Contacts of the helix formed by residues 456 - 462 (chain G) in PDB entry 4P0S
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 PHE 456 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272G CYS* 4.2 14.8 - - - -
301G ARG* 3.6 31.6 - - + -
303G LEU* 4.0 21.3 - - + -
309G VAL* 4.9 2.2 - - + -
311G VAL* 3.7 22.4 - - + -
325G GLU* 2.7 47.4 + - + +
326G LEU* 4.4 0.2 - - - +
327G VAL* 4.8 5.2 - - + +
454G LEU 3.8 0.8 + - - -
455G THR* 1.3 72.1 - - - +
457G SER* 1.3 63.6 + - - +
459G PHE* 3.5 13.4 + + - +
460G ASN* 3.0 58.2 + - + +
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Residues in contact with SER 457 (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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256G GLN* 3.4 22.3 + - - -
257G GLN* 3.1 29.5 + - - +
325G GLU* 5.3 2.3 + - - +
455G THR* 4.3 0.8 - - - -
456G PHE* 1.3 86.7 - - - +
458G ASP* 1.3 60.5 + - - +
460G ASN* 4.1 1.4 - - - +
461G ALA* 3.2 27.2 + - - +
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Residues in contact with ASP 458 (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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257G GLN* 2.7 30.3 + - - +
431G ARG 4.5 3.1 - - - +
432G PRO* 3.4 22.2 - - - +
433G TRP* 3.2 34.4 + - + +
454G LEU* 5.0 2.7 - - + -
455G THR* 3.2 17.0 + - - +
457G SER* 1.3 77.5 - - - +
459G PHE* 1.3 61.2 + - - +
461G ALA* 3.9 3.0 - - - +
462G GLY* 3.2 16.1 + - - -
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Residues in contact with PHE 459 (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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303G LEU* 3.8 24.7 - - + -
305G VAL* 3.7 38.6 - - + +
309G VAL* 4.1 25.8 - - + -
327G VAL* 4.3 13.2 - - + -
331G ILE* 4.3 1.6 - - + -
359G CYS* 3.3 36.3 - - + -
361G LEU* 3.9 13.0 - - + -
433G TRP* 4.7 4.5 - - - -
454G LEU* 4.3 14.3 - - + +
455G THR 3.2 13.3 + - - +
456G PHE* 3.7 13.7 - + - +
458G ASP* 1.3 76.5 - - - +
460G ASN* 1.3 75.1 + - + +
461G ALA 2.9 9.9 + - - -
462G GLY* 3.0 14.2 + - - -
463G ALA* 4.1 3.5 + - - +
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Residues in contact with ASN 460 (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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301G ARG* 5.6 0.6 - - - +
302G LYS 2.7 23.2 + - - +
303G LEU* 3.1 8.5 - - - +
304G HIS* 2.3 74.2 + - - +
305G VAL* 6.1 0.7 - - - -
456G PHE* 3.0 50.4 + - + +
457G SER* 4.6 2.2 - - - +
459G PHE* 1.3 81.7 - - + +
461G ALA* 1.3 51.9 + - - +
462G GLY 3.7 0.2 - - - -
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Residues in contact with ALA 461 (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* 4.2 5.7 + - + -
457G SER 3.2 18.5 + - - +
458G ASP* 3.9 3.8 - - - +
459G PHE 3.0 0.4 - - - -
460G ASN* 1.3 80.1 - - - +
462G GLY* 1.3 62.7 + - - +
463G ALA 3.2 9.9 + - - +
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Residues in contact with GLY 462 (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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433G TRP* 3.4 35.4 - - - -
458G ASP 3.2 4.4 + - - -
459G PHE 3.0 7.5 + - - -
461G ALA* 1.3 76.8 - - - +
463G ALA* 1.3 63.9 + - - +
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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