Contacts of the strand formed by residues 179 - 187 (chain M) in PDB entry 6G0L
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 ILE 179 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M PHE* 5.9 0.9 - - - -
178M GLY* 1.3 73.3 - - - -
180M ASP* 1.3 71.5 + - - +
181M ILE 4.6 3.8 - - - +
182M VAL* 5.5 1.6 - - + -
215M ILE* 3.7 32.1 - - + -
216M LYS 4.1 3.1 - - - -
217M TRP* 4.2 8.5 - - + -
218M THR* 4.4 3.5 - - - +
233M ILE* 4.1 11.4 - - + -
236M VAL* 3.7 20.2 - - + -
237M ARG 3.0 10.9 + - - +
238M GLY* 3.4 31.1 - - - +
239M LEU* 4.0 11.0 - - + -
241M ARG* 4.2 18.6 + - + -
242M LEU* 4.9 20.0 - - + +
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Residues in contact with ASP 180 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178M GLY 3.7 1.0 + - - -
179M ILE* 1.3 73.6 - - - +
181M ILE* 1.3 71.1 + - - +
216M LYS* 2.5 49.8 + - + +
218M THR* 3.5 27.6 + - - +
241M ARG* 2.4 46.8 + - - +
318M GLU* 5.5 3.5 - - - +
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Residues in contact with ILE 181 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M ILE* 5.0 1.6 - - - -
180M ASP* 1.3 95.6 - - - +
182M VAL* 1.3 67.2 + - - +
183M ILE* 4.2 14.6 - - + -
215M ILE* 3.9 4.5 - - - +
216M LYS* 2.9 45.5 + - + +
222M HIS* 4.2 22.0 - - + +
241M ARG* 4.5 7.0 - - - +
281M PHE* 4.8 13.5 - - + -
284M PHE* 5.2 4.7 - - + -
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Residues in contact with VAL 182 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179M ILE* 5.5 2.7 - - + -
181M ILE* 1.3 80.9 - - - +
183M ILE* 1.3 66.0 + - - +
184M ASN 4.3 7.9 - - - +
213M PHE* 4.9 2.2 - - + -
214M LEU 3.7 11.7 - - - +
215M ILE* 4.0 13.7 - - + -
241M ARG* 4.7 5.4 - - + +
242M LEU* 3.8 36.3 - - + +
245M TYR* 3.7 48.4 - - + -
281M PHE* 3.5 21.0 - - - -
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Residues in contact with ILE 183 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181M ILE* 4.2 15.0 - - + -
182M VAL* 1.3 79.5 - - - +
184M ASN* 1.3 62.8 + - + +
214M LEU* 2.9 33.7 + - + +
216M LYS* 3.7 28.0 - - + -
222M HIS* 4.5 7.9 - - + -
225M ASN* 3.5 27.6 - - - +
245M TYR* 4.1 10.6 + - - -
277M ARG* 5.6 0.7 - - - +
278M LEU* 5.4 4.5 - - + +
281M PHE* 3.2 51.1 - - + -
285M HIS* 5.4 4.7 - - - +
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Residues in contact with ASN 184 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182M VAL* 4.3 3.3 - - - +
183M ILE* 1.3 82.3 - - + +
185M HIS* 1.3 85.3 + - - +
186M ARG* 5.6 1.0 - - - +
213M PHE* 3.6 2.1 - - - +
214M LEU* 2.7 43.8 + - + +
227M TRP* 3.3 27.9 - - + -
278M LEU* 4.3 22.6 - - + +
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Residues in contact with HIS 185 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ASN* 1.3 96.1 + - - +
186M ARG* 1.3 67.4 + - - +
212M GLU 3.9 5.4 - - - -
213M PHE* 3.6 24.9 - - + -
227M TRP* 4.0 2.7 - - - -
245M TYR* 2.9 39.1 + + + -
249M PHE* 3.3 45.7 - + - -
252M GLU* 5.0 4.7 - - - -
274M ARG* 3.5 22.3 + - + -
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Residues in contact with ARG 186 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184M ASN* 5.6 0.7 - - - +
185M HIS* 1.3 78.9 - - - +
187M LEU* 1.3 66.0 + - + +
211M TYR* 3.3 16.6 - - - +
212M GLU* 2.7 58.4 + - + +
213M PHE* 4.9 0.3 - - - -
227M TRP* 3.6 56.5 - - + +
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Residues in contact with LEU 187 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186M ARG* 1.3 83.8 - - + +
188M LYS* 1.3 60.7 + - - +
189M THR 4.6 12.8 - - - +
190M SER* 4.2 21.3 - - - +
210M ASN 3.8 7.9 - - - +
211M TYR* 3.6 20.4 - - + -
212M GLU* 3.2 19.8 - - - +
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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