Contacts of the helix formed by residues 202 - 213 (chain C) in PDB entry 5G04
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 HIS 202 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ILE* 3.6 8.5 - - + +
43C THR* 3.9 14.6 - - + -
48C LEU* 4.0 12.4 - - + +
51C SER* 3.8 20.2 + - - -
170C PHE* 4.0 15.2 - + + -
173C TYR* 2.9 38.6 - + + +
199C LEU* 4.1 24.9 + - + +
200C PRO* 3.2 4.6 + - - +
201C LEU* 1.3 74.7 - - - +
203C TRP* 1.3 62.1 + - - +
204C GLY* 3.4 7.3 + - - -
205C ALA* 2.8 39.5 + - + +
206C TRP* 3.7 12.1 + - - -
229C MET* 4.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 6.0 1.6 - - + -
51C SER* 4.5 10.0 + - - +
54C TRP* 3.1 85.8 - + + +
55C SER* 4.9 8.0 + - - +
58C LEU* 4.2 16.8 - - + +
201C LEU* 3.4 8.6 + - + -
202C HIS* 1.3 73.8 - - - +
204C GLY* 1.3 54.2 + - - +
206C TRP* 3.1 12.6 + - + -
207C LEU* 2.7 53.4 + - + +
210C CYS* 4.5 4.0 - - - -
228C TRP* 6.1 0.8 - - - -
229C MET* 3.4 23.0 - - + +
232C PHE* 3.7 41.3 - + + +
233C PHE* 4.5 7.2 - - + -
236C HIS* 4.8 5.2 - - + -
264C TYR* 4.5 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 6.1 0.4 - - - -
51C SER* 3.8 12.9 - - - +
54C TRP* 5.7 0.7 - - - -
173C TYR* 3.3 20.7 - - - -
202C HIS* 3.3 13.0 + - - -
203C TRP* 1.3 78.7 - - - +
205C ALA* 1.3 56.4 + - - +
207C LEU* 3.7 8.5 - - - +
208C GLU* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C TYR* 3.5 19.5 - - + -
192C PHE* 3.9 17.4 - - + +
195C ALA* 4.4 18.6 - - + -
196C THR* 4.4 13.0 - - + +
199C LEU 5.5 2.7 - - - +
202C HIS* 2.8 31.8 + - + +
204C GLY* 1.3 71.7 - - - +
206C TRP* 1.3 63.4 + - + +
208C GLU 3.4 1.7 + - - -
209C LEU* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C THR* 3.8 21.5 - - + +
199C LEU 5.5 0.7 - - - -
200C PRO* 4.5 10.0 - - + +
201C LEU 4.7 2.2 - - - -
202C HIS 3.7 8.0 + - - -
203C TRP* 3.1 20.5 + - + +
205C ALA* 1.3 79.7 - - + +
207C LEU* 1.3 63.4 + - - +
209C LEU* 3.1 27.3 - - + +
210C CYS* 3.2 12.5 + - - -
224C LEU* 3.8 25.1 - - + -
225C PRO* 4.0 23.1 - - + -
227C THR* 5.0 1.3 - - - -
229C MET* 3.3 40.4 - - + +
230C LYS* 3.6 28.3 - - + -
233C PHE* 2.9 66.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU 4.4 11.0 - - - +
48A LEU* 5.0 6.3 - - + -
49A TRP* 4.3 31.4 - - + +
54C TRP* 3.1 40.6 - - + -
203C TRP* 2.7 26.2 + - + +
204C GLY* 3.7 8.5 - - - +
206C TRP* 1.3 71.6 - - - +
208C GLU* 1.3 66.4 + - + +
210C CYS* 3.0 23.0 + - + +
211C ASN* 3.5 9.3 + - - +
236C HIS* 3.8 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 4.1 6.8 - - - +
47A GLU* 4.1 16.7 - - - +
173C TYR* 4.7 2.2 - - + +
177C VAL* 4.6 11.1 - - + +
180C ARG* 2.7 45.5 + - - +
192C PHE* 3.3 41.1 - - + -
204C GLY 3.0 19.4 + - - +
205C ALA 4.0 0.2 - - - +
206C TRP 3.3 0.6 - - - -
207C LEU* 1.3 75.5 - - + +
209C LEU* 1.3 61.3 + - - +
211C ASN* 3.1 36.7 + - - +
212C LEU* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ILE* 4.2 18.6 - - + +
192C PHE* 3.7 32.2 - - + +
193C VAL* 4.2 18.4 - - + +
196C THR* 3.8 28.7 - - + -
205C ALA 3.4 5.7 + - - +
206C TRP* 3.1 17.8 + - + +
207C LEU 3.1 0.4 - - - -
208C GLU* 1.3 78.3 - - - +
210C CYS* 1.3 58.9 + - - +
212C LEU* 3.2 4.8 + - - +
213C ILE* 3.1 38.6 + - + +
222C LEU* 4.7 2.0 - - + -
224C LEU* 4.6 11.9 - - + -
233C PHE* 3.7 19.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
203C TRP* 4.5 2.9 - - - -
206C TRP 3.4 16.2 - - - -
207C LEU* 3.0 16.9 + - + +
209C LEU* 1.3 77.1 - - - +
211C ASN* 1.3 62.7 + - - +
213C ILE* 3.8 12.1 + - - +
233C PHE* 3.7 9.8 - - - -
236C HIS* 3.3 29.6 - - + +
237C ILE* 3.4 31.0 - - + +
240C GLU* 3.0 33.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 5.4 4.4 + - - -
47A GLU 5.5 0.8 + - - -
49A TRP* 4.3 27.2 - - - +
55A ALA* 6.1 0.9 - - - +
180C ARG* 5.4 4.9 - - - +
207C LEU* 3.5 8.0 + - - +
208C GLU* 3.1 29.8 + - - +
210C CYS* 1.3 76.9 - - - +
212C LEU* 1.3 69.5 + - + +
213C ILE 4.2 3.5 - - - +
214C THR* 4.9 4.7 - - - +
240C GLU* 3.3 21.3 - - - +
363C ARG* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ARG* 3.8 28.3 - - + -
185C VAL* 3.8 41.5 - - + +
188C ALA* 3.6 31.4 - - + -
189C ILE* 3.7 29.2 - - + +
192C PHE* 4.2 14.6 - - + -
208C GLU 3.3 12.9 + - - +
209C LEU* 3.2 5.1 + - - +
211C ASN* 1.3 81.3 - - + +
213C ILE* 1.3 63.0 + - - +
214C THR* 3.4 13.0 + - - +
218C MET* 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ILE* 4.0 24.0 - - + -
209C LEU* 3.1 24.6 + - + +
210C CYS* 3.8 12.7 + - - +
211C ASN 3.6 2.3 - - - +
212C LEU* 1.3 74.2 - - - +
214C THR* 1.3 62.7 + - - +
215C ASP 3.4 26.7 - - - +
218C MET* 4.1 13.5 - - + -
219C LEU* 4.2 15.0 - - + +
222C LEU* 3.7 29.4 - - + -
233C PHE* 4.7 12.1 - - + -
237C ILE* 4.7 16.2 - - + +
240C GLU* 5.0 2.4 - - - +
241C LEU* 4.6 7.0 - - + +
----------------------------------------------------------
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