Contacts of the helix formed by residues 215 - 234 (chain A) in PDB entry 1IN5
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 THR 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO 3.7 7.9 + - - +
61A GLY* 3.3 34.3 - - - +
62A LEU* 4.2 2.6 - - + +
179A PHE* 3.7 14.0 - - - -
185A LEU* 3.7 4.8 - - - +
212A SER 2.9 6.6 + - - +
213A ARG 2.9 11.3 + - - -
214A GLY* 1.3 77.7 + - - +
216A PRO* 1.3 65.4 - - + +
217A ARG* 3.6 8.3 - - + +
218A ILE* 3.2 32.3 + - + +
219A ALA* 2.9 22.2 + - - +
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Residues in contact with PRO 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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61A GLY 3.2 13.2 - - - +
62A LEU* 3.9 2.2 - - + -
180A TYR* 3.3 46.4 - - + -
185A LEU* 3.9 8.7 - - + -
188A ILE* 3.9 19.1 - - + -
214A GLY 3.9 0.2 - - - +
215A THR* 1.3 82.2 - - + +
217A ARG* 1.3 62.1 + - - +
219A ALA* 3.2 4.0 + - + +
220A ILE* 2.9 29.6 + - - +
600A ADP 3.6 36.3 - - + +
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Residues in contact with ARG 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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60A PRO* 3.9 19.0 - - - +
61A GLY* 3.2 31.0 + - - +
215A THR* 3.3 2.9 - - + -
216A PRO* 1.3 77.9 - - - +
218A ILE* 1.3 66.1 + - - +
220A ILE* 3.5 3.5 + - - +
221A ARG* 3.2 46.9 + - - +
600A ADP 2.6 61.2 + - + -
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Residues in contact with ILE 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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211A ARG 4.4 0.4 - - - +
212A SER* 3.4 32.1 - - - +
213A ARG* 3.9 44.0 - - + +
215A THR* 3.2 31.0 + - + +
217A ARG* 1.3 81.0 - - + +
219A ALA* 1.3 63.1 + - - +
221A ARG* 3.2 9.8 + - - +
222A LEU* 2.9 35.9 + - + +
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Residues in contact with ALA 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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185A LEU* 4.3 9.2 - - + +
188A ILE* 5.3 2.5 - - + -
189A ILE* 3.9 20.9 - - + -
208A ILE* 4.0 2.1 - - - +
212A SER* 3.1 30.9 + - - +
215A THR 2.9 12.5 + - - +
216A PRO* 3.2 9.2 + - + +
218A ILE* 1.3 78.3 - - - +
220A ILE* 1.3 52.5 + - + +
222A LEU* 3.5 3.9 + - - +
223A THR* 2.7 37.0 + - - -
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Residues in contact with ILE 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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19A LEU* 3.8 36.6 - - + +
188A ILE* 4.2 15.5 - - + -
189A ILE* 5.8 0.7 - - - -
192A ALA* 4.5 13.5 - - + -
196A MET* 6.1 0.2 - - + -
216A PRO 2.9 22.2 + - - +
217A ARG* 3.9 4.0 - - - +
219A ALA* 1.3 72.8 - - - +
221A ARG* 1.3 66.8 + - + +
223A THR* 3.2 7.8 + - - -
224A LYS* 3.0 32.9 + - + +
600A ADP 3.6 48.5 - - + +
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Residues in contact with ARG 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 ARG* 3.2 37.7 + - + +
218A ILE* 3.7 6.7 - - - +
220A ILE* 1.3 74.5 - - + +
222A LEU* 1.3 67.4 + - + +
224A LYS* 3.2 17.0 + - + +
225A ARG* 3.1 34.4 + - + +
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Residues in contact with LEU 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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208A ILE* 3.9 14.8 - - + +
211A ARG* 3.3 29.4 - - + +
212A SER* 3.7 16.6 - - - +
213A ARG* 6.3 0.7 - - - +
218A ILE* 2.9 27.6 + - + +
219A ALA 3.6 4.3 - - - +
221A ARG* 1.3 78.2 - - + +
223A THR* 1.3 62.8 + - - +
225A ARG* 3.0 7.5 + - + +
226A VAL* 2.9 28.0 + - - +
246A THR* 4.9 0.2 - - - +
247A MET* 4.2 18.2 - - + -
250A LEU* 3.6 26.2 - - + -
252A ILE* 4.4 15.7 - - + -
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Residues in contact with THR 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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189A ILE* 3.4 43.6 - - + +
192A ALA* 4.7 2.9 - - + -
193A ALA* 4.4 10.1 - - + +
196A MET* 3.6 20.9 - - + -
200A ILE* 5.4 0.9 - - + -
208A ILE* 4.1 9.1 - - + +
219A ALA 2.7 21.0 + - - -
220A ILE* 3.2 12.2 + - - -
222A LEU* 1.3 77.0 - - - +
224A LYS* 1.3 56.5 + - - +
226A VAL* 3.4 7.2 + - - +
227A ARG* 3.0 26.7 + - - +
238A ILE* 4.8 7.9 - - + +
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Residues in contact with LYS 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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18A PHE* 6.1 2.3 - - - -
