Contacts of the helix formed by residues 181 - 196 (chain G) in PDB entry 1F9E
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 181 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G ARG 3.0 0.4 + - - -
180G ASN* 1.3 74.3 - - - +
182G THR* 1.3 54.4 + - - +
183G HIS* 2.9 18.8 + - - -
184G LEU* 2.6 41.3 + - - +
185G ASP* 3.5 2.0 + - - -
341H ARG* 4.8 3.6 - - - -
342H ASN 4.6 3.8 - - - -
343H PRO* 3.8 17.7 + - - -
346H GLY* 4.2 7.3 - - - -
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Residues in contact with THR 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN* 3.2 33.7 - - - +
170G ASN 3.6 4.5 + - - +
171G HIS* 4.2 4.4 - - - +
179G ARG* 2.5 58.0 + - - +
180G ASN 4.1 0.2 + - - -
181G GLY* 1.3 73.2 - - - +
183G HIS* 1.3 57.7 + - - +
185G ASP* 2.6 35.8 + - - +
186G ALA 2.8 11.1 + - - -
235G LEU* 3.4 20.9 - - + -
341H ARG* 4.6 2.9 - - - +
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Residues in contact with HIS 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G ASN* 4.2 10.3 - - - +
171G HIS* 3.3 46.4 + + + -
180G ASN* 4.1 1.8 - - - -
181G GLY* 3.2 29.2 + - - -
182G THR* 1.3 74.7 - - - +
184G LEU* 1.3 64.6 + - + +
186G ALA* 3.3 3.5 + - - +
187G GLY* 2.8 27.4 + - - -
204G HIS* 6.4 0.4 - + - -
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Residues in contact with LEU 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G GLY* 2.6 20.2 + - - +
183G HIS* 1.3 83.4 - - + +
185G ASP* 1.3 54.4 + - - +
187G GLY* 3.4 1.4 + - - -
188G ALA* 2.9 30.5 + - - +
343H PRO 3.8 12.1 - - - +
344H ALA 3.5 33.4 - - - +
345H GLU* 3.7 13.0 - - - +
346H GLY 4.0 10.1 - - - +
351H GLN* 3.7 4.1 + - - +
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Residues in contact with ASP 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179G ARG* 4.6 1.6 + - - -
181G GLY 3.5 0.2 + - - -
182G THR* 2.6 22.0 + - - +
184G LEU* 1.3 69.9 - - - +
186G ALA* 1.3 55.7 + - - +
188G ALA* 3.1 2.4 + - - +
189G LEU* 2.7 40.1 + - - +
235G LEU* 3.6 15.7 - - + +
283G GLN* 4.3 2.8 - - - +
346H GLY* 3.6 2.8 - - - -
347H THR* 2.9 54.9 + - - +
350H ILE* 3.3 21.2 - - + +
351H GLN* 3.2 17.4 + - - +
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Residues in contact with ALA 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ILE* 4.1 12.4 - - + +
169G ASN* 3.1 31.2 - - + +
182G THR 2.8 4.2 + - - -
183G HIS* 3.5 8.1 - - - +
185G ASP* 1.3 76.4 - - - +
187G GLY* 1.3 54.5 + - - +
189G LEU* 3.5 6.1 - - - +
190G THR* 2.5 40.4 + - - +
202G PRO* 6.4 0.9 - - + -
204G HIS* 5.1 7.2 - - + -
235G LEU* 3.9 8.6 - - + +
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Residues in contact with GLY 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G HIS 2.8 19.7 + - - -
184G LEU* 3.7 2.0 - - - -
185G ASP 3.1 0.2 - - - -
186G ALA* 1.3 71.8 - - - +
188G ALA* 1.3 61.8 + - - +
190G THR* 3.1 9.0 + - - -
191G THR* 2.9 29.1 + - - -
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Residues in contact with ALA 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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184G LEU 2.9 18.1 + - - +
185G ASP* 3.5 3.1 - - - +
187G GLY* 1.3 74.6 - - - +
189G LEU* 1.3 59.2 + - - +
191G THR* 3.6 5.9 - - - -
192G THR* 2.6 34.5 + - - -
351H GLN* 3.9 21.5 - - - +
354H CYS* 3.6 18.6 - - + -
358H ARG* 4.8 9.1 + - - +
