Contacts of the helix formed by residues 301 - 306 (chain X) in PDB entry 1O1F
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 GLY 301 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154X ASP* 4.0 5.2 - - - -
155X SER 3.2 15.5 - - - -
156X GLY* 4.8 1.1 - - - -
300X SER* 1.3 76.8 - - - +
302X GLY* 1.3 68.4 + - - +
304X THR* 2.9 19.9 + - - -
305X MET* 3.9 5.5 + - - +
335X ARG* 3.1 12.7 + - - +
336X LYS* 4.2 7.6 - - - -
339X VAL* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 302 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155X SER 3.3 2.6 + - - -
156X GLY* 4.4 6.4 - - - -
301X GLY* 1.3 69.2 - - - -
303X THR* 1.3 61.6 + - - +
304X THR 3.2 1.6 + - - -
305X MET* 3.2 27.5 + - - +
306X TYR* 4.9 0.7 + - - -
336X LYS* 4.2 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155X SER* 3.1 29.3 + - - +
156X GLY 2.9 18.4 + - - -
181X ALA 4.3 1.6 - - - -
182X GLY* 3.1 21.4 - - - +
185X LEU* 3.8 26.2 - - + -
213X LYS* 5.1 1.4 + - - -
261X LEU* 4.1 11.6 - - + +
302X GLY* 1.3 75.9 - - - +
304X THR* 1.3 56.3 + - - +
305X MET 3.2 1.8 - - - -
306X TYR* 3.0 37.7 + - + -
309X ILE* 3.9 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 304 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153X LEU* 4.0 20.4 - - + -
155X SER* 3.6 21.3 - - - -
261X LEU* 6.5 0.2 - - + -
299X MET* 3.8 15.3 - - + -
300X SER 3.3 26.9 + - - +
301X GLY 2.9 13.5 + - - +
303X THR* 1.3 75.2 - - - +
305X MET* 1.3 55.0 + - - +
306X TYR 3.5 1.8 - - - -
309X ILE* 3.2 23.5 - - + +
335X ARG* 2.7 46.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 305 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301X GLY 3.9 7.2 - - - +
302X GLY* 3.2 24.0 - - - +
303X THR 3.2 1.4 - - - -
304X THR* 1.3 78.1 - - - +
306X TYR* 1.4 65.8 + - - +
307X PRO* 3.1 10.7 - - - +
333X PRO* 3.8 19.7 - - + +
335X ARG* 3.3 43.9 + - + +
336X LYS* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185X LEU* 3.0 35.7 - - + +
213X LYS* 3.7 43.7 + - + +
214X GLU* 5.6 3.1 - - - -
217X CYS* 4.0 16.4 - - + +
219X VAL* 3.6 18.4 - - + +
257X CYS* 5.5 0.4 - - - -
258X PRO* 3.6 31.0 - - + -
261X LEU* 4.0 9.6 - - + -
302X GLY 4.9 0.6 + - - -
303X THR* 3.0 37.9 + - + +
304X THR 3.5 0.6 - - - -
305X MET* 1.4 71.2 - - - +
307X PRO* 1.3 71.8 - - + +
309X ILE* 3.2 26.0 - - + +
----------------------------------------------------------
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