Contacts of the helix formed by residues 297 - 303 (chain R) 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 R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE* 4.4 16.2 - - + -
121H VAL* 3.4 26.0 - - + +
122H GLY* 2.7 14.8 + - - -
270H LEU* 6.6 0.2 - - + -
274H PHE* 6.0 1.6 - - - -
301H ILE* 4.3 19.7 - - + -
309H ILE* 4.1 26.0 - - + -
314H LEU* 5.9 0.7 - - + -
1477H EDO 4.1 20.6 - - - -
270R LEU* 3.9 15.3 - - + +
271R THR* 3.8 22.2 - - + -
295R ARG 3.2 0.2 + - - -
296R ALA* 1.3 73.1 - - - +
298R HIS* 1.3 63.0 + - - +
299R ALA 3.2 3.4 - - - -
300R VAL* 3.1 32.1 + - + +
301R ILE* 3.8 10.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 298 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H GLY 5.0 4.3 - - - -
123H ASN* 6.0 1.1 - - - -
126H GLY* 5.7 2.8 - - - -
270R LEU* 3.7 19.4 - - + +
295R ARG* 2.9 77.9 + - + +
296R ALA 3.4 0.8 + - - -
297R MET* 1.3 78.7 - - - +
299R ALA* 1.3 69.6 + - + +
301R ILE* 2.8 10.9 + - - +
302R ASP* 2.5 63.8 + - - +
311R PHE* 4.0 6.1 - + + -
314R LEU* 4.0 9.0 - - + -
335R LEU* 6.0 3.2 - - - +
336R GLU 5.7 3.1 - - - -
1476R CAP 4.1 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H GLY 5.5 2.4 + - - +
123H ASN 5.2 2.0 - - - +
125H PHE* 3.5 10.1 - - + +
126H GLY* 3.3 37.5 - - - +
307H HIS* 2.8 21.7 + - - -
297R MET 3.2 1.2 - - - -
298R HIS* 1.3 86.8 - - + +
300R VAL* 1.3 61.8 + - - +
301R ILE 3.1 1.7 + - - -
302R ASP* 3.2 14.4 - - - +
303R ARG* 3.2 13.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 3.7 29.2 - - + +
125H PHE* 3.7 27.0 - - + +
300H VAL 5.0 4.5 - - - +
301H ILE* 3.9 20.6 - - + +
307H HIS* 3.5 21.7 - - - -
308H GLY* 3.9 11.3 - - - -
309H ILE* 3.7 27.8 - - + -
297R MET* 3.1 24.4 + - + +
299R ALA* 1.3 77.0 - - - +
301R ILE* 1.3 58.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 301 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H MET* 4.3 15.9 - - + -
300H VAL* 3.9 17.2 - - + +
301H ILE* 4.0 20.2 - - + -
307H HIS* 5.9 0.4 - - - -
1477H EDO 4.7 9.9 - - - -
270R LEU* 4.8 8.3 - - + -
297R MET* 4.2 28.9 - - + +
298R HIS 2.8 7.4 + - - +
300R VAL* 1.3 83.2 - - + +
302R ASP* 1.3 58.8 + - - +
303R ARG 3.7 0.9 - - - -
304R GLN 5.2 0.2 + - - -
307R HIS 3.9 4.5 - - - +
308R GLY* 3.3 10.2 - - - -
309R ILE* 3.2 48.9 + - + +
314R LEU* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 302 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R ARG* 3.0 23.0 + - - +
298R HIS* 2.5 47.0 + - - +
299R ALA* 3.2 16.3 - - - +
301R ILE* 1.3 72.7 - - - +
303R ARG* 1.3 64.2 + - - +
304R GLN 3.6 1.8 - - - -
309R ILE 2.9 22.7 - - - +
310R HIS 4.0 0.2 - - - -
311R PHE* 3.2 35.7 + - - +
314R LEU* 4.1 3.8 - - + +
473R ASP* 4.1 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H GLN* 4.5 0.8 - - - +
125H PHE 2.9 26.0 + - - +
126H GLY* 3.4 14.9 - - - -
127H PHE 2.9 24.1 + - - -
128H LYS* 4.0 8.9 + - - +
130H LEU* 2.8 31.1 + - - +
131H ARG 4.8 1.9 - - - +
307H HIS* 3.6 11.8 + - + +
299R ALA* 3.2 21.4 + - - +
301R ILE 3.7 1.2 - - - -
302R ASP* 1.3 81.6 + - - +
304R GLN* 1.3 75.7 + - - +
336R GLU* 2.9 45.1 + - - +
472R ILE* 3.6 21.0 - - + +
473R ASP* 3.5 22.2 + - - +
----------------------------------------------------------
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