Contacts of the helix formed by residues 433 - 439 (chain N) in PDB entry 3H1J
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 ASP 433 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242N ARG* 3.1 8.6 - - - +
432N LEU* 1.3 104.2 - - + +
434N TYR* 1.3 65.4 + - - +
435N ASN* 2.5 33.6 + - - +
436N ARG* 3.2 19.2 + - + +
437N ILE* 3.1 16.3 + - - +
220P PRO* 3.3 17.7 - - + +
223P PRO* 4.0 2.8 - - - +
224P TYR* 2.9 42.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 434 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238N GLY 3.8 1.9 - - - -
239N SER* 3.7 14.8 - - - -
240N GLU* 3.2 44.1 + - + +
242N ARG* 3.7 0.6 - - - +
419N CYS* 3.5 8.7 - - - +
420N PRO* 2.6 56.9 + - + +
422N LEU* 4.9 6.1 - - + -
433N ASP* 1.3 73.9 + - - +
435N ASN* 1.3 51.6 + - - +
437N ILE* 3.0 11.0 + - + +
438N ARG* 2.6 48.5 + - + -
229Q VAL* 3.9 19.1 - - + +
17T SER* 5.7 0.2 - - - -
18T LEU 4.7 2.2 - - - -
19T SER* 3.5 38.0 - - - -
20T PRO* 4.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433N ASP* 2.5 17.9 + - - +
434N TYR* 1.3 70.9 - - - +
436N ARG* 1.3 66.9 + - - +
438N ARG* 2.7 20.3 + - - +
439N SER* 2.9 17.7 + - - -
223P PRO* 4.2 12.8 - - + +
224P TYR* 2.9 26.9 + - - -
226Q LYS* 3.0 48.8 + - + +
229Q VAL* 3.5 9.3 - - - +
20T PRO* 3.5 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 436 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N GLN* 5.0 1.2 + - - -
432N LEU 3.9 8.1 - - - +
433N ASP* 3.2 26.7 + - + +
435N ASN* 1.3 78.1 - - - +
437N ILE* 1.3 60.3 + - + +
439N SER* 3.6 8.0 + - - -
440N GLY* 3.6 13.9 + - - -
6P ARG* 3.5 22.2 - - - +
20P ILE* 2.9 35.7 + - - +
21P ASP* 2.6 24.4 + - - -
220P PRO* 3.3 18.6 - - + +
222P HIS* 2.8 35.4 + - - -
223P PRO* 3.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242N ARG* 3.7 25.4 - - - +
255N LEU* 4.3 22.7 - - + -
335N MET* 4.5 7.6 - - + -
339N GLN* 3.2 34.4 - - - +
420N PRO* 4.8 5.4 - - + -
422N LEU* 3.8 20.6 - - + -
431N LEU* 3.9 20.6 - - + -
432N LEU 3.8 7.6 - - - +
433N ASP 3.1 8.9 + - - +
434N TYR* 3.0 11.0 + - + +
435N ASN 3.0 0.6 - - - -
436N ARG* 1.3 73.6 - - + +
438N ARG* 1.3 66.2 + - - +
439N SER 3.1 1.8 - - - -
440N GLY* 3.1 9.0 + - - -
441N MET* 3.8 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417N ASP* 2.4 43.8 + - - -
418N LYS 3.3 25.1 + - - +
419N CYS* 3.4 23.8 - - - +
420N PRO* 3.8 7.8 - - - +
434N TYR* 2.6 34.4 + - + +
435N ASN* 2.7 15.0 + - - +
437N ILE* 1.3 73.5 - - - +
439N SER* 1.3 58.3 + - - +
441N MET* 3.1 24.4 - - - +
442N TYR* 4.0 9.4 - - + -
33R LYS* 3.6 14.8 - - - +
37R TYR* 4.1 1.8 + - - -
19T SER* 4.4 0.7 - - - +
20T PRO* 5.2 3.1 - - + -
21T PHE* 3.6 25.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 439 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435N ASN 2.9 15.3 + - - -
436N ARG* 3.8 10.0 - - - -
437N ILE 3.1 0.2 - - - -
438N ARG* 1.3 74.4 - - - +
440N GLY* 1.3 55.8 + - - +
441N MET 2.9 9.7 + - - -
442N TYR* 3.4 50.3 + - - +
3008N PEE 4.1 18.8 + - - -
226Q LYS* 4.2 12.8 + - - -
----------------------------------------------------------
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