Contacts of the helix formed by residues 216 - 229 (chain A) in PDB entry 1IAX
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LYS* 2.8 33.1 + - - +
214A THR 3.8 2.8 + - - -
215A LEU* 1.3 71.2 - - - +
217A LYS* 1.3 56.2 + - - +
218A ASP* 2.7 22.5 + - - +
219A THR* 2.4 65.9 + - - +
220A LEU* 3.0 9.9 + - - +
248A PRO* 6.6 0.2 - - - -
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Residues in contact with LYS 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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215A LEU 3.2 6.4 + - - -
216A ASP* 1.3 70.0 + - - +
218A ASP* 1.3 66.5 + - - +
220A LEU* 3.1 13.6 + - - +
221A LYS* 3.0 36.3 + - - +
251A VAL* 4.2 30.6 - - + +
255A GLU* 5.2 6.3 + - - +
256A ILE* 3.8 14.7 - - + +
259A GLU* 2.6 29.6 + - - +
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Residues in contact with ASP 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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216A ASP* 2.7 20.2 + - - +
217A LYS* 1.3 78.4 - - - +
219A THR* 1.3 56.3 + - - -
221A LYS* 3.2 32.7 + - - +
222A SER* 2.9 28.0 + - - +
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Residues in contact with THR 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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179A LYS* 3.7 11.9 + - + +
180A ILE* 3.6 31.2 - - + +
215A LEU* 5.2 14.8 - - + -
216A ASP* 2.4 55.5 + - - +
218A ASP* 1.3 64.8 - - - +
220A LEU* 1.3 61.8 + - - +
222A SER* 3.1 9.2 + - - -
223A VAL* 3.0 30.9 + - + +
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Residues in contact with LEU 220 (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 LEU* 4.0 24.7 - - + -
206A ASN* 3.9 17.9 - - + +
215A LEU* 4.0 18.2 - - + +
216A ASP 3.0 8.9 + - - +
217A LYS* 3.1 7.2 + - - +
219A THR* 1.3 76.0 - - - +
221A LYS* 1.3 65.2 + - - +
222A SER 3.0 0.3 + - - -
223A VAL* 3.2 6.5 + - - +
224A LEU* 2.9 26.9 + - - +
234A LEU* 5.3 0.6 - - + +
236A CYS* 5.1 4.9 - - - -
251A VAL* 3.2 45.3 - - + +
252A SER 4.8 1.3 - - - -
253A ILE* 4.4 17.9 - - + +
256A ILE* 4.2 17.9 - - + -
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Residues in contact with LYS 221 (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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217A LYS* 3.0 23.6 + - + +
218A ASP* 3.2 36.8 + - - +
220A LEU* 1.3 77.8 - - - +
222A SER* 1.3 52.9 + - - +
224A LEU* 4.0 2.1 - - - +
225A SER* 2.7 32.9 + - - -
256A ILE* 3.8 18.8 - - + +
259A GLU* 3.4 21.5 + - - +
261A GLU* 3.0 37.3 + - - +
262A MET* 3.8 25.7 - - - +
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Residues in contact with SER 222 (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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182A SER* 3.3 25.0 + - - -
218A ASP 2.9 15.8 + - - -
219A THR* 3.4 10.4 - - - -
220A LEU 3.0 0.6 - - - -
221A LYS* 1.3 73.7 - - - +
223A VAL* 1.3 69.3 + - - +
224A LEU 3.0 1.3 - - - -
225A SER* 2.9 15.8 + - - -
226A PHE* 3.1 15.6 + - - +
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Residues in contact with VAL 223 (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 ILE* 4.4 22.7 - - + +
182A SER* 4.7 2.7 + - - +
185A VAL* 4.9 10.1 - - + -
202A LEU* 3.9 20.4 - - + -
204A LEU* 3.9 24.0 - - + -
219A THR* 3.0 22.2 + - + +
220A LEU 3.7 5.8 - - - +
222A SER* 1.3 78.5 - - - +
224A LEU* 1.3 56.9 + - - +
226A PHE* 4.1 5.9 - - - +
227A THR* 2.8 33.7 + - - +
234A LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 224 (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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220A LEU 2.9 15.8 + - - +
221A LYS 4.1 4.0 - - - +
223A VAL* 1.3 76.0 - - - +
225A SER* 1.3 54.7 + - - +
227A THR* 3.9 9.2 - - + -
228A ASN* 2.8 39.4 + - + +
234A LEU* 4.0 17.0 - - + -
253A ILE* 3.8 12.3 - - + -
256A ILE* 3.6 28.9 - - + -
257A LEU* 4.0 19.1 - - + -
262A MET* 4.5 8.1 - - + -
265A CYS* 4.0 18.2 - - + -
266A ASN 5.9 0.2 - - - +
270A VAL* 3.6 29.6 - - + -
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Residues in contact with SER 225 (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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221A LYS 2.7 22.7 + - - -
222A SER* 2.9 7.7 + - - -
224A LEU* 1.3 73.2 - - - +
226A PHE* 1.3 56.3 + - - +
228A ASN* 3.1 5.9 + - - +
229A GLN* 2.7 42.1 + - - +
262A MET* 3.8 17.4 - - - +
265A CYS* 4.9 1.8 - - - -
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Residues in contact with PHE 226 (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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146A LEU* 4.6 2.0 - - + -
182A SER* 5.5 6.1 - - - +
185A VAL* 3.3 34.3 - - + -
186A LYS* 4.0 34.5 - - + -
189A TYR* 3.4 40.2 - + + -
202A LEU* 5.2 1.6 - - + -
222A SER 3.1 11.8 + - - +
223A VAL* 4.1 5.2 - - - +
225A SER* 1.3 78.3 - - - +
227A THR* 1.3 68.6 + - - +
229A GLN* 3.3 13.8 + - - -
230A HIS* 2.9 69.0 - + - +
232A ILE* 4.4 13.9 - - + -
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Residues in contact with THR 227 (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 LEU* 4.3 13.9 - - - +
223A VAL* 2.8 28.7 + - - +
224A LEU* 3.5 15.0 - - + +
226A PHE* 1.3 82.7 - - - +
228A ASN* 1.3 66.3 + - + +
230A HIS 3.3 3.5 + - - -
232A ILE* 3.3 57.3 + - - +
233A HIS 4.5 0.2 + - - -
234A LEU* 3.6 29.6 - - + +
269A LEU* 4.8 4.3 - - + +
270A VAL* 5.5 0.4 - - + -
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Residues in contact with ASN 228 (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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224A LEU* 2.8 24.5 + - + +
225A SER* 3.7 2.6 - - - +
227A THR* 1.3 77.9 - - + +
229A GLN* 1.3 61.9 + - - +
230A HIS 3.2 1.4 + - - -
231A ASN* 3.4 9.2 + - - +
264A TYR 4.1 5.3 + - - +
265A CYS* 3.9 22.4 - - + -
266A ASN* 2.7 49.7 + - - +
269A LEU* 4.3 9.6 - - - +
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Residues in contact with GLN 229 (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* 5.7 3.9 - - - +
225A SER* 2.7 22.2 + - - +
226A PHE* 3.6 17.6 + - - +
227A THR 3.2 0.2 - - - -
228A ASN* 1.3 74.9 + - - +
230A HIS* 1.3 78.5 + - - +
231A ASN 3.6 0.2 - - - -
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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