Contacts of the helix formed by residues 204 - 219 (chain A) in PDB entry 1MUC
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 ASP 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A TYR 4.2 0.2 + - - -
203A TRP* 1.3 78.5 - - - +
205A GLU* 1.3 65.4 + - - +
206A SER* 2.5 29.6 + - - -
207A GLN* 2.9 34.5 + - - +
208A ALA* 3.1 9.7 + - - +
227A ILE* 3.8 3.6 - - - -
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Residues in contact with GLU 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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204A ASP* 1.3 74.9 - - - +
206A SER* 1.3 62.0 + - - +
208A ALA* 3.2 1.6 + - - -
209A ILE* 3.1 41.1 + - + +
227A ILE* 3.9 15.0 - - + +
231A ASN* 3.4 25.5 + - - +
234A GLY* 3.4 12.2 - - - +
237A ARG* 2.8 52.8 + - - +
238A LEU* 4.8 9.4 - - + +
241A ARG* 5.6 2.6 + - - -
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 2.5 25.2 + - - -
205A GLU* 1.3 77.2 - - - +
207A GLN* 1.3 62.7 + - - +
209A ILE* 4.0 20.2 + - - +
210A ARG* 4.7 2.9 + - - +
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Residues in contact with GLN 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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175A VAL* 4.1 25.0 - - + +
202A TYR 4.1 2.6 - - - +
203A TRP* 3.4 23.5 - - + -
204A ASP* 2.9 43.8 + - - +
206A SER* 1.3 80.4 - - - +
208A ALA* 1.3 63.4 + - - +
209A ILE 3.3 0.4 + - - -
210A ARG* 3.8 4.0 + - - +
211A ALA* 3.4 22.0 + - - +
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Residues in contact with ALA 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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203A TRP* 3.9 22.9 - - + +
204A ASP 3.1 15.3 + - - +
205A GLU 3.2 4.0 + - - +
207A GLN* 1.3 76.2 - - - +
209A ILE* 1.3 66.4 + - - +
211A ALA* 4.3 0.2 - - - -
212A CYS* 2.8 32.8 + - - +
226A PRO* 4.5 0.7 - - + -
227A ILE* 3.8 20.6 - - + -
238A LEU* 3.9 15.5 - - + -
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Residues in contact with ILE 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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205A GLU* 3.1 38.0 + - + +
206A SER* 4.1 13.7 - - - +
207A GLN 3.3 0.4 - - - -
208A ALA* 1.3 78.7 - - - +
210A ARG* 1.3 64.2 + - + +
212A CYS* 4.2 2.1 - - - +
213A GLN* 3.7 15.8 + - - +
238A LEU* 4.5 11.4 - - + +
241A ARG* 3.6 45.3 + - - +
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Residues in contact with ARG 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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175A VAL* 5.4 1.4 - - - +
176A GLU* 2.9 29.2 + - - +
179A LEU* 3.6 19.2 - - - +
206A SER 4.7 2.4 + - - +
207A GLN 3.8 5.5 + - - +
209A ILE* 1.3 79.4 - - + +
211A ALA* 1.3 65.6 + - - +
213A GLN* 3.2 8.5 + - + +
214A VAL* 3.1 37.5 + - + +
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Residues in contact with ALA 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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175A VAL* 4.1 14.5 - - + +
179A LEU* 4.1 14.4 - - + -
203A TRP* 3.5 34.8 - - + -
207A GLN 3.4 18.2 + - - +
208A ALA 3.3 1.9 + - - +
210A ARG* 1.3 77.7 - - - +
212A CYS* 1.3 64.1 + - - +
214A VAL* 3.4 1.9 + - - +
215A LEU* 3.0 30.4 + - - +
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Residues in contact with CYS 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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203A TRP* 4.7 2.9 - - - -
208A ALA* 2.8 39.3 + - - +
209A ILE 4.2 2.9 - - - +
211A ALA* 1.3 72.9 - - - +
213A GLN* 1.3 57.7 + - - +
215A LEU* 4.9 0.2 - - - -
216A GLY* 2.9 23.4 + - - -
223A ILE* 3.7 35.2 - - - +
226A PRO* 4.4 7.0 - - - -
238A LEU* 4.3 13.0 - - + -
242A THR* 3.5 25.9 + - - +
243A PRO* 3.4 9.8 - - - +
246A ILE* 4.5 3.4 - - - -
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Residues in contact with GLN 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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209A ILE 3.7 11.3 + - - +
210A ARG* 3.2 13.6 + - + +
212A CYS* 1.3 80.2 - - - +
214A VAL* 1.3 60.5 + - + +
216A GLY* 3.3 1.2 + - - -
217A ASP* 2.8 69.7 + - - +
241A ARG 4.8 4.0 - - - +
243A PRO* 3.4 25.4 - - - +
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Residues in contact with VAL 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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179A LEU* 4.1 20.6 - - + -
183A VAL* 4.4 14.8 - - + -
210A ARG* 3.1 46.7 + - + +
211A ALA 3.8 6.1 - - - +
213A GLN* 1.3 78.8 - - + +
215A LEU* 1.3 64.1 + - - +
217A ASP* 3.3 4.3 + - - -
218A ASN* 2.8 42.0 + - - +
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Residues in contact with LEU 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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170A ILE* 4.4 2.5 - - + -
179A LEU* 3.7 19.7 - - + -
182A VAL* 4.0 32.1 - - + -
183A VAL* 4.7 7.9 - - + -
197A VAL* 3.9 28.3 - - + -
203A TRP* 4.0 22.4 - - + -
211A ALA 3.0 21.2 + - - +
212A CYS 4.0 2.7 - - - +
214A VAL* 1.3 74.4 - - - +
216A GLY* 1.3 64.3 + - - +
218A ASN* 3.0 13.1 + - - -
219A GLY 3.6 0.2 + - - -
220A ILE* 3.2 34.9 + - + +
223A ILE* 4.3 15.5 - - + -
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Residues in contact with GLY 216 (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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212A CYS 2.9 18.7 + - - -
213A GLN 3.7 0.9 - - - -
215A LEU* 1.3 76.9 - - - +
217A ASP* 1.3 61.1 + - - +
218A ASN 3.4 0.7 + - - -
219A GLY* 3.7 8.5 + - - -
220A ILE 4.5 3.9 + - - +
243A PRO* 3.9 18.9 - - - +
244A ALA* 3.9 19.6 - - - +
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Residues in contact with ASP 217 (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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213A GLN* 2.8 50.6 + - - +
214A VAL* 3.7 6.7 - - - +
215A LEU 3.2 0.2 - - - -
216A GLY* 1.3 76.9 - - - +
218A ASN* 1.3 67.4 + - - +
219A GLY 3.4 1.4 + - - -
243A PRO* 4.3 4.9 - - - +
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Residues in contact with ASN 218 (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 VAL* 3.6 37.0 - - + +
186A LYS* 3.4 18.9 - - - +
214A VAL* 2.8 36.7 + - - +
215A LEU 3.0 5.2 + - - +
217A ASP* 1.3 88.2 - - - +
219A GLY* 1.3 59.8 + - - +
220A ILE* 3.5 6.7 + - + +
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Residues in contact with GLY 219 (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 LYS* 3.5 27.7 + - - +
195A VAL 4.4 1.4 + - - +
215A LEU 3.6 0.8 + - - -
216A GLY 3.7 5.7 + - - -
217A ASP 3.4 4.0 + - - -
218A ASN* 1.3 78.1 - - - +
220A ILE* 1.3 65.2 + - - +
221A ASP* 3.4 11.0 + - - +
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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