19A LEU* 3.8 28.3 - - - +
196A MET* 3.8 20.6 - - - -
220A ILE* 3.0 26.0 + - + +
221A ARG* 3.5 16.8 - - + +
222A LEU 3.2 0.4 - - - -
223A THR* 1.3 75.9 - - - +
225A ARG* 1.3 78.9 + - - +
227A ARG* 3.2 12.3 + - - +
228A ASP* 3.1 26.0 + - - +
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Residues in contact with ARG 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 ARG* 3.1 23.3 + - + +
222A LEU* 3.0 7.3 + - - +
224A LYS* 1.3 91.5 + - - +
226A VAL* 1.3 65.6 + - - +
227A ARG 3.1 0.4 - - - -
228A ASP* 2.7 42.4 + - - +
229A MET* 3.2 8.7 + - - +
246A THR* 3.7 11.1 - - + +
250A LEU* 3.9 41.1 - - + -
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Residues in contact with VAL 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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208A ILE* 3.9 19.1 - - + -
222A LEU 2.9 19.0 + - - +
223A THR 3.7 6.1 - - - +
225A ARG* 1.3 76.1 - - - +
227A ARG* 1.3 58.2 + - - +
229A MET* 3.2 3.3 + - - +
230A LEU* 3.0 25.6 + - - +
238A ILE* 3.5 39.3 - - + -
242A ILE* 3.8 10.9 - - + +
243A VAL* 4.2 8.7 - - + -
246A THR* 3.5 27.8 - - + +
247A MET* 4.1 12.8 - - + -
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Residues in contact with ARG 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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196A MET* 3.7 55.1 + - + +
198A VAL* 4.6 15.8 - - + +
223A THR 3.0 15.0 + - - +
224A LYS* 3.2 12.9 + - - +
226A VAL* 1.3 77.3 - - - +
228A ASP* 1.3 68.3 + - - +
230A LEU* 3.3 11.0 + - + +
231A THR* 2.9 36.1 + - - +
238A ILE* 4.4 8.5 - - + -
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LYS 3.1 11.3 + - - +
225A ARG* 2.7 43.3 + - - +
227A ARG* 1.3 88.9 + - - +
229A MET* 1.3 63.8 + - - +
231A THR* 3.1 10.2 + - - -
232A VAL* 3.0 29.0 + - + +
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Residues in contact with MET 229 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A ARG 3.2 7.6 + - - +
226A VAL 3.2 3.8 + - - +
228A ASP* 1.3 72.7 - - - +
230A LEU* 1.3 67.0 + - - +
232A VAL* 3.0 23.3 - - + +
233A VAL* 2.9 43.1 + - + +
242A ILE* 3.7 17.7 - - + +
245A LYS* 3.8 41.5 - - + +
246A THR* 3.2 30.7 - - + +
249A VAL* 3.8 19.7 - - + -
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Residues in contact with LEU 230 (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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198A VAL* 3.9 20.4 - - + -
226A VAL 3.0 13.2 + - - +
227A ARG* 3.4 12.8 - - + +
229A MET* 1.3 77.7 - - - +
231A THR* 1.3 68.0 + - - +
233A VAL* 3.9 7.9 - - - -
234A LYS* 3.1 16.5 + - - -
235A ALA* 3.2 28.9 + - + +
236A ASP 4.4 0.9 - - - -
237A ARG* 3.4 44.4 - - - +
238A ILE* 3.5 19.3 - - + +
242A ILE* 3.9 6.2 - - + +
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Residues in contact with THR 231 (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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227A ARG* 2.9 23.8 + - - +
228A ASP* 3.4 12.3 + - - -
229A MET 3.1 0.4 - - - -
230A LEU* 1.3 83.9 - - - +
232A VAL* 1.3 67.0 + - + +
234A LYS* 3.2 17.0 + - - +
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Residues in contact with VAL 232 (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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228A ASP* 3.0 16.8 + - + +
229A MET* 3.0 42.8 - - - +
231A THR* 1.3 81.1 - - + +
233A VAL* 1.3 62.2 + - + +
234A LYS* 3.2 9.7 + - - +
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Residues in contact with VAL 233 (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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229A MET* 2.9 45.0 + - + +
230A LEU* 3.6 7.2 - - - +
232A VAL* 1.3 77.4 - - + +
234A LYS* 1.3 71.6 + - - +
235A ALA* 3.8 10.4 - - + -
242A ILE* 3.5 30.1 - - + -
245A LYS* 4.9 9.9 - - + +
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Residues in contact with LYS 234 (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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230A LEU 3.1 8.8 + - - -
231A THR 3.2 12.1 + - - +
232A VAL 3.2 7.3 - - - +
233A VAL* 1.3 82.8 - - - +
235A ALA* 1.3 61.3 + - - +
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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