Contacts of the helix formed by residues 204 - 218 (chain A) in PDB entry 1MDF
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 HIS 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 4.0 1.1 - - - +
26A THR* 3.5 19.2 - - - -
27A PHE* 3.2 46.4 + + + -
28A GLY 5.1 0.2 - - - -
96A PHE* 4.3 15.4 + + + -
99A GLY* 5.9 1.8 - - - -
179A VAL* 3.7 17.2 - - + +
180A LYS 3.5 14.4 - - - -
181A SER* 3.2 18.2 + - - +
183A ASP* 3.4 25.9 + - + +
184A VAL 4.5 1.6 + - - -
185A ALA* 3.4 24.4 - - + +
203A THR* 1.3 74.7 - - - +
205A ASP* 1.3 60.0 + - - +
208A ILE* 2.9 37.3 + - + +
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Residues in contact with ASP 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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17A ARG* 5.0 4.5 + - - -
21A CYS 4.3 1.7 - - - +
22A TRP* 3.4 34.9 - - + +
23A ALA* 2.9 14.9 + - - +
24A GLY* 2.8 24.8 + - - -
25A GLU 4.2 2.4 + - - +
181A SER* 2.7 40.7 + - - +
182A SER* 4.0 5.3 + - - -
203A THR* 3.2 4.0 - - - +
204A HIS* 1.3 77.8 - - - +
206A ASP* 1.3 63.5 - - - +
208A ILE* 3.9 2.8 - - - +
209A TYR* 3.0 24.6 + - - +
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Residues in contact with ASP 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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8A TRP* 3.5 20.7 - - + -
22A TRP* 3.9 7.8 - - + +
202A ARG* 2.6 40.3 + - - -
203A THR* 2.4 47.3 + - - +
205A ASP* 1.3 79.3 - - - +
207A TYR* 1.3 58.4 + - - +
209A TYR* 3.4 2.2 + - - +
210A SER* 3.1 20.4 + - - -
386A PRO 3.1 27.1 - - - +
387A TYR* 3.3 17.8 - - - +
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Residues in contact with TYR 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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27A PHE* 3.6 20.4 - + + -
186A PHE* 3.3 41.5 - + + -
188A GLN* 4.7 1.0 + - - -
202A ARG* 3.4 32.8 - - + -
203A THR 3.2 16.1 + - - +
206A ASP* 1.3 78.3 - - - +
208A ILE* 1.3 66.0 + - - +
209A TYR 3.1 1.6 - - - -
210A SER* 2.5 26.1 + - - -
211A LEU* 3.0 14.6 + - + +
235A ASN* 2.7 29.9 + - - -
238A LEU* 3.7 16.8 - - + +
239A SER* 3.0 28.6 + - - -
244A LEU* 4.3 15.5 - - + -
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Residues in contact with ILE 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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23A ALA* 5.6 2.9 - - + -
25A GLU* 3.2 50.7 - - + +
26A THR* 3.6 23.8 - - - +
27A PHE* 3.8 28.0 - - + +
30A LEU* 4.4 7.6 - - + -
204A HIS 2.9 20.9 + - - +
205A ASP* 3.9 3.4 - - - +
207A TYR* 1.3 75.1 - - - +
209A TYR* 1.3 58.3 + - - +
211A LEU* 3.3 9.1 + - - +
212A LYS* 3.0 25.5 + - + +
248A TYR* 4.0 18.9 - - + +
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Residues in contact with TYR 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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20A GLY 4.7 2.7 - - - -
21A CYS* 3.0 61.3 - - + +
22A TRP* 4.7 0.9 - - + -
205A ASP 3.0 14.5 + - - +
206A ASP* 3.5 5.8 - - - +
207A TYR 3.1 0.2 - - - -
208A ILE* 1.3 76.4 - - - +
210A SER* 1.3 65.6 + - - +
212A LYS* 3.2 15.4 + - + +
213A ARG* 3.0 48.8 + - + +
358A SER* 2.5 36.4 + - - -
359A PRO* 4.3 3.1 - - - +
360A TYR* 4.4 1.2 - - - -
386A PRO* 4.1 13.0 - - + -
387A TYR* 3.6 30.7 - + + -
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Residues in contact with SER 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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202A ARG* 4.4 3.8 - - - -
206A ASP 3.1 14.2 + - - -
207A TYR* 2.5 36.2 + - - -
209A TYR* 1.3 83.6 - - - +
211A LEU* 1.3 64.5 + - - +
213A ARG 3.6 0.2 + - - -
214A SER* 2.7 30.6 + - - -
239A SER* 4.7 5.2 - - - -
