ALA* 3.4 44.2 - - + -
380G ASP* 4.0 20.8 - - + +
424G ASP* 3.0 40.1 + - - -
426G GLU* 1.3 78.0 - - - +
428G LEU* 1.3 93.2 + - + +
430G ALA* 3.5 17.7 - - - +
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Residues in contact with LEU 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307G ALA* 5.3 1.1 - - + -
311G LEU* 5.6 1.3 - - + -
373G ALA* 3.9 20.9 - - + -
376G MET* 3.7 17.5 - - + +
421G LEU* 3.5 31.6 - - + -
425G ARG* 3.1 11.1 + - - +
426G GLU 3.0 0.6 - - - -
427G PHE* 1.3 123.4 - - + +
429G LYS* 1.3 60.2 + - - +
430G ALA 3.1 10.4 + - - +
433G VAL* 3.6 3.1 - - - +
434G PHE* 3.0 57.9 + - + +
439G ILE* 4.2 3.8 - - + -
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Residues in contact with LYS 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425G ARG* 3.5 29.5 - - + +
426G GLU* 3.0 35.5 + - - +
428G LEU* 1.3 72.3 - - - +
430G ALA* 1.3 67.2 + - - +
431G GLY 3.5 0.2 + - - -
432G GLY* 2.9 19.1 + - - -
434G PHE 3.1 20.5 - - - +
435G THR 4.8 1.1 - - - -
436G ASP* 3.0 41.3 + - - +
439G ILE* 4.2 10.8 - - + -
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Residues in contact with ALA 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G TYR* 3.6 24.2 - - + +
376G MET* 3.4 5.1 - - + +
383G LYS* 5.7 3.1 - - - +
426G GLU 3.5 6.0 + - - +
427G PHE* 3.5 20.4 - - - +
428G LEU 3.1 0.2 - - - -
429G LYS* 1.3 79.8 - - - +
431G GLY* 1.3 60.0 + - - +
432G GLY 2.9 6.1 + - - -
433G VAL* 3.1 18.4 + - - +
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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