Contacts of the helix formed by residues 185 - 202 (chain A) in PDB entry 1GAJ
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 ALA 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLY 4.1 1.4 + - - -
184A VAL* 1.3 72.6 - - - +
186A PRO* 1.4 65.4 - - + +
187A GLY 3.3 2.2 - - - +
188A LEU* 2.8 36.7 + - + +
189A ALA 3.0 7.7 + - - -
212A ARG* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL 3.5 0.6 - - - -
185A ALA* 1.4 84.7 - - + -
187A GLY* 1.3 54.3 + - - +
189A ALA* 3.3 7.8 - - + +
190A HIS* 2.7 47.4 + - + +
212A ARG* 3.8 18.8 - - - +
215A ILE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ALA* 2.9 4.2 + - - +
186A PRO* 1.3 78.9 - - - +
188A LEU* 1.3 62.1 + - - +
190A HIS* 3.7 6.3 + - - +
191A ASP* 3.3 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 3.7 24.7 - - - +
157A GLY* 3.7 24.9 - - - +
158A GLN* 4.2 11.4 - - + +
161A LEU* 5.8 6.3 - - + -
184A VAL* 3.6 8.3 - - + -
185A ALA* 2.8 18.0 + - + +
187A GLY* 1.3 71.2 - - - -
189A ALA* 1.3 58.6 + - - +
191A ASP* 3.1 20.3 + - + +
192A ILE* 2.8 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 3.8 20.9 - - + -
184A VAL* 3.4 17.6 - - + +
185A ALA 3.0 11.4 + - - +
186A PRO* 3.3 10.1 - - + +
188A LEU* 1.3 73.8 - - - +
190A HIS* 1.3 65.9 + - - +
192A ILE* 3.1 5.0 + - - +
193A PHE* 3.0 27.7 + - - -
215A ILE* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 2.7 38.9 + - + +
187A GLY* 4.0 5.6 - - - +
189A ALA* 1.3 76.3 - - - +
191A ASP* 1.3 53.0 + - - +
193A PHE 3.4 0.3 + - - -
194A ASN* 2.7 35.1 + - - +
214A ASP 5.0 2.6 + - - -
215A ILE* 3.5 39.5 - - + +
218A ASN* 5.7 4.9 - - - -
219A TYR* 3.0 35.9 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 5.5 2.4 - - - +
187A GLY 3.3 12.9 + - - +
188A LEU* 3.1 28.0 + - + +
190A HIS* 1.3 77.7 - - - +
192A ILE* 1.3 63.8 + - - +
194A ASN* 3.2 16.7 + - - +
195A HIS* 3.0 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A GLY* 3.5 32.3 - - - +
160A LYS* 3.7 18.8 - - + -
161A LEU* 4.2 15.7 - - + +
164A ILE* 3.8 25.0 - - + +
180A PRO* 4.3 8.5 - - + +
181A ILE* 3.9 25.8 - - + -
184A VAL* 4.2 4.7 - - + -
188A LEU* 2.8 21.2 + - + +
189A ALA 3.4 7.4 - - - +
191A ASP* 1.3 74.9 - - - +
193A PHE* 1.3 62.6 + - + +
195A HIS* 2.8 28.9 + - - +
196A VAL* 3.1 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 5.2 3.6 - - + -
180A PRO* 3.8 21.3 - - + -
181A ILE* 3.4 44.2 - - + -
189A ALA 3.0 17.4 + - - +
190A HIS 3.9 1.3 - - - +
192A ILE* 1.3 76.9 - - + +
194A ASN* 1.3 66.2 + - - +
196A VAL* 3.0 28.3 + - + +
197A LEU* 3.0 18.2 + - - +
208A ILE* 3.9 24.5 - - + -
210A GLU* 4.9 1.3 - - - -
215A ILE* 5.1 1.6 - - + -
216A VAL* 3.5 28.0 - - + -
219A TYR* 3.7 45.9 - + + -
