Contacts of the helix formed by residues 204 - 219 (chain A) in PDB entry 4IRX
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 LYS 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.2 16.6 + - - -
48A SER* 2.8 33.1 + - - -
49A GLN* 4.5 9.6 - - - +
77A ASN* 6.2 2.2 - - - +
201A ALA 3.0 9.9 + - - +
202A ASN* 3.4 14.8 - - + +
203A SER* 1.3 87.1 + - - +
205A ARG* 1.3 59.4 + - - +
206A ASP* 3.3 18.8 - - - +
207A GLN* 3.9 22.7 - - + +
208A ALA* 2.9 28.2 + - - +
233A ASP* 4.7 1.3 - - - +
234A MSE 3.8 5.5 - - - +
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Residues in contact with ARG 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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50A PRO* 5.2 2.6 - - - +
204A LYS* 1.3 71.9 - - - +
206A ASP* 1.3 59.0 + - - +
208A ALA* 3.2 5.1 + - - +
209A LEU* 3.0 27.9 + - - +
233A ASP* 2.8 64.1 + - - +
236A MSE 3.4 28.0 - - - +
237A GLY* 3.7 12.8 - - - +
240A GLU* 4.6 15.5 + - - +
260A ILE* 4.6 5.5 - - - +
262A GLU* 2.8 43.0 + - - -
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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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204A LYS* 3.3 22.2 - - - +
205A ARG* 1.3 75.2 + - - +
207A GLN* 1.3 70.7 + - - +
209A LEU* 3.4 15.4 + - - +
210A THR* 3.4 18.4 + - - +
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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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200A THR 5.1 0.5 - - - +
201A ALA* 3.6 23.2 - - + +
202A ASN* 2.8 34.2 + - - +
204A LYS* 3.4 22.0 + - + +
205A ARG 3.4 0.4 - - - -
206A ASP* 1.3 84.4 + - - +
208A ALA* 1.3 61.7 + - - +
209A LEU 3.2 0.2 + - - -
210A THR* 3.3 6.7 + - - +
211A VAL* 2.8 41.4 + - + +
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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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166A ILE* 5.0 3.1 - - + -
201A ALA* 3.5 10.5 - - + +
204A LYS 2.9 15.1 + - - +
205A ARG 3.2 8.9 + - - +
207A GLN* 1.3 78.0 - - - +
209A LEU* 1.3 62.3 + - - +
211A VAL* 4.6 0.9 - - - -
212A THR* 2.8 33.4 + - - +
234A MSE 3.3 43.5 - - + +
237A GLY* 4.2 2.8 - - - -
238A ALA* 4.4 0.9 - - + +
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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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205A ARG 3.0 12.8 + - - +
206A ASP* 3.7 11.9 - - - +
207A GLN 3.2 0.6 - - - -
208A ALA* 1.3 76.8 - - - +
210A THR* 1.3 63.5 + - + +
213A GLN* 2.9 52.6 + - - +
237A GLY* 3.7 13.9 - - - +
240A GLU* 4.0 18.4 - - + +
241A ALA* 3.5 33.1 - - - +
244A ALA* 5.2 1.6 - - + -
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Residues in contact with THR 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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206A ASP 3.4 12.1 + - - +
207A GLN* 3.3 10.9 + - - -
209A LEU* 1.3 80.8 - - + +
211A VAL* 1.3 69.4 + - - +
213A GLN* 3.3 16.9 + - - +
214A ASN* 3.0 35.2 + - - -
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Residues in contact with VAL 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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166A ILE* 4.0 13.2 - - + -
199A GLN* 3.8 29.1 - - + +
200A THR 4.0 18.8 - - - +
201A ALA* 4.5 2.7 - - + -
207A GLN* 2.8 35.3 + - + +
208A ALA* 4.2 3.4 - - - +
210A THR* 1.3 76.2 + - - +
212A THR* 1.3 61.2 + - - +
214A ASN* 3.4 6.1 + - - +
