Contacts of the helix formed by residues 178 - 189 (chain G) in PDB entry 4GTU
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 178 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174G LEU 4.1 0.4 - - - -
175G ASP 4.4 6.7 - - - +
176G ALA 3.3 12.1 - - - +
177G PHE* 1.3 82.8 - - - +
179G ASN* 1.3 62.4 + - - +
181G LYS* 3.1 14.9 + - + +
182G ASP* 3.0 30.0 + - - +
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Residues in contact with ASN 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G SER* 3.3 20.2 + - - +
141G LEU* 3.4 25.2 - - + +
142G GLY* 2.8 48.3 + - - +
144G ARG 4.9 1.0 - - - +
177G PHE 2.9 1.0 + - - -
178G PRO* 1.3 79.9 - - - +
180G LEU* 1.3 61.9 + - - +
182G ASP* 3.7 5.0 + - - +
183G PHE 3.3 15.1 + - - -
186G ARG* 4.5 7.4 + - - -
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Residues in contact with LEU 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G MET* 3.9 24.9 - - + +
137G PHE* 4.1 12.1 - - + -
138G SER* 3.8 24.7 - - - +
141G LEU* 4.6 5.4 - - + -
147G PHE* 4.3 16.2 - - + -
163G LEU* 4.5 12.1 - - + -
174G LEU* 4.1 27.1 - - + -
177G PHE* 2.8 38.8 + - + +
179G ASN* 1.3 73.7 - - - +
181G LYS* 1.3 66.8 + - - +
183G PHE* 3.2 13.2 + - - +
184G ILE* 3.0 23.0 + - - +
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Residues in contact with LYS 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ASP* 3.6 32.6 + - - -
185F SER* 4.9 8.1 - - - -
167G ARG* 6.1 5.0 - - - +
174G LEU* 3.8 35.2 - - + +
175G ASP* 4.6 15.5 - - - +
177G PHE 3.4 1.2 + - - -
178G PRO* 3.1 16.7 + - + +
180G LEU* 1.3 79.8 - - - +
182G ASP* 1.3 63.7 + - - +
184G ILE* 3.0 39.5 + - + +
185G SER* 3.3 11.7 + - - -
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Residues in contact with ASP 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F SER* 3.4 20.5 + - - +
188F GLU* 4.5 23.7 - - - +
189F GLY* 5.2 0.5 - - - -
178G PRO* 3.0 18.0 + - - +
179G ASN* 4.2 4.5 - - - +
181G LYS* 1.3 75.6 - - - +
183G PHE* 1.3 55.4 + - - +
185G SER* 3.1 8.5 + - - -
186G ARG* 2.7 51.4 + - - +
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Residues in contact with PHE 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G LEU* 4.1 11.9 - - + -
145G PRO 3.9 16.6 - - - -
146G TRP* 3.7 17.3 - + - -
147G PHE* 3.8 29.2 - + - -
156G ASP* 3.5 41.5 - - + -
159G ALA* 4.1 0.7 - - + -
160G TYR* 3.8 30.1 - - + -
163G LEU* 3.7 19.5 - - + -
179G ASN 3.3 14.1 + - - +
180G LEU* 3.2 11.4 + - - +
181G LYS 3.2 0.4 - - - -
182G ASP* 1.3 76.0 - - - +
184G ILE* 1.3 55.6 + - + +
186G ARG* 3.1 11.7 + - - +
187G PHE* 2.8 39.6 + + - +
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Residues in contact with ILE 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G TYR* 4.2 20.9 - - + -
163G LEU* 3.3 31.2 - - + -
167G ARG* 4.3 21.8 - - - +
174G LEU* 3.7 20.2 - - + -
180G LEU 3.0 25.6 + - - +
181G LYS* 3.0 23.0 + - + +
183G PHE* 1.3 81.9 - - + +
185G SER* 1.3 64.3 + - - +
187G PHE* 3.7 0.5 + - - +
188G GLU* 3.1 52.6 + - - +
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Residues in contact with SER 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F ASP* 5.3 2.1 + - - -
185F SER* 3.0 48.7 + - - -
186F ARG* 4.1 9.7 + - - +
189F GLY* 3.4 12.5 - - - -
181G LYS* 3.3 9.9 + - - -
182G ASP* 3.1 9.5 + - - -
184G ILE* 1.3 81.3 - - - +
186G ARG* 1.3 56.8 + - - +
188G GLU* 3.7 6.1 + - - +
189G GLY* 3.1 22.0 + - - -
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Residues in contact with ARG 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F GLU 5.6 3.8 + - - -
189F GLY* 3.6 22.8 - - - +
194F SER* 4.5 16.3 + - - +
141G LEU* 4.6 1.4 - - - +
144G ARG 4.5 2.0 + - - -
145G PRO* 3.0 49.7 + - - +
146G TRP* 3.9 22.7 - - + -
179G ASN* 4.5 14.1 + - - -
182G ASP* 2.7 32.1 + - - +
183G PHE* 3.1 24.2 + - - +
185G SER* 1.3 74.8 - - - +
187G PHE* 1.3 65.4 + - - +
189G GLY* 3.1 10.0 + - - -
190G LEU* 3.7 11.5 + - + +
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Residues in contact with PHE 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G LEU* 3.7 13.7 - - + -
146G TRP* 4.3 23.7 - + + -
152G ILE* 5.1 2.7 - - + -
156G ASP* 3.4 16.4 - - + -
157G PHE* 3.4 60.8 - + - -
160G TYR* 3.4 42.0 - + + -
183G PHE* 2.8 24.0 + + + +
184G ILE 4.2 2.7 - - - +
186G ARG* 1.3 74.7 - - - +
188G GLU* 1.3 61.0 + - - +
189G GLY 3.1 1.1 + - - -
190G LEU* 3.7 5.3 + - + +
193G ILE* 3.4 40.0 - - + +
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Residues in contact with GLU 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160G TYR* 3.2 28.6 + - + +
167G ARG* 3.2 18.6 + - - -
184G ILE* 3.1 40.6 + - - +
185G SER* 3.8 5.5 - - - +
187G PHE* 1.3 75.8 - - - +
189G GLY* 1.3 57.3 + - - +
190G LEU 3.5 1.3 - - - -
193G ILE* 4.2 8.3 - - - -
194G SER* 3.4 26.2 - - - -
197G MET* 3.9 15.3 - - + +
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Residues in contact with GLY 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F GLY 3.5 22.4 - - - -
190F LEU* 4.0 15.4 - - - +
191F GLU* 3.4 19.3 + - - +
185G SER 3.1 11.0 + - - -
186G ARG 3.1 0.6 + - - -
187G PHE 3.1 1.4 - - - -
188G GLU* 1.3 78.8 - - - +
190G LEU* 1.3 65.3 + - - +
191G GLU* 3.2 4.7 + - - -
194G SER* 4.7 3.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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