Contacts of the helix formed by residues 297 - 303 (chain H) in PDB entry 1UW9
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 MET 297 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H LEU* 3.9 14.6 - - + +
271H THR* 3.9 21.3 - - + -
296H ALA* 1.3 73.8 - - - +
298H HIS* 1.3 65.2 + - - +
299H ALA 3.2 3.1 - - - +
300H VAL* 3.0 31.8 + - + +
301H ILE* 3.8 11.1 + - + +
1477H EDO 4.0 22.4 - - - -
117R PHE* 4.4 17.7 - - + -
121R VAL* 3.4 25.8 - - + +
122R GLY 2.7 15.2 + - - -
274R PHE* 6.0 0.7 - - - -
301R ILE* 4.3 20.0 - - + -
309R ILE* 4.1 26.0 - - + -
314R LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 298 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H LEU* 3.7 19.2 - - + +
295H ARG* 2.9 76.7 + - + +
296H ALA 3.3 1.0 + - - -
297H MET* 1.3 78.6 - - - +
299H ALA* 1.3 71.9 + - + +
301H ILE* 2.9 10.1 + - - +
302H ASP* 2.4 62.9 + - - +
311H PHE* 3.9 6.9 - - + -
314H LEU* 4.0 9.5 - - + +
335H LEU* 5.9 2.4 - - - +
336H GLU 5.7 0.4 - - - -
1482H EDO 3.6 12.3 - - - -
1478O CAP 4.1 6.5 + - - -
122R GLY 5.0 4.7 - - - -
123R ASN* 6.0 1.1 - - - -
126R GLY* 5.7 2.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H MET 3.2 0.8 - - - -
298H HIS* 1.3 87.6 - - + +
300H VAL* 1.3 63.2 + - - +
301H ILE 3.1 2.0 + - - -
302H ASP* 3.1 14.4 - - - +
303H ARG* 3.3 13.4 + - + +
122R GLY 5.4 2.4 + - - +
123R ASN 5.1 2.0 - - - +
125R PHE* 3.5 10.1 - - + +
126R GLY* 3.4 37.2 - - - +
307R HIS* 2.8 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H MET* 3.0 23.7 + - + +
299H ALA* 1.3 78.8 - - - +
301H ILE* 1.3 57.8 + - - +
121R VAL* 3.8 24.5 - - + +
125R PHE* 3.7 31.1 - - + +
300R VAL 5.0 4.7 - - - +
301R ILE* 3.9 20.4 - - + +
307R HIS* 3.5 21.4 - - - -
308R GLY* 3.9 11.3 - - - -
309R ILE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H ARG* 5.5 0.2 + - - -
270H LEU* 4.8 8.7 - - + -
297H MET* 4.2 26.5 - - + +
298H HIS 2.9 7.0 + - - +
300H VAL* 1.3 82.0 - - + +
302H ASP* 1.3 58.1 + - - +
303H ARG 3.7 1.3 - - - -
304H GLN 5.2 0.4 + - - -
307H HIS 3.9 4.3 - - - +
308H GLY* 3.3 10.2 - - - -
309H ILE* 3.1 54.2 + - + +
314H LEU* 4.0 18.4 - - + -
1477H EDO 4.6 10.8 - - - -
297R MET* 4.3 16.4 - - + -
300R VAL* 3.9 17.7 - - + +
301R ILE* 4.0 20.4 - - + -
307R HIS* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H ARG* 3.0 22.6 + - - +
298H HIS* 2.4 48.2 + - - +
299H ALA* 3.1 15.8 - - - +
301H ILE* 1.3 77.9 - - - +
303H ARG* 1.3 64.9 + - - +
304H GLN 3.6 1.8 - - - -
309H ILE 2.9 22.2 - - - +
310H HIS* 4.9 0.2 - - - -
311H PHE* 3.3 34.3 + - - +
314H LEU* 4.0 3.7 - - + +
473H ASP* 4.1 7.6 - - - +
1482H EDO 4.4 7.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H ALA* 3.3 21.1 + - - +
301H ILE 3.7 1.2 - - - -
302H ASP* 1.3 83.5 + - - +
304H GLN* 1.3 76.3 + - - +
336H GLU* 2.9 43.4 + - - +
472H ILE* 3.6 22.3 - - + +
473H ASP* 3.5 21.8 + - - +
45R GLN* 4.5 0.4 - - - +
125R PHE 2.9 26.7 + - - +
126R GLY* 3.4 15.0 - - - -
127R PHE 2.9 26.3 + - - -
128R LYS* 3.9 6.3 + - - +
130R LEU* 2.8 31.5 + - - +
131R ARG 4.7 2.4 + - - +
307R HIS* 3.5 12.5 + - + +
----------------------------------------------------------
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