Contacts of the helix formed by residues 445 - 457 (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 LEU 445 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 3.7 37.2 - - - +
179B ARG* 3.8 40.4 - - + +
182B LEU* 4.1 4.3 - - + -
183B LEU* 3.8 29.6 - - + +
440B ILE* 3.6 23.1 - - + +
441B ASP 3.3 4.1 + - - +
442B HIS* 3.0 22.1 + - - +
444B ILE* 1.3 75.1 - - - +
446B HIS* 1.3 63.6 + - - +
448B ALA* 3.2 11.5 + - + +
449B VAL* 3.3 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 5.6 7.4 - - - +
442B HIS 4.4 1.8 + - - -
443B HIS 3.4 23.2 + - - -
444B ILE* 3.0 6.0 + - + -
445B LEU* 1.3 80.4 - - - +
447B VAL* 1.3 82.7 + - + +
449B VAL* 3.0 14.7 + - - +
450B ASP* 2.9 36.1 + - - +
601B HEM 4.2 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B HIS* 4.2 6.5 - - + -
388B HIS* 3.6 34.3 - - + +
444B ILE* 2.9 16.8 + - + +
446B HIS* 1.3 98.3 - - + +
448B ALA* 1.3 58.6 + - - +
450B ASP* 2.7 29.5 + - - +
451B VAL* 2.9 13.4 + - + +
601B HEM 3.7 49.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 4.3 0.2 - - - -
182B LEU* 3.8 15.5 - - + -
388B HIS* 5.5 2.8 + - + +
440B ILE* 3.5 33.0 - - + -
444B ILE 4.0 0.8 + - - -
445B LEU* 3.2 11.9 + - + +
447B VAL* 1.3 77.9 - - - +
449B VAL* 1.3 62.2 + - - +
451B VAL* 3.2 12.3 + - - +
452B ILE* 3.1 29.8 + - - +
504B TYR* 4.0 10.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA* 4.0 4.4 - - + +
175B GLU* 3.9 39.3 - - + +
178B SER* 3.3 31.9 - - - +
179B ARG* 5.9 0.4 - - - +
445B LEU* 3.3 16.4 + - + +
446B HIS* 3.0 17.6 + - - +
448B ALA* 1.3 79.0 - - - +
450B ASP* 1.3 62.0 + - - +
452B ILE* 3.3 5.0 + - - +
453B LYS* 3.1 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B HIS* 2.9 31.4 + - - +
447B VAL* 2.7 16.4 + - - +
449B VAL* 1.3 73.4 - - - +
451B VAL* 1.3 55.1 + - - +
453B LYS* 3.3 16.8 + - - +
454B GLU* 2.8 30.5 + - - +
601B HEM 3.1 26.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 3.6 21.4 - - - +
386B HIS* 3.4 42.2 - - + +
447B VAL* 2.9 17.4 + - + +
448B ALA* 3.3 11.9 - - - +
450B ASP* 1.3 72.1 - - - +
452B ILE* 1.3 61.4 + - - +
454B GLU* 3.0 10.2 + - - +
455B SER 2.9 24.6 + - - -
504B TYR* 3.6 34.3 - - + -
601B HEM 5.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO 5.8 0.7 - - - +
174B ALA* 4.1 22.9 - - + +
177B LEU* 4.7 12.6 - - + -
178B SER* 3.3 26.9 - - - +
182B LEU* 4.1 13.5 - - + -
448B ALA 3.1 12.7 + - - +
449B VAL* 3.3 5.6 + - - +
451B VAL* 1.3 74.9 - - - +
453B LYS* 1.3 62.8 + - - +
455B SER* 3.1 12.1 + - - -
456B ARG* 3.1 22.3 + - + +
502B GLU* 3.6 26.5 - - - +
504B TYR* 4.0 10.1 - - + -
505B PRO* 4.0 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ALA* 3.9 16.4 - - + -
449B VAL* 3.1 30.5 + - + +
450B ASP* 3.5 17.1 + - - +
452B ILE* 1.3 76.3 - - - +
454B GLU* 1.3 60.5 + - - +
456B ARG* 3.2 11.5 + - - +
457B VAL* 3.0 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B THR* 4.7 17.2 + - - +
218B PRO* 4.0 22.2 - - + +
382B ASN* 4.4 9.0 - - - +
383B GLN* 3.4 20.2 + - - +
386B HIS* 5.6 2.5 - - - -
450B ASP* 2.8 15.2 + - - +
451B VAL* 3.4 10.7 - - - +
453B LYS* 1.3 71.4 - - - +
455B SER* 1.3 67.0 + - - +
456B ARG 3.0 1.3 - - - -
457B VAL* 2.9 16.7 + - + +
458B LEU* 2.9 35.3 + - + +
601B HEM 5.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 2.8 24.2 + - - -
451B VAL 2.9 9.4 + - - -
452B ILE* 3.2 12.7 - - - -
454B GLU* 1.3 72.6 - - - +
456B ARG* 1.3 60.9 + - - +
458B LEU* 3.5 6.1 - - - +
459B ARG* 2.9 21.8 + - - -
460B LEU* 3.0 28.0 + - - +
502B GLU* 4.0 15.3 - - - -
503B PHE* 4.9 2.6 + - - +
504B TYR* 4.2 18.4 + - - +
505B PRO* 5.2 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 5.5 0.2 - - - +
162B PRO* 3.4 25.3 + - - +
163B MET* 3.7 14.5 - - - +
171B LEU* 3.5 27.5 - - + +
452B ILE* 3.1 14.4 + - + +
453B LYS* 3.2 13.7 - - - +
454B GLU 3.0 0.6 - - - -
455B SER* 1.3 84.9 + - - +
457B VAL* 1.3 64.9 + - + +
459B ARG* 3.1 37.1 + - - +
460B LEU 3.6 21.8 + - - -
502B GLU* 3.2 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE* 5.2 3.0 - - + +
157B ARG* 4.6 5.5 + - - -
218B PRO* 4.3 27.8 - - + -
453B LYS* 3.0 15.3 + - + +
454B GLU* 2.9 13.1 + - - +
456B ARG* 1.3 71.8 - - + +
458B LEU* 1.3 63.4 + - + +
459B ARG* 3.0 12.9 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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