Contacts of the helix formed by residues 178 - 192 (chain A) in PDB entry 4BOS
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 CYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A THR* 4.1 15.0 - - - -
166A TYR* 3.6 53.2 - - + -
175A ASN* 3.0 30.8 + - - +
176A PRO 3.0 1.7 + - - -
177A ALA* 1.3 76.6 - - - +
179A ALA* 1.3 69.9 + - - +
180A PRO 3.5 0.2 - - - -
181A GLU* 3.2 16.5 + - - +
182A MET* 3.0 32.6 + - + +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 3.5 35.2 - - - +
162A PHE* 4.3 15.9 - - + -
163A THR* 4.6 3.4 - - - +
176A PRO 3.2 11.2 + - - +
177A ALA 3.2 0.8 - - - -
178A CYS* 1.3 82.0 - - - +
180A PRO* 1.4 70.9 - - + +
182A MET* 3.2 1.8 + - - +
183A ARG* 2.9 33.5 + - - +
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A PRO 4.4 1.3 - - - +
177A ALA* 3.3 19.5 - - - +
179A ALA* 1.4 93.6 - - + +
181A GLU* 1.3 58.3 + - + +
183A ARG* 3.4 13.5 + - - +
184A ARG* 3.1 34.4 + - + +
214A LYS 5.5 2.3 - - - +
216A ASP* 6.2 4.0 - - + -
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ALA 4.3 13.6 - - - +
178A CYS* 3.2 11.8 + - - +
180A PRO* 1.3 75.7 - - + +
182A MET* 1.3 62.5 + - + +
184A ARG* 3.2 10.4 + - - +
185A LEU* 2.9 27.9 + - - +
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Residues in contact with MET 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 3.4 44.2 - - + +
165A VAL* 4.0 12.8 - - + -
166A TYR* 3.9 13.7 - - + +
178A CYS* 3.0 36.4 + - + +
179A ALA 3.8 3.1 - - - +
181A GLU* 1.3 77.7 - - + +
183A ARG* 1.3 61.1 + - - +
185A LEU* 3.2 12.1 + - + +
186A ILE* 3.0 27.7 + - - +
228A LEU* 3.9 37.2 - - + +
232A TYR* 4.1 15.5 - - - +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ASN 3.4 10.3 + - - -
159A SER* 3.0 28.3 + - - -
162A PHE* 3.4 29.9 - - + -
179A ALA* 2.9 24.8 + - - +
180A PRO* 3.7 9.2 - - - +
182A MET* 1.3 76.3 - - - +
184A ARG* 1.3 58.4 + - - +
186A ILE* 3.1 12.3 + - - +
187A ALA* 2.9 26.9 + - - +
213A ILE* 2.8 36.4 + - - +
214A LYS* 3.9 15.3 - - + -
215A ARG 2.9 25.1 + - - -
216A ASP* 4.0 10.2 + - - +
218A THR* 2.9 33.1 + - - -
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PRO* 3.1 22.6 + - - +
181A GLU* 3.2 11.0 + - - +
183A ARG* 1.3 75.9 - - - +
185A LEU* 1.3 62.8 + - - +
187A ALA* 3.3 2.9 + - - +
188A GLN* 3.0 25.4 + - - +
214A LYS* 3.7 42.6 - - + +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU 2.9 13.2 + - - +
182A MET* 3.4 11.7 - - + +
183A ARG 3.2 0.2 - - - -
184A ARG* 1.3 74.9 - - - +
186A ILE* 1.3 66.1 + - + +
188A GLN* 3.2 9.7 + - + +
189A ILE* 3.1 41.2 + - + +
227A ILE* 5.9 0.2 - - + -
228A LEU* 4.3 18.4 - - + -
231A PHE* 3.8 49.6 - - + -
232A TYR* 5.2 3.6 - - - +
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Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A PHE* 4.1 5.4 - - + -
182A MET 3.0 19.0 + - - +
183A ARG* 3.3 12.6 - - - +
185A LEU* 1.3 75.5 - - + +
187A ALA* 1.3 58.6 + - - +
189A ILE* 3.0 3.8 + - - +
190A VAL* 2.8 42.3 + - + +
209A TYR* 4.8 0.2 - - + -
213A ILE* 4.0 14.1 - - + -
224A GLU* 3.8 42.0 - - + +
227A ILE* 3.8 31.6 - - + +
228A LEU* 3.8 31.2 - - + -
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG 2.9 9.4 + - - +
184A ARG 3.7 6.5 - - - +
185A LEU 3.3 0.4 - - - -
186A ILE* 1.3 77.5 - - - +
188A GLN* 1.3 57.7 + - - +
190A VAL* 4.5 1.3 - - - -
191A ALA* 2.9 30.1 + - - +
210A CYS* 3.3 30.9 - - + +
213A ILE* 4.2 4.9 - - + +
214A LYS* 3.5 34.1 - - + +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 3.0 14.9 + - - +
185A LEU* 3.4 17.0 - - + +
186A ILE 3.1 0.2 - - - -
187A ALA* 1.3 76.4 - - - +
189A ILE* 1.3 65.0 + - + +
191A ALA* 4.1 4.5 - - - +
192A SER* 3.3 22.9 + - - -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.1 33.1 + - + +
186A ILE 3.0 6.5 + - - +
188A GLN* 1.3 79.5 - - + +
190A VAL* 1.3 65.0 + - - +
192A SER* 3.0 25.1 + - - +
193A ASP* 3.6 4.2 + - + +
197A TYR* 4.0 13.0 - - + +
227A ILE* 3.6 43.3 - - + +
231A PHE* 4.9 12.1 - - + -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 2.8 29.5 + - + +
187A ALA* 4.8 0.4 - - - -
189A ILE* 1.3 76.5 - - - +
191A ALA* 1.3 63.1 + - - +
192A SER 3.2 0.5 + - - -
193A ASP 3.3 8.7 + - - -
197A TYR* 3.8 27.0 - - + -
202A LEU* 4.2 10.8 - - + -
206A ASN* 2.9 39.1 + - - +
209A TYR* 4.2 19.7 - - + -
210A CYS* 3.8 14.4 - - - -
223A ILE* 4.6 3.4 - - + -
227A ILE* 3.9 20.2 - - + -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ALA 2.9 19.5 + - - +
188A GLN* 4.2 4.7 - - - +
190A VAL* 1.3 77.5 - - - +
192A SER* 1.3 59.4 + - - +
194A PRO* 3.3 15.6 - - - +
206A ASN* 3.2 16.8 + - - +
210A CYS* 3.7 7.4 - - - -
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A GLN* 3.3 18.8 + - - -
189A ILE* 3.0 18.2 + - - +
190A VAL 3.1 1.6 - - - -
191A ALA* 1.3 77.0 - - - +
193A ASP* 1.3 59.2 + - - +
194A PRO* 3.6 4.6 - - - +
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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
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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