Contacts of the helix formed by residues 203 - 215 (chain A) in PDB entry 1GQT
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 GLU 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASN* 2.9 15.1 + - - +
202A ASP* 1.3 75.5 - - - +
204A ASP* 1.3 66.3 + - - +
206A ALA* 3.4 7.2 + - + +
207A LYS* 3.2 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.3 6.0 - - + +
198A ARG 3.2 22.7 - - - +
199A VAL* 3.7 5.7 - - + +
200A GLU* 2.7 41.5 + - - +
201A ASN* 2.6 29.3 + - - +
203A GLU* 1.3 71.8 - - - +
205A ALA* 1.3 68.6 + - - +
207A LYS* 3.0 12.2 + - - +
208A ALA* 2.9 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 4.0 17.2 - - + +
201A ASN 2.8 11.2 + - - +
202A ASP* 3.2 13.2 + - - +
204A ASP* 1.3 77.3 - - - +
206A ALA* 1.3 58.8 + - - +
208A ALA 3.2 0.7 + - - -
209A ALA* 3.0 29.1 + - - +
222A ILE* 3.6 13.5 - - + +
224A LEU* 4.7 6.7 - - + -
230A TRP* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP 3.0 12.7 + - - +
203A GLU* 3.8 7.2 - - - +
204A ASP 3.1 0.2 - - - -
205A ALA* 1.3 78.5 - - - +
207A LYS* 1.3 56.9 + - + +
209A ALA* 3.6 3.4 - - - +
210A GLN* 3.1 26.0 + - - +
230A TRP* 3.5 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.3 21.2 - - + +
203A GLU* 3.2 43.4 + - + +
204A ASP* 3.0 14.4 + - - +
206A ALA* 1.3 75.9 - - + +
208A ALA* 1.3 65.8 + - - +
210A GLN* 3.1 15.3 + - - +
211A VAL* 3.2 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 4.2 4.0 - - + -
195A THR* 3.4 38.6 - - + +
197A ILE* 4.4 7.0 - - + +
199A VAL* 4.0 15.9 - - + -
204A ASP 2.9 17.4 + - - +
205A ALA 3.9 3.4 - - - +
207A LYS* 1.3 72.4 - - - +
209A ALA* 1.3 63.3 + - - +
211A VAL 3.3 2.8 + - - +
212A LEU* 3.1 19.1 + - - +
222A ILE* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A ALA 3.0 17.1 + - - +
206A ALA* 3.6 9.0 - - - +
208A ALA* 1.3 77.1 - - - +
210A GLN* 1.3 57.1 + - - +
212A LEU* 3.0 5.3 + - - +
213A HIS* 2.7 35.4 + - + +
220A VAL* 4.1 27.2 - - + +
222A ILE* 4.2 1.5 - - + +
230A TRP* 4.3 4.7 - - + +
232A SER* 4.1 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 3.1 12.7 + - - +
207A LYS* 3.1 10.7 + - + +
209A ALA* 1.3 76.5 - - - +
211A VAL* 1.3 65.3 + - + +
213A HIS* 2.9 24.1 + - - +
214A GLU* 2.7 49.9 + - - +
234A ASN 5.4 0.2 - - - -
235A GLY* 4.2 19.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU 4.8 3.6 - - - +
195A THR* 3.9 30.5 - - + +
197A ILE* 4.5 16.4 - - + -
207A LYS 3.2 10.6 + - - +
208A ALA 3.3 7.4 + - - +
210A GLN* 1.3 77.4 - - + +
212A LEU* 1.3 62.7 + - + +
214A GLU* 3.4 12.6 + - - +
215A LYS* 3.2 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 4.4 13.7 - - + -
184A ILE* 4.1 22.0 - - + -
186A PRO* 4.2 17.0 - - + -
191A ALA* 5.3 3.8 - - + -
194A LEU* 4.3 25.6 - - + +
195A THR* 3.8 18.6 - - + -
208A ALA 3.1 16.2 + - - +
209A ALA 3.0 8.2 + - - +
211A VAL* 1.3 77.1 - - + +
213A HIS* 1.3 65.4 + - - +
215A LYS* 3.1 15.3 + - + +
217A ILE* 3.2 35.9 + - + +
220A VAL* 3.9 20.0 - - + -
222A ILE* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 2.7 32.1 + - + +
210A GLN* 2.9 18.1 + - - +
212A LEU* 1.3 73.0 - - - +
214A GLU* 1.3 58.5 + - - +
216A GLY* 3.1 18.5 + - - -
217A ILE 2.8 27.6 + - - +
218A ARG 3.0 8.5 + - - -
220A VAL* 3.7 9.3 - - + +
232A SER* 2.6 50.3 + - - -
234A ASN* 3.0 37.4 + - - +
235A GLY* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 2.7 46.1 + - - +
211A VAL* 4.0 13.0 - - - +
212A LEU 3.2 0.2 - - - -
213A HIS* 1.3 75.7 - - - +
215A LYS* 1.3 60.3 + - - +
216A GLY* 3.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 2.7 40.8 + - + +
178A LEU* 4.1 30.7 - - + -
179A ALA* 3.4 27.5 + - - +
194A LEU 5.2 6.7 - - - -
211A VAL* 3.2 28.2 + - + +
212A LEU* 3.1 14.5 + - + +
214A GLU* 1.3 79.0 - - - +
216A GLY* 1.3 56.9 + - - +
217A ILE* 3.6 2.9 - - + -
----------------------------------------------------------
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