Contacts of the helix formed by residues 196 - 215 (chain A) in PDB entry 4O6M
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 SER 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU 4.4 4.0 + - - -
195A ASN* 1.3 78.8 - - - +
197A TYR* 1.3 65.7 + - - +
198A LEU* 3.7 6.9 + - - +
199A THR* 2.9 32.1 + - - +
200A THR* 2.8 27.1 + - - -
315A ASN* 4.8 1.1 - - - -
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Residues in contact with TYR 197 (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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196A SER* 1.3 72.1 - - - +
198A LEU* 1.3 57.5 + - + +
200A THR* 3.0 1.6 + - - -
201A LEU* 2.7 60.8 + - + +
312A SER 3.9 6.3 - - - -
313A VAL 2.7 29.5 + - - -
314A VAL 4.4 0.9 - - - -
315A ASN* 3.5 51.3 + - + +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A SER* 3.3 7.0 + - - +
197A TYR* 1.3 83.3 - - + +
199A THR* 1.3 62.5 + - + +
201A LEU* 3.4 14.8 + - + +
202A LEU* 3.0 54.5 + - + +
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Residues in contact with THR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A LEU* 3.4 36.4 + - + +
194A LEU* 3.7 26.9 - - + +
196A SER* 2.9 33.1 + - - +
197A TYR 3.2 0.2 - - - -
198A LEU* 1.3 83.7 - - + +
200A THR* 1.3 59.3 + - - +
202A LEU* 3.8 9.6 - - + -
203A ALA* 2.8 29.1 + - - +
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Residues in contact with THR 200 (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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191A LEU 5.0 0.2 - - - -
192A PHE* 4.0 20.3 + - + -
195A ASN* 5.1 1.2 - - - -
196A SER 2.8 23.2 + - - -
197A TYR 3.4 3.6 - - - +
199A THR* 1.3 75.7 + - - +
201A LEU* 1.3 58.0 + - - +
203A ALA* 3.3 7.0 + - - +
204A GLY 2.9 23.7 + - - -
312A SER* 3.5 34.2 - - - +
315A ASN* 3.8 18.2 + - - +
317A PRO* 4.1 20.8 - - + +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A TYR* 2.7 46.6 + - + +
198A LEU* 3.5 15.9 - - + +
200A THR* 1.3 72.7 - - - +
202A LEU* 1.3 66.3 + - + +
204A GLY* 3.2 2.9 + - - -
205A VAL* 3.0 31.0 + - + +
312A SER 4.2 7.8 + - - -
313A VAL* 3.6 35.2 - - + +
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Residues in contact with LEU 202 (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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191A LEU* 4.0 21.5 - - + -
198A LEU* 3.0 44.1 + - + +
199A THR* 3.8 9.6 - - + +
201A LEU* 1.3 80.8 - - + +
203A ALA* 1.3 57.5 + - - +
205A VAL* 3.3 11.7 + - + +
206A ILE* 2.9 38.0 + - + +
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Residues in contact with ALA 203 (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 GLY* 3.3 26.5 - - - +
191A LEU* 3.7 11.4 - - + +
192A PHE* 3.6 24.0 - - + -
199A THR 2.8 18.1 + - - +
200A THR 3.4 6.3 - - - +
202A LEU* 1.3 77.6 - - - +
204A GLY* 1.3 56.7 + - - +
206A ILE* 3.3 2.4 + - - +
207A ILE* 2.8 36.4 + - - +
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Residues in contact with GLY 204 (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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192A PHE* 4.3 2.0 - - - -
200A THR 2.9 11.1 + - - -
201A LEU 3.2 4.0 + - - -
203A ALA* 1.3 76.9 - - - +
205A VAL* 1.3 60.8 + - - +
207A ILE* 3.2 5.2 + - - +
208A GLN 3.1 18.0 + - - -
308A ILE 5.1 0.2 - - - -
309A PHE* 3.2 27.5 - - - +
312A SER* 3.8 23.7 - - - -
313A VAL* 5.7 0.2 - - - -
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Residues in contact with VAL 205 (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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201A LEU* 3.0 26.2 + - + +
202A LEU* 3.6 15.0 - - + +
204A GLY* 1.3 75.2 - - - +
206A ILE* 1.3 62.9 + - + +
208A GLN* 3.2 4.2 + - - +
209A LEU* 2.9 31.0 + - + +
309A PHE* 3.7 22.0 - - + -
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Residues in contact with ILE 206 (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 LEU* 3.3 42.5 - - + +
187A VAL* 4.0 11.9 - - + -
188A GLY* 3.8 11.4 - - - +
191A LEU* 3.2 31.9 - - + -
202A LEU* 2.9 20.7 + - + +
203A ALA 3.8 2.5 - - - +
205A VAL* 1.3 80.0 - - + +
207A ILE* 1.3 57.9 + - - +
209A LEU* 3.5 14.7 - - + +
210A HIS* 2.8 26.7 + - - +
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Residues in contact with ILE 207 (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 SER* 4.0 12.8 - - - +
