Contacts of the helix formed by residues 184 - 200 (chain G) in PDB entry 1O1F
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 GLY 184 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ASN* 4.8 6.3 - - - -
180G GLU 4.4 0.2 + - - -
181G SER 4.6 3.0 + - - -
182G GLY 3.1 6.3 + - - -
183G ALA* 1.3 80.2 - - - +
185G LYS* 1.3 65.0 + - - +
186G THR* 5.8 0.2 - - - -
187G VAL* 3.3 28.5 - - - +
188G ASN* 3.1 19.0 + - - -
240G ASN* 4.9 10.5 - - - -
674G CYS* 4.8 0.4 - - - -
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Residues in contact with LYS 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ILE* 3.6 21.1 - - + +
178G THR* 4.3 2.5 - - - -
179G GLY* 2.9 45.5 - - - +
180G GLU 3.9 10.7 + - - +
181G SER* 4.8 9.2 + - - +
184G GLY* 1.3 76.5 - - - +
186G THR* 1.3 55.3 + - - +
187G VAL 3.0 1.8 - - - -
188G ASN* 2.6 29.9 + - - +
189G THR* 2.5 23.9 + - - +
243G SER* 5.8 0.6 + - - -
244G SER* 4.6 19.2 + - - +
463G ASP* 4.4 16.5 + - - +
464G ILE 3.8 18.2 + - - +
465G ALA* 4.6 8.6 - - - +
674G CYS* 4.2 6.5 - - + -
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Residues in contact with THR 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G GLY* 3.7 0.4 - - - -
185G LYS* 1.3 76.0 + - - +
187G VAL* 1.3 57.9 - - - +
189G THR* 3.1 6.9 + - - -
190G MLY 2.6 46.8 + - + +
230G GLU* 3.6 23.6 - - + +
234G ASN* 4.8 4.7 - - - +
240G ASN* 5.5 2.3 + - - -
242G ASN* 4.5 9.3 + - - -
244G SER* 3.7 28.6 + - - +
248G MLY 3.3 31.9 - - - -
463G ASP* 3.8 5.2 + - - +
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Residues in contact with VAL 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TYR* 5.5 7.0 - - + +
184G GLY* 3.3 32.5 - - - +
186G THR* 1.3 77.8 - - - +
188G ASN* 1.3 62.5 + - - +
190G MLY 3.7 15.3 - - - +
191G ARG* 3.0 47.9 + - - +
240G ASN* 5.5 5.2 - - - +
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Residues in contact with ASN 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G TYR* 4.4 1.0 + - - -
125G THR* 4.2 13.9 - - - +
135G TYR* 3.9 17.3 + - - -
155G ILE* 3.3 31.3 - - + +
177G ILE* 4.8 7.6 - - + -
184G GLY 3.1 14.8 + - - -
185G LYS* 2.6 11.8 + - - +
187G VAL* 1.3 74.0 - - - +
189G THR* 1.3 55.4 + - - +
191G ARG* 2.8 7.6 + - - +
192G VAL* 2.6 41.2 + - + +
674G CYS* 2.9 35.5 - - - +
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Residues in contact with THR 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ILE* 4.4 9.2 - - + +
185G LYS* 2.5 27.0 + - - +
186G THR* 3.3 6.1 - - - -
188G ASN* 1.3 71.9 - - - +
190G MLY 1.3 64.9 + - - +
192G VAL* 3.0 10.2 + - - +
193G ILE* 2.9 30.4 + - + +
248G MLY 4.8 16.2 - - - -
250G ILE* 5.0 2.2 - - + -
461G VAL* 3.7 26.7 - - + +
463G ASP* 3.1 35.8 + - + +
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Residues in contact with MLY 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G THR* 2.6 39.2 + - + +
187G VAL* 3.7 15.9 - - - +
189G THR* 1.3 72.5 - - - +
191G ARG* 1.3 99.5 + - - +
193G ILE* 2.8 26.3 + - - +
194G GLN* 2.9 21.2 + - - +
226G ASN* 4.1 29.8 - - + +
227G PRO* 6.1 1.6 - - - -
230G GLU* 2.8 44.9 - - - +
242G ASN* 4.0 8.7 - - - -
248G MLY 4.8 6.0 - - - -
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Residues in contact with ARG 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TYR* 3.1 49.1 - - + -
155G ILE* 5.8 5.2 - - + -
156G PHE* 4.4 14.7 - - + -
187G VAL* 3.0 36.0 + - - +
188G ASN* 2.8 6.3 + - - +
190G MLY 1.3 114.9 + - - +
192G VAL* 1.3 60.8 + - - +
194G GLN* 3.6 29.0 + - + +
195G TYR* 3.3 17.8 + - - +
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Residues in contact with VAL 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155G ILE* 4.4 26.9 - - + -
158G ILE* 6.5 0.9 - - + -
159G SER* 4.0 14.4 - - - -
175G ILE* 4.7 11.9 - - + -
177G ILE* 4.4 13.9 - - + -
188G ASN 2.6 25.9 + - - +
189G THR* 3.3 9.6 - - - +
191G ARG* 1.3 74.0 - - - +
193G ILE* 1.3 62.5 + - + +
195G TYR* 2.8 28.3 - - - +
196G PHE* 3.1 30.8 + - + -
461G VAL* 4.8 10.1 - - + -
