Contacts of the helix formed by residues 247 - 258 (chain C) in PDB entry 3UDB
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 SER 247 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 2.6 31.9 + - - -
246C ILE* 1.3 75.8 - - - +
248C PRO* 1.3 71.2 - - - +
249C GLU* 2.9 23.2 + - - -
250C CYS* 3.2 11.1 + - - +
251C ARG* 3.0 16.8 + - - +
276C TRP* 3.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ILE 3.7 2.0 - - - +
247C SER* 1.3 84.9 - - - +
249C GLU* 1.3 75.3 + - + +
251C ARG* 3.2 13.6 + - + +
252C HIS* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C SER* 2.9 30.5 + - - +
248C PRO* 1.3 89.8 - - - +
250C CYS* 1.3 62.8 + - - +
252C HIS* 3.1 8.8 + - - +
253C LEU 3.0 19.2 + - - -
274C HIS* 3.4 15.8 - - + -
275C GLU* 3.4 26.7 - - + +
276C TRP* 4.1 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 3.6 4.3 - - - +
207C LEU* 5.2 1.6 - - - -
211C LEU* 3.6 31.4 - - - -
246C ILE* 3.9 17.3 - - + -
247C SER* 3.1 22.8 + - - +
249C GLU* 1.3 80.2 - - - +
251C ARG* 1.3 61.8 + - - +
253C LEU* 3.4 4.0 + - - +
254C ILE* 3.1 26.4 + - - +
276C TRP* 3.2 37.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 5.0 1.0 + - - -
240C ILE* 3.8 32.0 + - + +
241C PRO 5.5 1.2 + - - -
244C VAL 3.8 20.2 + - - -
245C HIS* 4.7 2.4 + - - +
246C ILE* 3.8 42.3 + - + +
247C SER 3.0 9.2 + - - +
248C PRO* 3.5 13.6 - - + +
250C CYS* 1.3 77.2 - - - +
252C HIS* 1.3 62.8 + - - +
254C ILE* 3.7 5.8 + - - +
255C SER* 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C PRO 2.8 13.4 + - - +
249C GLU* 3.1 11.6 + - - +
251C ARG* 1.3 74.4 - - - +
253C LEU* 1.3 65.9 + - - +
255C SER* 2.7 30.0 + - - -
256C ARG* 3.0 32.8 + - + +
274C HIS* 3.0 26.5 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 4.0 20.2 - - + -
207C LEU* 4.2 8.1 - - + -
249C GLU 3.0 9.8 + - - +
250C CYS* 3.4 8.5 + - - +
252C HIS* 1.3 74.9 - - - +
254C ILE* 1.3 65.5 + - - +
256C ARG* 2.9 14.1 + - - +
257C ILE* 3.1 30.2 + - + +
266C ILE* 4.3 6.1 - - + -
271C ILE* 4.2 22.9 - - + -
274C HIS* 3.6 34.7 + - + +
276C TRP* 3.6 33.0 - - + -
277C PHE* 5.3 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLY* 5.8 2.5 - - - +
207C LEU* 4.2 20.0 - - + -
208C TYR* 5.0 11.9 - - + +
211C LEU* 4.1 25.4 - - + -
238C TYR* 4.2 18.2 - - + +
240C ILE* 4.1 21.3 - - + -
246C ILE* 4.3 5.6 - - + -
250C CYS* 3.1 16.2 + - - +
251C ARG* 3.8 5.8 - - - +
252C HIS 3.3 0.2 - - - -
253C LEU* 1.3 77.6 - - - +
255C SER* 1.3 57.7 + - - +
257C ILE* 3.2 8.9 + - - +
258C PHE* 3.0 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 3.5 20.2 - - - -
251C ARG 3.2 9.4 + - - -
252C HIS* 2.7 31.0 + - - -
254C ILE* 1.3 79.1 - - - +
256C ARG* 1.3 62.4 + - - +
257C ILE 3.3 0.4 + - - -
258C PHE* 3.9 7.7 - - - +
259C VAL* 3.4 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C HIS* 3.0 42.2 + - + +
253C LEU* 2.9 10.8 + - - +
255C SER* 1.3 80.6 + - - +
257C ILE* 1.3 60.7 + - - +
259C VAL* 3.6 17.7 - - - +
264C LYS* 2.9 29.3 + - - +
265C ARG 4.4 0.4 + - - -
266C ILE* 3.1 68.5 + - + +
270C GLU* 4.6 9.1 + - - -
274C HIS* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 4.4 12.6 - - + -
200C VAL* 3.6 27.8 - - + +
201C TRP* 3.8 11.3 - - - -
203C CYS* 5.8 0.2 - - + -
204C GLY* 3.7 27.1 - - - +
207C LEU* 4.9 3.4 - - + -
253C LEU* 3.1 30.7 + - + +
254C ILE* 3.2 9.8 + - - +
256C ARG* 1.3 77.7 - - - +
258C PHE* 1.3 62.0 + - + +
259C VAL 2.9 11.3 + - - -
265C ARG* 3.2 22.5 + - - +
266C ILE* 3.6 21.3 - - + -
271C ILE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C TRP* 3.8 33.0 - + + -
204C GLY* 3.6 26.2 - - - -
205C VAL* 3.7 31.0 - - + -
208C TYR* 4.3 18.8 - + + -
216C PRO* 4.4 5.2 - - + -
217C PHE* 4.0 17.3 - + + -
236C VAL* 3.1 23.8 - - + +
238C TYR* 3.8 28.1 - + + -
254C ILE* 3.0 38.5 + - + +
255C SER 3.9 5.4 - - - +
256C ARG 3.6 0.2 - - - -
257C ILE* 1.3 74.7 - - + +
259C VAL* 1.3 61.6 + - - +
----------------------------------------------------------
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