188A GLY* 3.9 23.8 - - - -
192A PHE* 4.1 17.3 - - + -
203A ALA 2.8 19.2 + - - +
204A GLY* 3.7 6.5 - - - +
205A VAL 3.2 0.2 - - - -
206A ILE* 1.3 78.4 - - - +
208A GLN* 1.3 56.0 + - - +
210A HIS* 3.3 7.2 - - + +
211A SER* 3.0 25.1 + - - -
246A ILE* 3.8 29.4 - - + -
305A LEU* 3.7 41.5 - - + +
308A ILE* 4.3 12.8 - - + -
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Residues in contact with GLN 208 (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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151A ILE* 5.2 3.2 - - - +
155A ILE* 5.6 1.8 - - - +
156A ASN* 3.0 32.7 + - - +
204A GLY 3.1 6.1 + - - -
205A VAL 3.2 6.7 + - - +
207A ILE* 1.3 74.1 - - - +
209A LEU* 1.3 65.5 + - - +
211A SER* 3.2 9.2 + - - -
212A ILE* 3.0 36.7 + - + +
302A ASP 5.0 0.3 - - - +
305A LEU 4.0 1.5 - - - -
306A LEU* 3.7 40.7 + - - +
309A PHE* 3.8 34.3 - - + +
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Residues in contact with LEU 209 (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 VAL* 6.4 1.1 - - + -
163A ILE* 5.4 4.5 - - + -
184A LEU* 4.1 20.2 - - + -
205A VAL* 2.9 18.7 + - + +
206A ILE* 3.5 17.9 - - + +
208A GLN* 1.3 76.8 - - - +
210A HIS* 1.3 57.0 + - - +
212A ILE* 3.2 15.3 + - + +
213A ILE* 2.9 59.3 + - + +
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Residues in contact with HIS 210 (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 SER* 2.8 48.5 + - - -
182A PHE* 4.4 0.9 - - - -
184A LEU* 4.2 20.8 - - + +
185A SER* 3.8 24.3 - - - +
206A ILE 2.8 18.1 + - - +
207A ILE* 3.3 8.5 - - - +
209A LEU* 1.3 76.0 - - - +
211A SER* 1.3 58.6 + - - +
213A ILE* 3.8 0.8 - - - +
214A ASP* 2.9 37.3 + - - +
239A ASP* 4.7 2.5 - - - -
242A SER* 4.1 4.7 - - - -
246A ILE* 4.8 6.7 - - + -
301A ARG* 3.0 40.0 + - - -
305A LEU* 3.9 12.3 - - + -
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Residues in contact with SER 211 (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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156A ASN* 3.3 23.4 + - - +
207A ILE 3.0 9.3 + - - -
208A GLN* 3.2 17.8 + - - -
210A HIS* 1.3 78.9 - - - +
212A ILE* 1.3 61.1 + - - +
214A ASP* 3.6 13.1 + - - +
215A GLY* 3.9 2.8 + - - -
301A ARG* 5.3 0.4 - - - +
302A ASP* 4.2 10.9 + - - +
305A LEU* 3.5 36.9 - - - +
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Residues in contact with ILE 212 (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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156A ASN* 3.8 33.2 - - + +
159A VAL* 3.8 43.3 - - + -
160A SER* 3.5 26.6 - - - +
163A ILE* 4.3 7.9 - - + -
208A GLN* 3.0 35.6 + - + +
209A LEU* 3.6 14.6 - - + +
211A SER* 1.3 75.9 - - - +
213A ILE* 1.3 64.6 + - + +
215A GLY* 3.1 12.0 + - - -
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Residues in contact with ILE 213 (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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163A ILE* 4.1 19.3 - - + -
177A ILE* 3.8 15.9 - - + +
180A PHE* 4.3 19.1 - - + -
181A SER* 4.4 9.4 - - - -
184A LEU* 3.7 14.1 - - + -
209A LEU* 2.9 51.6 + - + +
210A HIS* 4.1 3.8 - - - +
212A ILE* 1.3 74.1 - - + +
214A ASP* 1.3 57.0 - - - +
216A CYS* 2.8 32.8 + - - +
403A MPG 4.3 23.6 - - + -
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Residues in contact with ASP 214 (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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148A ASP* 4.7 7.6 - - - +
177A ILE* 5.4 0.4 - - - -
178A THR* 5.0 1.2 - - - +
181A SER* 3.0 26.3 + - - +
210A HIS* 2.9 20.0 + - - +
211A SER 3.7 7.4 - - - +
212A ILE 3.2 0.6 - - - -
213A ILE* 1.3 77.6 - - - +
215A GLY* 1.3 52.0 + - - +
217A ASP* 2.6 17.5 - - - +
235A ASP* 3.1 14.8 - - - +
239A ASP* 3.2 28.6 - - - +
301A ARG* 4.1 12.6 + - - +
401A CA 2.3 47.4 - - - -
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Residues in contact with GLY 215 (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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157A ARG* 3.5 19.2 + - - -
160A SER* 4.7 0.9 - - - -
211A SER 3.9 3.7 + - - -
212A ILE 3.1 10.8 + - - -
213A ILE 3.0 1.4 - - - -
214A ASP* 1.3 77.7 - - - +
216A CYS* 1.3 62.1 + - - +
217A ASP* 3.2 3.1 + - - -
218A GLY* 3.5 2.8 + - - -
219A GLU* 3.3 30.4 + - - +
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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