Contacts of the helix formed by residues 202 - 214 (chain C) in PDB entry 2PGW
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 202 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C GLY 4.2 0.4 + - - -
201C TRP* 1.3 78.9 - - - +
203C VAL* 1.3 65.3 + - - +
204C HIS* 3.6 10.9 + - - -
205C ASP* 3.2 32.8 + - - +
206C ALA* 2.9 18.6 + - - +
225C THR* 4.5 0.4 - - - -
292D GLY 5.8 0.9 - - - -
294D LYS* 3.4 36.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C SER* 1.3 74.7 - - - +
204C HIS* 1.3 63.4 + - - +
206C ALA* 3.4 2.6 + - - +
207C ILE* 3.2 24.1 + - + +
225C THR* 4.4 5.1 - - + +
232C ALA* 4.3 18.4 - - + +
235C HIS* 3.6 37.0 - - + +
236C VAL* 4.0 21.2 - - + +
266D ASP* 3.8 20.6 + - - +
292D GLY 3.4 26.0 + - - +
293D LEU* 4.0 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C SER* 3.5 11.3 + - - -
203C VAL* 1.3 76.8 - - - +
205C ASP* 1.3 84.2 + - - +
207C ILE* 3.3 6.7 + - - +
208C ASN* 3.1 31.5 + - - -
219D GLU* 2.9 47.8 + - + -
220D PHE* 4.0 11.5 - + + -
243D PRO* 3.7 22.2 - - + +
245D VAL* 5.8 0.7 - - + -
266D ASP* 3.9 16.7 + - + +
267D MSE 4.1 31.6 - - + +
294D LYS* 5.7 3.6 - - - -
321D ASP* 4.5 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C TRP* 4.3 11.2 - - + -
202C SER* 3.2 28.7 + - - +
203C VAL 3.3 0.6 - - - -
204C HIS* 1.3 99.6 + - - +
206C ALA* 1.3 60.7 + - - +
208C ASN* 3.3 6.7 + - - +
209C MSE 2.8 40.0 + - + +
192D ARG* 5.7 0.5 + - - -
219D GLU* 4.2 5.5 - - - +
294D LYS* 4.9 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C TRP* 3.6 29.1 - - + +
202C SER 2.9 18.1 + - - +
203C VAL 3.6 5.8 - - - +
204C HIS 3.3 0.2 - - - -
205C ASP* 1.3 77.6 - - - +
207C ILE* 1.3 62.0 + - - +
209C MSE 3.9 0.7 - - - +
210C CYS* 3.0 32.2 + - - -
224C PRO* 4.2 7.4 - - + -
225C THR* 4.4 2.2 - - + -
236C VAL* 4.0 23.8 - - + -
240C VAL* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C VAL* 3.2 20.8 + - + +
204C HIS* 3.6 8.3 - - - +
205C ASP 3.2 0.6 - - - -
206C ALA* 1.3 79.1 - - - +
208C ASN* 1.3 61.3 + - - +
210C CYS* 3.4 2.6 + - - +
211C ARG* 3.2 22.0 + - + +
235C HIS* 4.8 2.7 - - + +
236C VAL* 4.9 6.3 - - + -
239C LYS* 3.7 39.0 - - + +
240C VAL* 3.7 18.0 - - + +
241D GLY 4.1 13.2 - - - +
243D PRO* 4.0 15.9 - - + -
266D ASP* 3.5 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 5.7 2.0 - - - +
204C HIS* 3.1 24.8 + - - +
205C ASP* 3.9 6.5 + - - +
207C ILE* 1.3 74.9 - - - +
209C MSE 1.3 66.6 + - + +
211C ARG* 3.3 20.4 + - - +
212C LYS* 3.0 40.2 + - - +
218D ILE 4.0 8.0 - - - +
219D GLU* 2.9 41.7 + - - +
241D GLY 5.2 0.2 - - - +
243D PRO* 3.2 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 3.7 40.6 - - - +
177C ASP* 3.7 35.4 - - + +
178C LEU* 4.2 15.3 - - + -
201C TRP* 3.6 40.2 - - + +
205C ASP* 2.8 28.3 + - + +
208C ASN* 1.3 74.7 - - + +
210C CYS* 1.3 57.2 + - - +
212C LYS* 3.2 5.0 + - - +
213C LEU* 2.9 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C TRP* 4.7 5.4 - - - -
206C ALA* 3.0 26.5 + - - +
207C ILE 3.7 0.2 - - - +
208C ASN 3.3 0.2 - - - -
209C MSE 1.3 76.4 - - - +
211C ARG* 1.3 62.9 + - - +
213C LEU* 4.6 1.1 - - - -
214C GLU* 3.0 31.1 + - - +
221C ILE* 3.7 25.1 - - - -
224C PRO* 5.8 0.7 - - - -
236C VAL* 5.3 1.8 - - - -
240C VAL* 3.6 40.6 - - + -
241C GLY 5.2 0.9 - - - +
242C ILE* 3.4 16.8 - - + +
244C ILE* 4.6 9.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ILE* 3.2 11.7 + - + +
208C ASN* 3.4 20.6 + - - +
210C CYS* 1.3 80.2 - - - +
212C LYS* 1.3 84.2 + - - +
213C LEU 3.5 0.2 + - - -
214C GLU* 3.7 26.4 + - - +
215C LYS* 4.6 4.3 + - - -
214D GLU* 4.3 25.9 + - - -
217D ASP* 2.7 40.0 + - - +
218D ILE 4.8 6.6 + - - +
241D GLY 5.1 10.1 - - - -
242D ILE* 6.4 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLU* 2.7 46.9 + - + +
178C LEU* 3.8 27.7 - - + +
208C ASN* 3.0 24.2 + - - +
209C MSE 3.8 5.8 - - - +
211C ARG* 1.3 97.1 - - - +
213C LEU* 1.3 60.4 + - - +
215C LYS* 3.0 31.4 + - - +
216C TYR* 4.0 1.6 - - - -
192D ARG* 6.3 1.4 - - - +
217D ASP* 3.2 37.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C VAL* 5.3 3.4 - - + -
177C ASP* 4.5 3.8 - - + +
178C LEU* 3.7 23.3 - - + -
181C THR* 3.4 37.2 - - + +
195C LEU* 3.8 17.7 - - + -
201C TRP* 3.9 26.0 - - + -
209C MSE 2.9 29.7 + - + +
210C CYS 4.0 2.5 - - - +
212C LYS* 1.3 74.3 - - - +
214C GLU* 1.3 65.6 + - - +
215C LYS 3.2 3.6 - - - -
216C TYR* 2.9 24.9 + - + +
218C ILE* 3.5 13.5 - - + +
221C ILE* 4.1 7.4 - - + -
242C ILE* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ARG* 4.6 22.1 + - - -
210C CYS 3.0 22.5 + - - +
211C ARG* 3.8 22.6 - - - +
212C LYS 3.5 0.8 - - - -
213C LEU* 1.3 77.4 - - - +
215C LYS* 1.3 57.9 + - - +
216C TYR 2.9 5.9 + - - -
217C ASP* 3.0 14.9 + - - -
218C ILE* 4.5 1.5 + - - +
241C GLY* 3.6 28.8 - - - +
242C ILE* 3.6 21.1 - - + -
----------------------------------------------------------
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