337A VAL* 5.9 0.7 - - - -
357A MET* 3.8 24.7 - - - +
387A TYR* 4.2 13.0 - - - -
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Residues in contact with LEU 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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27A PHE* 4.0 24.2 - - + -
30A LEU* 4.9 4.0 - - + -
207A TYR* 3.0 16.6 + - + +
208A ILE* 3.5 10.3 - - - +
209A TYR 3.1 0.2 - - - -
210A SER* 1.3 80.6 + - - +
212A LYS* 1.3 57.9 + - - +
214A SER* 3.0 7.1 + - - -
215A VAL* 2.9 34.1 + - - +
239A SER* 3.4 41.7 - - - +
244A LEU* 3.8 28.3 - - + +
245A GLY* 3.7 20.4 - - - +
248A TYR* 4.4 15.5 - - + -
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Residues in contact with LYS 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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20A GLY 4.9 9.6 + - - -
23A ALA* 6.3 2.1 - - + +
208A ILE* 3.0 12.9 + - + +
209A TYR* 3.2 19.9 + - + +
211A LEU* 1.3 75.2 - - - +
213A ARG* 1.3 65.0 + - + +
215A VAL* 3.1 12.5 + - - +
216A GLU* 3.1 43.7 + - + +
248A TYR* 3.3 41.0 + - + +
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Residues in contact with ARG 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 TYR* 3.0 54.8 + - + +
212A LYS* 1.3 78.4 - - + +
214A SER* 1.3 57.8 + - - +
216A GLU* 2.9 42.3 + - - +
217A VAL* 2.9 43.7 + - - +
357A MET* 2.8 44.0 + - + +
358A SER* 4.1 2.5 - - - +
359A PRO* 4.2 15.6 - - - +
996A SO4 3.2 37.6 + - - -
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Residues in contact with SER 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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210A SER 2.7 22.6 + - - -
211A LEU* 3.0 6.2 + - - -
213A ARG* 1.3 77.7 - - - +
215A VAL* 1.3 60.0 + - - +
217A VAL 3.5 0.3 + - - -
218A CYS* 2.9 34.7 + - - +
239A SER 3.3 17.0 + - - -
240A SER* 4.9 0.2 + - - -
241A PRO* 3.8 11.0 - - - -
339A TYR* 2.6 31.2 + - - -
357A MET* 3.4 12.3 - - - +
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Residues in contact with VAL 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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211A LEU 2.9 20.6 + - - +
212A LYS* 3.1 7.6 + - - +
214A SER* 1.3 77.5 - - - +
216A GLU* 1.3 59.0 + - + +
219A TRP* 2.8 25.6 + - - -
220A LEU* 3.0 50.1 + - + +
241A PRO* 4.9 0.4 - - + -
245A GLY* 3.2 33.0 - - - +
248A TYR* 4.3 13.2 - - + -
249A ALA* 3.4 13.0 - - + -
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Residues in contact with GLU 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 LYS* 3.1 39.7 + - + +
213A ARG* 2.9 50.3 + - - +
215A VAL* 1.3 78.6 - - + +
217A VAL* 1.3 58.0 + - - +
219A TRP* 3.0 27.6 + - - +
996A SO4 5.6 0.9 - - - -
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Residues in contact with VAL 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 ARG* 2.9 42.4 + - - +
214A SER 4.0 2.9 - - - +
216A GLU* 1.3 78.5 - - - +
218A CYS* 1.3 57.4 + - - +
219A TRP* 3.4 10.5 + - - +
327A GLN* 4.2 3.7 + - - +
339A TYR* 3.8 31.9 - - + -
341A ARG* 3.5 36.7 - - - +
342A LEU* 3.8 15.1 + - - +
357A MET* 4.2 15.0 - - + +
996A SO4 4.7 4.7 - - - +
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Residues in contact with CYS 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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214A SER 2.9 20.7 + - - +
217A VAL* 1.3 76.3 - - - +
219A TRP* 1.3 70.3 + - - +
220A LEU* 3.4 14.6 + - + +
241A PRO* 3.7 25.8 - - + -
275A ILE* 4.9 8.7 - - + +
302A VAL* 5.1 1.9 - - - +
327A GLN* 3.6 29.2 - - - +
339A TYR* 3.6 26.9 - - - -
342A LEU* 3.6 14.5 - - + +
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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