220A ILE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS 2.7 21.1 + - - +
191A ASP* 3.2 21.6 + - - +
193A PHE* 1.3 75.5 - - - +
195A HIS* 1.3 59.9 + - - +
197A LEU* 3.2 13.6 + - - +
198A GLU* 3.0 40.1 + - - +
219A TYR* 4.5 7.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.8 17.3 + + + -
141A LEU* 3.4 46.9 + - + -
142A LYS* 4.5 13.0 - - + +
161A LEU* 4.0 23.6 - - + +
164A ILE* 6.0 2.7 - - + -
191A ASP* 3.0 36.0 + - - -
192A ILE 2.8 9.5 + - - +
194A ASN* 1.3 82.3 - - - +
196A VAL* 1.3 56.0 + - + +
198A GLU* 3.0 32.8 + - - +
199A LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.1 20.0 - - + -
164A ILE* 5.2 5.6 - - + -
177A MET* 4.3 21.5 - - + -
192A ILE* 3.1 17.4 + - + +
193A PHE* 3.0 26.1 + - + +
195A HIS* 1.3 76.1 - - - +
197A LEU* 1.3 53.8 + - + +
199A LEU* 2.9 11.0 + - + +
200A LYS* 2.6 31.0 + - - +
206A PHE* 3.6 37.8 - - + -
208A ILE* 5.0 2.0 - - + -
219A TYR* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.9 4.0 - - + -
193A PHE 3.0 7.5 + - - +
194A ASN* 3.5 13.2 - - - +
196A VAL* 1.3 76.1 - - + +
198A GLU* 1.3 67.8 + - - +
200A LYS* 3.3 24.8 - - + +
201A ALA* 2.8 24.8 + - - +
218A ASN 5.7 0.9 - - - +
219A TYR* 3.2 56.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.1 37.5 - - + +
142A LYS* 5.3 8.0 - - - -
194A ASN* 3.0 22.1 + - - +
195A HIS* 3.0 43.0 + - - +
197A LEU* 1.3 76.6 - - - +
199A LEU* 1.3 55.5 + - - +
201A ALA* 2.9 24.7 - - - +
202A LYS* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.9 23.6 - - + -
141A LEU* 5.5 0.7 - - + -
164A ILE* 4.7 10.8 - - + -
168A LEU* 3.9 33.4 - - + -
175A ILE* 4.9 0.9 - - + -
195A HIS* 2.9 19.4 + - + +
196A VAL* 2.9 8.5 + - + +
198A GLU* 1.3 74.7 - - - +
200A LYS* 1.3 65.1 + - - +
201A ALA 3.0 1.3 - - - -
202A LYS* 2.9 28.6 + - + +
203A GLY 3.3 0.3 + - - -
204A ILE* 3.1 40.6 + - + +
206A PHE* 3.9 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 2.8 30.7 - - - +
34A ASP* 4.3 2.4 + - - +
35A VAL* 3.9 20.0 - - + -
196A VAL 2.6 15.4 + - - +
197A LEU* 3.3 25.7 - - + +
199A LEU* 1.3 70.2 - - - +
201A ALA* 1.3 55.9 + - - +
203A GLY* 2.7 27.9 + - - -
204A ILE 3.5 15.1 + - - +
206A PHE* 4.2 0.4 - - - -
219A TYR 5.4 0.8 + - - -
221A ASP* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 2.8 11.9 + - - +
198A GLU* 2.9 20.4 - - - +
200A LYS* 1.3 78.8 - - - +
202A LYS* 1.3 59.7 + - + +
203A GLY 3.1 1.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.0 43.8 - - - -
198A GLU* 3.7 11.2 - - - +
199A LEU* 2.9 22.6 + - + +
201A ALA* 1.3 78.1 - - + +
203A GLY* 1.3 58.5 + - - +
204A ILE* 3.6 7.6 - - + +
----------------------------------------------------------
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