Contacts of the helix formed by residues 438 - 449 (chain R) in PDB entry 1P3Q
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 ARG 438 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436Q ALA* 3.1 43.0 - - + +
437Q SER* 3.1 26.2 + - - -
441Q PRO* 3.6 26.0 - - - +
434R ALA 3.0 10.5 + - - -
435R ALA* 3.1 8.9 + - - +
437R SER* 1.3 77.6 - - - +
439R ILE* 1.3 64.3 + - - +
440R GLY 3.1 2.4 + - - -
441R PRO* 3.1 36.3 - - + +
442R CYS* 3.3 23.2 + - - -
73V LEU* 3.2 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 439 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412Q THR* 4.6 8.7 - - + -
415Q THR* 3.6 15.3 - - + -
416Q LEU* 4.2 11.7 - - + -
419Q MSE 3.4 33.2 - - + -
433R ILE 5.3 0.7 - - - +
434R ALA* 3.4 23.3 + - + +
437R SER* 3.1 16.2 - - - +
438R ARG* 1.3 76.6 - - - +
440R GLY* 1.3 68.6 + - - +
442R CYS* 3.4 6.5 + - - +
443R VAL* 3.0 29.3 + - + +
69V LEU 5.7 0.7 - - - +
70V VAL* 4.4 15.5 - - + -
71V LEU 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 440 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434R ALA 4.4 2.2 + - - -
438R ARG* 3.1 1.6 - - - +
439R ILE* 1.3 85.2 - - - +
441R PRO* 1.3 63.6 - - - +
443R VAL* 3.1 2.9 + - - +
444R ASP* 2.9 32.2 + - - +
42V ARG* 3.3 14.6 + - - -
70V VAL* 4.3 10.5 - - - -
71V LEU 5.1 4.9 - - - -
73V LEU* 5.8 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 441 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435Q ALA* 4.7 2.4 - - + +
436Q ALA* 3.8 24.7 - - + +
434R ALA 5.6 0.2 - - - +
438R ARG* 3.1 52.7 - - + +
440R GLY* 1.3 86.4 - - - +
442R CYS* 1.3 64.1 + - - +
444R ASP* 3.0 20.5 + - + +
445R ALA* 3.0 15.4 + - - +
73V LEU* 5.9 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 442 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412Q THR* 4.2 10.8 - - - -
416Q LEU* 3.6 26.5 - - + -
431Q VAL* 4.3 2.6 - - + +
432Q CYS* 4.0 16.2 - - - -
435Q ALA* 3.1 32.8 - - - -
436Q ALA 5.5 0.2 - - - -
437R SER 4.6 2.7 - - - -
438R ARG* 3.3 16.9 + - - -
439R ILE* 3.6 8.7 - - - +
440R GLY 3.2 0.6 - - - -
441R PRO* 1.3 78.7 - - - +
443R VAL* 1.3 57.7 + - - +
445R ALA* 3.2 5.6 + - - +
446R LEU* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416Q LEU* 3.9 10.5 - - + -
419Q MSE 3.8 27.6 - - - -
420Q PHE* 4.4 6.3 - - + -
439R ILE* 3.0 23.1 + - + +
440R GLY* 3.4 9.0 - - - +
442R CYS* 1.3 71.6 - - - +
444R ASP* 1.3 68.0 + - - +
445R ALA 3.0 2.0 - - - -
446R LEU* 4.2 4.7 - - - +
447R LEU* 3.1 43.3 + - + +
42V ARG* 3.9 14.8 - - - +
44V ILE* 4.2 18.2 - - + -
70V VAL* 4.3 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 444 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440R GLY 2.9 19.7 + - - +
441R PRO* 3.0 13.9 + - + +
443R VAL* 1.3 78.5 - - - +
445R ALA* 1.3 60.1 + - - +
447R LEU* 4.0 4.7 - - - +
448R SER* 3.3 21.3 + - - -
42V ARG* 2.5 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431Q VAL* 3.4 27.6 - - + +
435Q ALA* 5.6 2.5 - - + -
441R PRO 3.0 10.5 + - - +
442R CYS* 3.5 5.8 - - - +
443R VAL 3.0 0.2 - - - -
444R ASP* 1.3 76.3 - - - +
446R LEU* 1.3 64.6 + - - +
448R SER* 2.6 25.0 + - - -
449R LEU* 3.4 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416Q LEU* 3.9 30.3 - - + -
420Q PHE* 3.6 45.8 - - + -
423Q MSE 3.6 30.4 - - - +
428Q ILE* 4.1 17.9 - - + -
431Q VAL* 3.7 34.1 - - + -
442R CYS 3.0 17.0 + - - +
443R VAL 3.5 0.6 + - - +
445R ALA* 1.3 75.4 - - - +
447R LEU* 1.3 65.2 + - - +
449R LEU* 3.2 20.7 + - + +
450R SER* 4.3 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420Q PHE* 3.8 23.3 - - + -
443R VAL* 3.1 37.3 + - + +
444R ASP* 4.0 4.3 - - - +
446R LEU* 1.3 76.2 - - - +
448R SER* 1.3 64.9 + - - +
449R LEU 3.2 0.3 + - - -
450R SER* 3.3 15.3 + - - -
451R GLU* 4.1 6.1 + - - +
42V ARG* 3.7 8.5 - - - +
44V ILE* 5.2 2.5 - - + -
47V GLY 3.9 13.2 - - - +
48V LYS* 4.2 2.2 - - - -
49V GLN* 3.7 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 448 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444R ASP 3.3 12.7 + - - -
445R ALA* 2.6 22.8 + - - -
446R LEU 3.1 0.8 - - - -
447R LEU* 1.3 80.5 - - - +
449R LEU* 1.3 63.4 + - - +
450R SER 2.9 4.2 + - - -
451R GLU* 2.8 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423Q MSE 4.3 19.1 - - + -
427Q LEU* 4.0 36.1 - - + -
431Q VAL* 4.3 16.4 - - + -
445R ALA 3.5 15.0 - - - +
446R LEU* 3.2 10.3 + - + +
448R SER* 1.3 80.0 + - - +
450R SER* 1.3 59.1 + - - +
451R GLU* 3.5 3.2 + - - +
----------------------------------------------------------
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