Contacts of the helix formed by residues 463 - 469 (chain B) in PDB entry 1PRH
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 463 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B PRO* 1.2 74.4 - - - +
464B ASN* 1.3 66.7 + - + +
466B TYR* 2.7 33.8 + - - +
467B ARG* 2.9 31.1 + - + -
475B TYR* 4.6 10.8 - + - -
481B LEU* 5.5 0.4 - - + -
498B ILE 5.9 0.2 - - - +
501B LEU* 3.0 32.7 + - + +
502B GLU 3.6 2.5 - - - +
503B PHE* 3.2 26.5 - + - +
506B GLY* 2.7 50.5 - - - -
507B LEU* 2.8 12.1 - - + -
510B GLU* 4.5 4.9 - - - -
521B SER* 3.8 24.0 - - - -
525B MET* 4.5 4.6 - - + +
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Residues in contact with ASN 464 (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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462B PRO* 5.2 2.2 - - + -
463B PHE* 1.3 80.2 - - + +
465B GLU* 1.3 69.6 + - - +
466B TYR 2.9 1.6 - - - -
467B ARG* 2.6 32.9 + - - +
468B LYS* 2.7 20.0 + - - +
474B PRO* 2.7 45.6 - - + +
475B TYR* 2.9 27.1 + - - +
498B ILE* 4.8 6.8 + - - +
499B ASP* 4.2 26.4 + - - +
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Residues in contact with GLU 465 (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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39B TYR* 3.4 32.1 - - + +
152B LEU* 3.9 8.6 - - + +
461B GLN* 3.3 20.9 - - - +
462B PRO* 3.0 41.8 - - + +
463B PHE 3.2 0.2 - - - -
464B ASN* 1.3 76.9 - - - +
466B TYR* 1.3 58.4 + - - +
468B LYS* 3.0 41.3 + - - +
469B ARG* 3.0 28.1 + - - +
499B ASP* 4.4 10.7 - - - +
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Residues in contact with TYR 466 (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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150B ARG* 4.2 0.9 + - - -
151B ILE* 4.0 4.9 - - + -
152B LEU* 3.6 33.5 + - + +
380B GLU* 2.6 48.2 + - + +
460B LEU* 3.5 16.9 - - + +
461B GLN* 3.8 23.1 + - + -
462B PRO 2.9 25.1 - - - -
463B PHE 2.7 10.6 + - - +
465B GLU* 1.3 77.4 - - - +
467B ARG* 1.3 59.0 + - - +
469B ARG* 3.7 4.0 - - - -
470B PHE* 2.9 54.5 + + - +
503B PHE* 3.8 30.7 - + + -
525B MET* 3.6 5.3 - - + +
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Residues in contact with ARG 467 (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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463B PHE* 2.9 24.5 + - + -
464B ASN* 2.6 42.2 + - - +
466B TYR* 1.3 70.3 - - - +
468B LYS* 1.3 56.1 + - - +
470B PHE* 3.2 6.9 + - - -
471B GLY 3.4 0.2 + - - -
472B MET* 2.8 59.8 + - + +
473B LYS* 2.8 51.5 + - - +
474B PRO* 4.2 1.6 - - + -
475B TYR* 2.9 45.1 + - - -
510B GLU* 3.3 7.5 + - - -
520B GLU* 2.6 24.5 + - - -
521B SER* 3.6 5.0 + - - +
525B MET* 3.7 12.1 - - + -
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Residues in contact with LYS 468 (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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39B TYR* 5.3 3.6 + - - +
42B GLN* 4.6 21.3 + - - +
43B HIS* 6.0 2.8 - - - -
464B ASN 2.7 19.4 + - - +
465B GLU* 3.0 45.9 + - - +
467B ARG* 1.3 74.8 - - - +
469B ARG* 1.4 59.4 + - - +
471B GLY* 3.1 18.9 + - - -
472B MET 3.2 11.7 + - - +
474B PRO* 4.4 30.1 - - + -
499B ASP* 4.9 7.7 + - - -
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Residues in contact with ARG 469 (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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44B GLN* 3.4 56.8 + - - +
123B LEU* 2.8 46.2 + - - +
125B PRO* 4.6 7.5 - - - +
151B ILE* 3.6 46.8 + - + +
152B LEU* 3.8 25.5 - - + +
465B GLU 3.0 15.9 + - - +
466B TYR* 3.5 7.4 - - - +
468B LYS* 1.4 78.8 - - - +
470B PHE* 1.3 61.6 + - + +
471B GLY 3.1 4.8 + - - -
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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