Contacts of the helix formed by residues 179 - 190 (chain G) in PDB entry 1GUL
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 PRO 179 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 4.3 37.7 - - + +
137G GLU* 3.2 11.9 - - - +
176G SER 4.2 2.9 - - - +
177G ALA* 3.0 13.0 - - - +
178G PHE* 1.3 91.0 - - - +
180G PHE* 1.3 71.8 + - + +
182G GLN* 3.2 15.5 + - - +
183G GLU* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G GLU* 3.0 29.0 + - + +
140G LEU* 4.2 22.3 - - + +
141G ARG* 3.5 58.8 - - + -
144G GLY* 5.6 5.4 - - - -
179G PRO* 1.3 86.9 - - + +
181G LEU* 1.3 58.7 + - - +
183G GLU* 3.1 12.6 + - - +
184G TYR* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G PHE* 3.5 55.6 - - + +
136G PHE* 3.9 16.8 - - + -
137G GLU* 2.7 19.6 + - - +
140G LEU* 3.8 18.8 - - + -
160G LEU* 4.6 4.0 - - + -
164G ILE* 4.4 10.8 - - + -
175G LEU* 3.7 13.7 - - + -
178G PHE* 3.0 18.8 + - + +
180G PHE* 1.3 72.6 - - - +
182G GLN* 1.3 63.5 + - - +
184G TYR* 3.5 13.9 - - + +
185G THR* 2.7 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E TYR* 4.4 8.9 + - - -
175G LEU* 2.9 46.1 + - + +
176G SER* 3.2 18.8 + - - +
178G PHE 2.6 19.2 + - - +
179G PRO* 3.6 14.8 - - - +
180G PHE 3.1 0.4 - - - -
181G LEU* 1.3 75.8 - - - +
183G GLU* 1.3 63.9 + - - +
185G THR* 3.4 2.0 - - - -
186G VAL* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 183 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G PRO 3.0 10.9 + - - +
180G PHE* 3.7 13.0 - - - +
182G GLN* 1.3 79.0 - - - +
184G TYR* 1.3 65.3 + - - +
186G VAL* 3.0 10.7 + - + +
187G LYS* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 184 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 3.7 32.1 - - + -
146G SER* 3.3 28.8 - - - +
148G LEU* 3.5 15.9 - - + +
157G ASP* 2.6 45.1 + - - -
160G LEU* 4.0 21.5 - - + +
161G LEU* 5.2 1.1 - - - -
164G ILE* 4.9 3.1 - - + -
180G PHE 2.8 17.6 + - - +
181G LEU* 3.5 16.4 - - + +
183G GLU* 1.3 76.3 - - - +
185G THR* 1.3 62.8 + - - +
187G LYS* 3.3 13.9 + - - +
188G LEU* 2.8 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G LEU* 4.0 22.2 - - + +
164G ILE* 3.9 21.0 - - + +
165G LEU* 4.1 17.5 - - + -
168G GLU* 5.2 3.4 - - - +
175G LEU* 3.8 12.1 - - + +
181G LEU 2.7 22.1 + - - -
182G GLN* 3.4 7.0 - - - +
184G TYR* 1.3 81.4 - - - +
186G VAL* 1.3 62.4 + - + +
188G LEU* 3.8 1.4 - - - +
189G SER* 2.4 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G GLN* 3.1 17.2 + - + +
183G GLU* 3.0 13.6 + - + +
185G THR* 1.3 85.6 - - + +
187G LYS* 1.3 67.4 + - + +
189G SER* 3.1 11.2 + - - -
190G ASN* 2.8 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 4.9 12.8 - - + -
200B PRO* 4.5 24.9 - - + +
145G GLN 4.6 3.0 + - - -
146G SER* 3.3 41.0 + - - +
183G GLU* 2.9 40.7 + - + +
184G TYR* 3.6 16.6 - - - +
186G VAL* 1.3 82.8 - - + +
188G LEU* 1.3 64.5 + - + +
190G ASN* 2.8 20.3 + - - +
191G ILE* 3.4 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 188 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PRO* 6.0 0.9 - - + -
146G SER* 4.2 10.3 - - - +
147G PHE* 4.1 13.7 - - + -
153G LEU* 4.0 17.0 - - + -
157G ASP* 3.9 18.6 - - + +
161G LEU* 4.0 22.9 - - + -
184G TYR* 2.8 59.4 + - + +
185G THR 3.8 3.8 - - - +
187G LYS* 1.3 75.5 - - + +
189G SER* 1.3 64.3 + - - +
190G ASN 2.9 0.9 + - - -
191G ILE* 3.0 39.9 + - + +
194G ILE* 3.5 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G LEU* 4.0 12.2 - - - +
165G LEU* 5.1 3.3 - - - +
185G THR* 2.4 32.5 + - - +
186G VAL* 3.7 6.3 - - - -
187G LYS 3.0 0.4 - - - -
188G LEU* 1.3 78.4 - - - +
190G ASN* 1.3 63.3 + - - +
191G ILE 3.3 0.4 - - - -
194G ILE* 3.9 9.6 - - - -
195G LYS* 3.5 23.7 + - - +
198G LEU* 3.7 21.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 190 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLU* 6.1 0.7 - - - +
200B PRO 4.5 6.3 - - - +
186G VAL* 2.8 37.8 + - - +
187G LYS* 2.8 12.0 + - - +
189G SER* 1.3 83.4 - - - +
191G ILE* 1.3 65.1 + - - +
192G PRO* 3.2 8.8 - - - +
195G LYS* 4.1 27.9 - - + +
----------------------------------------------------------
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