Contacts of the helix formed by residues 445 - 457 (chain A) 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 LEU 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A SER* 3.7 37.5 - - - +
179A ARG* 3.8 40.8 - - - +
182A LEU* 4.1 3.8 - - + -
183A LEU* 3.8 30.3 - - + +
440A ILE* 3.6 22.2 - - + +
441A ASP 3.3 4.1 + - - +
442A HIS* 3.0 23.0 + - - +
444A ILE* 1.3 75.7 - - - +
446A HIS* 1.3 63.1 + - - +
447A VAL 3.2 0.7 + - - -
448A ALA* 3.2 10.4 + - + +
449A VAL* 3.3 13.6 + - + +
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Residues in contact with HIS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ARG* 5.6 7.5 - - - +
442A HIS 4.4 2.0 + - - +
443A HIS 3.4 24.3 + - - -
444A ILE* 3.0 4.9 + - + -
445A LEU* 1.3 81.6 - - - +
447A VAL* 1.3 82.4 + - + +
449A VAL* 3.0 14.5 + - - +
450A ASP* 2.9 36.2 + - - +
601A HEM 4.2 16.4 - - + +
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A HIS* 4.2 6.5 - - + -
388A HIS* 3.6 33.7 - - + +
444A ILE* 2.9 17.0 + - + +
446A HIS* 1.3 97.9 - - + +
448A ALA* 1.3 55.0 + - - +
450A ASP* 2.7 31.6 + - - +
451A VAL* 2.9 13.7 + - - +
601A HEM 3.7 49.1 - - + +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER* 4.3 0.4 - - - +
182A LEU* 3.8 14.4 - - + -
388A HIS* 5.5 2.5 + - + +
440A ILE* 3.5 33.8 - - + +
444A ILE 4.0 0.8 + - - -
445A LEU* 3.2 12.1 + - + +
447A VAL* 1.3 77.8 - - - +
449A VAL* 1.3 63.5 + - - +
451A VAL* 3.2 11.8 + - - +
452A ILE* 3.1 29.7 + - - +
504A TYR* 4.0 10.9 - - + +
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA* 4.0 4.9 - - + -
175A GLU* 3.9 40.6 - - + +
178A SER* 3.3 31.9 - - - +
179A ARG* 5.9 0.7 - - - +
445A LEU* 3.6 15.9 - - + +
446A HIS* 3.0 17.1 + - + +
448A ALA* 1.3 79.0 - - - +
450A ASP* 1.3 61.1 + - - +
452A ILE* 3.3 5.7 + - - +
453A LYS* 3.1 34.5 + - + +
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Residues in contact with ASP 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A HIS* 2.9 30.9 + - - +
447A VAL* 2.7 17.0 + - - +
449A VAL* 1.3 72.2 - - - +
451A VAL* 1.3 55.1 + - - +
453A LYS* 3.3 18.2 + - - +
454A GLU* 2.8 32.0 + - - +
601A HEM 3.1 28.3 - - - +
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Residues in contact with VAL 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLN* 3.6 22.3 - - + +
386A HIS* 3.4 41.3 - - + +
447A VAL* 2.9 17.4 + - + +
448A ALA* 3.3 12.1 - - - +
450A ASP* 1.3 73.6 - - - +
452A ILE* 1.3 60.9 + - - +
454A GLU* 3.0 10.7 + - - +
455A SER 2.9 25.1 + - - -
504A TYR* 3.6 34.5 - - + -
601A HEM 5.1 2.7 - - - +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PRO 5.8 0.4 - - - +
174A ALA* 4.1 22.7 - - + +
177A LEU* 4.7 12.1 - - + -
178A SER* 3.3 26.5 - - - +
182A LEU* 4.1 13.9 - - + -
448A ALA 3.1 12.4 + - - +
449A VAL* 3.7 5.4 - - - +
451A VAL* 1.3 74.3 - - - +
453A LYS* 1.3 64.0 + - - +
455A SER* 3.1 11.9 + - - -
456A ARG* 3.1 22.7 + - + +
502A GLU* 3.6 26.5 - - - +
504A TYR* 4.0 10.5 - - + -
505A PRO* 4.0 25.1 - - + -
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ALA* 3.9 16.4 - - + -
449A VAL* 3.1 29.9 + - + +
450A ASP* 3.5 18.2 + - - +
451A VAL 3.2 0.2 - - - -
452A ILE* 1.3 76.2 - - - +
454A GLU* 1.3 59.9 + - - +
456A ARG* 3.2 12.1 + - - +
457A VAL* 3.0 27.1 + - + +
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A THR* 4.7 16.8 + - - +
218A PRO* 4.0 22.7 - - + +
382A ASN* 4.5 9.0 - - - +
383A GLN* 3.5 19.9 + - - +
386A HIS* 5.6 2.7 - - - -
450A ASP* 2.8 14.8 + - - +
451A VAL* 3.0 11.8 + - - +
453A LYS* 1.3 71.4 - - - +
455A SER* 1.3 66.1 + - - +
456A ARG 3.0 1.1 - - - -
457A VAL* 2.9 17.2 + - - +
458A LEU* 2.9 35.0 + - + +
601A HEM 5.4 4.2 - - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLN* 2.8 24.6 + - - -
451A VAL 2.9 10.2 + - - -
452A ILE* 3.2 13.9 - - - -
454A GLU* 1.3 73.0 - - - +
456A ARG* 1.3 60.6 + - - +
458A LEU* 3.5 5.3 - - - +
459A ARG* 2.9 21.8 + - - -
460A LEU* 3.0 28.8 + - - +
502A GLU* 4.0 14.4 - - - -
503A PHE* 4.9 3.2 + - - +
504A TYR* 4.2 18.0 + - - +
505A PRO* 5.2 0.7 - - - +
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Residues in contact with ARG 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 5.5 0.2 - - - +
162A PRO* 3.4 24.7 + - - +
163A MET* 3.7 14.3 - - - +
171A LEU* 3.5 28.6 - - + +
452A ILE* 3.1 13.6 + - + +
453A LYS* 3.2 14.6 - - - +
454A GLU 3.0 0.2 - - - -
455A SER* 1.3 84.7 + - - +
457A VAL* 1.3 66.1 + - + +
459A ARG* 3.1 37.3 + - - +
460A LEU 3.6 21.6 + - - -
502A GLU* 3.2 27.6 + - - +
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 5.2 3.4 - - + +
157A ARG* 4.6 5.4 + - - -
218A PRO* 4.3 26.2 - - + -
453A LYS* 3.0 14.8 + - + +
454A GLU* 2.9 14.4 + - - +
456A ARG* 1.3 71.5 - - + +
458A LEU* 1.3 62.2 + - + +
459A ARG* 3.0 13.2 + - - +
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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