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Residues in contact with LEU 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ILE* 3.8 16.2 - - + -
185G ASP 2.7 23.2 + - - +
186G ALA 3.5 3.8 - - - +
188G ALA* 1.3 72.5 - - - +
190G THR* 1.3 66.9 + - - +
192G THR* 4.4 0.2 - - - -
193G PHE* 2.8 56.5 + - + +
200G ILE* 5.4 0.2 - - - -
233G CYS* 4.0 29.2 - - + -
235G LEU* 4.0 23.1 - - + -
350H ILE* 3.7 25.8 - - + -
353H LEU* 4.9 7.0 - - + -
354H CYS* 3.7 15.0 - - - -
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Residues in contact with THR 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G ILE* 4.0 3.7 - - - +
186G ALA* 2.5 26.1 + - - +
187G GLY* 3.3 8.7 - - - -
189G LEU* 1.3 73.7 - - - +
191G THR* 1.3 57.8 + - - +
194G GLU* 2.8 48.7 + - - +
200G ILE* 3.6 40.0 - - + +
202G PRO* 6.0 1.8 - - + +
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Residues in contact with THR 191 (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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187G GLY 2.9 15.3 + - - -
188G ALA* 3.6 9.1 - - - -
190G THR* 1.3 76.3 - - - +
192G THR* 1.3 60.0 + - - +
194G GLU* 3.5 7.5 - - - +
195G GLU* 2.9 58.7 + - + +
358H ARG* 4.3 13.2 - - - +
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Residues in contact with THR 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ALA 2.6 24.8 + - - -
189G LEU* 3.6 2.7 - - - -
191G THR* 1.3 76.2 - - - +
193G PHE* 1.3 65.6 + - + +
195G GLU* 3.2 12.3 + - - +
196G LEU* 3.2 26.2 + - + +
354H CYS* 3.4 23.5 - - - +
357H LEU* 3.8 37.5 - - + -
358H ARG* 3.8 24.6 + - + +
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Residues in contact with PHE 193 (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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165G CYS* 4.0 15.9 - - - -
189G LEU* 2.8 47.9 + - + +
192G THR* 1.3 74.7 - - - +
194G GLU* 1.3 67.0 + - - +
196G LEU* 3.1 24.7 + - + +
197G HIS 3.2 0.3 + - - -
198G PHE* 2.9 34.6 + + + +
200G ILE* 3.8 16.6 - - + -
231G ILE* 3.4 26.2 - - + -
233G CYS* 4.6 4.9 - - - -
281G PHE* 3.8 24.7 - + - -
353H LEU* 5.4 0.2 - - + -
357H LEU* 3.7 25.6 - - + -
400H PHE* 4.1 15.9 - + - -
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Residues in contact with GLU 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR* 2.8 37.8 + - - +
191G THR* 3.5 8.1 - - - +
193G PHE* 1.3 75.8 - - - +
195G GLU* 1.3 56.1 + - + +
197G HIS* 2.7 30.0 + - - -
198G PHE 3.8 11.7 + - - +
200G ILE* 3.8 12.6 - - + +
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Residues in contact with GLU 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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191G THR* 2.9 46.8 + - + +
192G THR* 3.4 6.3 - - - +
194G GLU* 1.3 76.8 - - + +
196G LEU* 1.3 59.4 + - + +
197G HIS* 3.1 19.1 + - - -
358H ARG* 3.8 31.8 + - - +
402H SER* 4.2 13.0 + - - +
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Residues in contact with LEU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162G ARG* 3.6 12.1 + - - -
192G THR* 3.2 19.0 + - + +
193G PHE* 3.1 27.3 + - + +
194G GLU 3.0 1.2 + - - -
195G GLU* 1.3 80.0 - - + +
197G HIS* 1.3 74.7 + - - +
198G PHE* 3.5 16.9 - - + -
357H LEU* 4.6 5.8 - - + +
361H CYS* 4.0 19.7 - - + -
362H PRO* 5.8 0.7 - - + -
400H PHE* 3.5 53.1 - - + +
401H PRO 4.2 8.5 - - - +
402H SER* 4.5 9.6 - - - +
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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