Contacts of the helix formed by residues 250 - 257 (chain C) in PDB entry 4QG0
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 ILE 250 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 4.3 6.3 - - + -
134C ARG* 3.9 39.3 - - + +
135C ILE* 4.1 17.3 - - + -
244C LEU* 4.0 12.1 - - + -
245C ILE* 3.3 48.2 + - + +
248C ASN* 4.0 20.9 - - + +
249C GLY* 1.3 76.7 - - - +
251C LYS* 1.3 60.3 + - - +
253C VAL* 2.9 22.4 + - + +
254C MET* 2.9 27.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C GLU* 5.3 3.5 + - - -
245C ILE* 4.0 13.0 - - + +
246C ASN* 3.6 24.3 + - - +
249C GLY 3.5 0.2 - - - -
250C ILE* 1.3 76.9 - - - +
252C PRO* 1.3 63.4 - - + +
254C MET* 3.3 11.6 + - - +
255C GLU* 2.9 38.1 + - - +
261C PRO* 4.0 21.7 - - + +
265C ILE* 3.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C GLY* 3.2 25.6 - - - +
251C LYS* 1.3 95.4 - - + +
253C VAL* 1.3 56.5 + - + +
255C GLU* 3.5 12.7 + - + +
256C GLN* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASP* 5.4 2.2 - - - +
130C PRO 5.4 0.2 - - - +
131C LEU* 3.9 17.9 - - + -
134C ARG* 3.7 46.9 - - + +
249C GLY 3.7 18.6 - - - +
250C ILE* 2.9 10.1 + - - +
252C PRO* 1.3 74.9 - - + +
254C MET* 1.3 67.3 + - - +
256C GLN* 3.0 18.4 + - - +
257C TYR* 3.0 48.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LEU* 4.0 15.6 - - + +
135C ILE* 4.8 1.3 - - + -
201C ILE* 4.3 13.0 - - + -
241C PHE* 4.5 2.0 - - + -
245C ILE* 4.1 22.2 - - + -
250C ILE* 2.9 26.6 + - + +
251C LYS* 3.3 17.9 - - - +
253C VAL* 1.3 76.0 - - - +
255C GLU* 1.3 60.5 + - - +
257C TYR* 3.0 9.9 + - - +
258C GLY 3.1 0.3 + - - -
259C LEU* 2.9 46.9 + - + +
261C PRO* 4.4 13.7 - - + -
264C ASP* 6.0 0.9 - - + -
265C ILE* 4.4 23.6 - - + +
268C ILE* 4.2 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LYS* 2.9 26.9 + - - +
252C PRO* 3.8 10.8 - - + +
254C MET* 1.3 71.7 - - - +
256C GLN* 1.3 66.3 + - - +
258C GLY* 3.0 14.0 + - - -
259C LEU 3.7 9.8 - - - +
261C PRO* 3.7 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASP* 5.0 7.9 + - - +
134C ARG* 5.1 4.7 + - - -
252C PRO 2.9 13.7 + - - +
253C VAL* 3.1 27.6 - - - +
255C GLU* 1.3 75.9 - - - +
257C TYR* 1.3 90.1 + - + +
258C GLY 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ASP* 3.8 17.4 + - - +
129C HIS* 3.6 30.3 - + + +
130C PRO* 3.4 32.3 - - + +
131C LEU* 4.1 15.7 - - + -
194C ARG* 5.4 1.0 - - - +
197C LEU* 4.6 6.4 - - + +
253C VAL* 3.0 46.4 + - + +
254C MET 3.0 4.8 + - - +
256C GLN* 1.3 105.9 + - + +
258C GLY* 1.3 58.7 + - - +
259C LEU* 3.3 16.4 + - + +
----------------------------------------------------------
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