215A ILE* 3.1 33.7 + - + +
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Residues in contact with THR 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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164A VAL* 6.0 0.9 - - + -
166A ILE* 4.0 16.5 - - + +
208A ALA* 2.8 24.6 + - - +
211A VAL* 1.3 73.0 - - - +
213A GLN* 1.3 60.7 + - - +
215A ILE* 3.2 9.9 + - + +
216A LEU* 2.8 41.0 + - + +
227A ILE* 3.9 30.5 - - + -
238A ALA* 3.7 19.9 - - + +
241A ALA* 3.6 21.3 - - + -
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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 LEU* 2.9 39.6 + - - +
210A THR* 3.6 16.8 - - - +
212A THR* 1.3 76.8 - - - +
214A ASN* 1.3 60.9 + - - +
216A LEU* 3.2 8.1 + - - +
217A THR* 2.9 33.6 + - - +
241A ALA* 3.6 18.6 - - + +
244A ALA* 3.6 26.1 - - - +
245A ALA* 6.4 0.9 - - + -
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Residues in contact with ASN 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 THR* 3.0 24.6 + - - +
211A VAL* 3.8 6.1 - - - +
213A GLN* 1.3 79.7 - - - +
215A ILE* 1.3 58.0 + - + +
217A THR* 3.3 9.5 + - - +
218A SER* 3.0 28.3 + - - -
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Residues in contact with ILE 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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164A VAL* 3.8 15.5 - - + -
166A ILE* 3.7 29.2 - - + -
197A THR* 3.6 31.6 - - + -
199A GLN* 3.7 31.9 - - + +
211A VAL* 3.1 17.7 + - + +
212A THR* 3.6 8.3 - - + +
214A ASN* 1.3 77.1 - - + +
216A LEU* 1.3 67.6 + - + +
218A SER* 2.7 24.0 + - - +
219A MSE 2.9 29.6 - - + +
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Residues in contact with LEU 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 THR* 2.8 31.3 + - + +
213A GLN* 3.6 5.6 - - - +
215A ILE* 1.3 80.2 - - + +
217A THR* 1.3 61.1 + - - +
219A MSE 3.1 6.4 + - - -
220A ARG* 3.0 24.7 + - - +
223A PRO* 5.3 1.2 - - + +
224A PRO* 3.7 35.4 - - + -
227A ILE* 4.5 9.4 - - + -
241A ALA* 3.7 32.1 - - + +
242A VAL* 4.0 10.8 - - + +
245A ALA* 4.2 9.0 - - + -
247A LEU* 4.0 22.7 - - + -
252A VAL* 4.8 1.8 - - + -
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Residues in contact with THR 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* 2.9 18.7 + - - +
214A ASN* 3.6 10.6 + - - +
215A ILE 3.3 0.2 - - - -
216A LEU* 1.3 76.0 - - - +
218A SER* 1.3 62.6 + - - +
219A MSE 3.2 1.0 + - - -
220A ARG* 3.4 33.5 + - - +
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Residues in contact with SER 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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197A THR* 5.8 1.4 - - - +
214A ASN 3.0 13.6 + - - -
215A ILE* 2.7 23.6 + - - +
217A THR* 1.3 78.3 - - - +
219A MSE 1.3 60.7 + - - +
220A ARG 3.7 0.8 + - - -
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Residues in contact with MSE 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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162A ARG* 3.1 35.2 - - - +
164A VAL* 3.7 15.0 - - - -
196A VAL* 3.4 35.2 - - + -
197A THR* 4.9 2.0 - - - -
215A ILE* 2.9 32.5 - - - +
216A LEU* 3.1 8.5 + - - +
217A THR 3.1 0.6 - - - -
218A SER* 1.3 82.8 - - - +
220A ARG* 1.3 57.8 + - - +
221A ASP 3.1 3.4 - - - -
222A THR* 2.9 35.2 + - - +
223A PRO* 3.2 4.5 - - - +
224A PRO* 3.4 38.6 - - + -
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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