672G VAL* 6.4 1.1 - - + -
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Residues in contact with ILE 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G THR* 3.0 19.5 - - + +
190G MLY 2.8 13.1 + - - +
192G VAL* 1.3 77.9 - - + +
194G GLN* 1.3 64.5 + - - +
196G PHE* 3.0 17.7 + - - +
197G ALA* 3.0 12.2 + - + +
222G ILE* 4.0 28.0 - - + +
223G ILE* 5.3 6.5 - - + -
226G ASN* 5.6 8.1 - - - +
248G MLY 5.6 2.9 - - - -
250G ILE* 3.1 38.4 - - + -
252G ILE* 3.9 24.2 - - + -
461G VAL* 4.7 7.9 - - + -
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Residues in contact with GLN 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G MLY 2.9 16.8 + - - +
191G ARG* 3.8 37.7 + - + +
193G ILE* 1.3 73.0 - - - +
195G TYR* 1.3 55.1 + - - +
197G ALA* 2.9 5.0 + - - +
198G THR* 2.5 43.6 + - + +
223G ILE* 3.2 39.3 - - + +
226G ASN* 6.0 0.2 + - - -
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Residues in contact with TYR 195 (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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140G VAL* 3.4 37.0 + - + -
143G TYR* 3.9 5.7 + - - +
144G ARG* 4.0 0.7 - - - -
156G PHE* 2.9 40.4 - + + -
159G SER* 2.8 33.7 - - - +
160G ASP* 2.4 32.4 + - + +
191G ARG 3.3 10.5 + - - +
192G VAL* 2.8 17.0 + - - +
194G GLN* 1.3 78.6 - - - +
196G PHE* 1.3 62.3 + + - -
198G THR* 3.0 13.9 + - - -
199G ILE* 2.9 55.2 + - + +
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Residues in contact with PHE 196 (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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159G SER* 3.1 33.4 - - - -
162G ALA* 4.3 4.9 - - + -
163G TYR* 4.0 14.8 - + + -
175G ILE* 4.2 5.6 - - + -
192G VAL* 3.1 37.7 + - + -
193G ILE* 3.0 8.0 + - - +
195G TYR* 1.3 82.5 - + + +
197G ALA* 1.3 66.5 + - - +
198G THR 3.2 0.2 + - - -
199G ILE* 3.6 12.9 + - + -
200G ALA* 3.3 23.4 + - - +
252G ILE* 4.6 17.9 - - + -
254G PHE* 3.6 28.4 - + + -
260G LEU* 4.7 2.9 - - + +
459G ILE* 3.7 41.7 - - + -
461G VAL* 4.9 1.6 - - + -
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Residues in contact with ALA 197 (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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193G ILE 3.0 10.2 + - - +
194G GLN* 2.9 11.7 + - - +
196G PHE* 1.3 79.4 - - - +
198G THR* 1.3 64.0 + - + +
201G ALA* 3.0 28.2 + - - +
219G GLU* 4.3 24.7 - - + +
222G ILE* 5.2 5.8 - - + -
223G ILE* 4.9 6.5 - - + -
260G LEU* 3.9 19.1 - - + -
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Residues in contact with THR 198 (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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140G VAL* 5.1 12.2 - - + +
194G GLN* 2.5 33.6 + - + +
195G TYR* 3.0 11.6 + - - -
197G ALA* 1.3 76.5 - - + +
199G ILE* 1.3 60.1 + - - +
200G ALA 2.8 7.3 + - - -
201G ALA* 3.7 8.6 + - - +
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Residues in contact with ILE 199 (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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140G VAL* 4.8 8.5 - - + +
144G ARG* 4.5 17.4 + - + +
160G ASP* 4.1 6.5 - - - +
163G TYR* 4.3 22.7 + - + -
195G TYR* 2.9 70.1 + - + +
196G PHE* 4.1 18.8 - - + +
198G THR* 1.3 75.1 - - - +
200G ALA* 1.3 62.9 + - + +
259G LYS* 4.5 4.9 + - - -
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Residues in contact with ALA 200 (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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163G TYR* 3.1 35.4 - - + +
196G PHE 3.3 11.5 + - - +
197G ALA 3.8 2.9 - - - -
198G THR 2.8 8.9 + - - -
199G ILE* 1.3 80.0 - - + +
201G ALA* 1.3 60.6 + - - +
254G PHE* 4.3 6.1 - - + -
258G GLY 3.6 7.0 - - - +
259G LYS* 3.7 12.8 - - - +
260G LEU* 3.1 28.6 + - - +
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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
------------------------------------------------------------
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