Contacts of the helix formed by residues 503 - 509 (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 PHE 503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLU* 3.7 35.9 - - + -
383A GLN* 4.0 15.9 - - + -
384A LEU* 4.4 9.2 - - + -
455A SER* 4.9 3.5 + - - +
460A LEU* 4.3 19.3 - - + +
461A GLN 4.4 15.3 + - - +
462A PRO 4.4 0.4 - - - +
463A PHE* 3.2 21.3 - + - +
466A TYR* 3.8 33.4 - + + -
470A PHE* 6.1 0.2 - + - -
501A LEU 3.7 1.2 + - - -
502A GLU* 1.3 71.8 - - - +
504A TYR* 1.3 66.6 + - - +
507A LEU* 3.1 44.8 + - + +
525A MET* 3.4 31.9 - - + -
529A PHE* 5.7 1.8 - + - -
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Residues in contact with TYR 504 (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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182A LEU* 4.4 5.6 - - + -
383A GLN* 3.4 24.2 - - + +
384A LEU* 5.5 0.7 - - - -
386A HIS* 3.1 39.7 + - + +
388A HIS* 4.8 1.2 + - - -
440A ILE* 4.1 3.3 - - - +
448A ALA* 4.0 28.2 - - + +
451A VAL* 3.6 28.0 - - + -
452A ILE* 4.0 14.6 - - + -
455A SER* 4.2 12.1 + - - +
503A PHE* 1.3 81.5 - - - +
505A PRO* 1.4 71.5 - - + +
507A LEU* 3.0 19.4 + - + +
508A LEU* 3.1 52.4 + - + +
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Residues in contact with PRO 505 (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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177A LEU* 4.8 7.9 - - + -
182A LEU* 5.2 6.1 - - + -
452A ILE* 4.0 28.3 - - + -
455A SER* 5.2 1.8 - - - +
495A TYR* 3.9 15.0 - - - +
501A LEU* 4.5 7.9 - - + -
502A GLU* 3.5 28.3 - - + +
504A TYR* 1.4 97.3 - - + +
506A GLY* 1.3 57.2 + - - +
508A LEU* 3.1 4.1 + - + -
509A LEU* 2.8 45.5 + - + +
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Residues in contact with GLY 506 (chain A).
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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463A PHE* 2.7 27.9 - - - -
481A LEU* 4.1 4.5 - - - +
501A LEU* 3.7 22.1 - - - +
502A GLU 3.2 8.9 + - - -
505A PRO* 1.3 78.5 - - - +
507A LEU* 1.3 61.1 + - - +
509A LEU* 4.5 1.1 - - - -
510A GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 507 (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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384A LEU* 3.8 28.9 - - + +
435A GLY* 5.0 4.5 - - - -
463A PHE* 2.8 11.6 - - + -
503A PHE* 3.1 35.1 + - + +
504A TYR* 3.0 16.5 + - + +
506A GLY* 1.3 78.3 - - - +
508A LEU* 1.3 65.0 + - + +
510A GLU* 4.0 13.5 + - - +
518A PHE* 5.9 0.9 - - - +
519A GLY 5.8 1.6 + - - -
521A SER* 4.0 23.8 - - - -
522A MET* 4.1 26.9 + - + +
525A MET* 3.9 26.9 - - - -
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Residues in contact with LEU 508 (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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182A LEU* 4.1 15.5 - - + -
384A LEU 5.8 0.9 - - - +
386A HIS 5.3 0.7 - - - +
387A TRP* 5.2 5.8 - - + -
389A PRO* 4.6 8.3 - - + -
434A ILE* 4.2 20.0 - - + +
435A GLY* 3.7 3.7 - - - -
436A GLY 3.1 10.4 + - - -
437A GLY* 3.1 23.6 + - - +
440A ILE* 3.9 20.0 - - + -
504A TYR* 3.1 53.8 + - + +
505A PRO 3.1 7.1 + - - +
507A LEU* 1.3 82.7 - - + +
509A LEU* 1.3 58.6 + - - +
510A GLU 3.5 0.2 - - - -
522A MET* 4.2 21.8 - - + -
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Residues in contact with LEU 509 (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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177A LEU* 5.7 2.7 - - + -
181A PHE* 3.7 32.3 - - + +
182A LEU* 3.9 18.4 - - + -
436A GLY 4.3 10.3 - - - +
437A GLY* 4.0 16.2 - - - -
481A LEU* 4.0 5.1 - - + +
482A THR* 4.0 19.0 - - + +
487A MET* 4.6 9.8 - - + +
491A LEU* 3.9 40.8 - - + -
501A LEU* 5.2 2.7 - - + -
505A PRO* 2.8 35.8 + - + +
506A GLY* 3.8 3.6 - - - +
508A LEU* 1.3 70.5 - - - +
510A GLU* 1.3 63.7 + - - +
511A LYS 3.8 0.5 + - - -
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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