Contacts of the helix formed by residues 213 - 228 (chain A) in PDB entry 1R4N
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 PRO 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A TYR* 4.1 13.9 - - + +
211A HIS 4.1 3.4 - - - +
212A THR* 1.3 94.3 - - + +
214A TRP* 1.3 65.9 + - - +
215A ILE 3.2 0.7 + - - +
216A VAL* 3.4 14.4 + - + +
217A ILE* 3.2 16.3 + - - +
332A MET* 3.2 25.8 - - + -
333A ILE 4.2 1.3 - - - +
334A ALA* 3.6 24.6 - - + -
338A LYS* 4.3 20.0 - - + +
339A TYR* 4.3 2.9 - - - -
342A LEU* 3.7 15.9 - - + -
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Residues in contact with TRP 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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181A GLU* 6.1 0.7 - - + -
183A LEU* 4.7 12.4 - - + +
185A LEU* 6.0 0.4 - - - +
212A THR 3.3 2.9 + - - -
213A PRO* 1.3 68.9 - - - +
215A ILE* 1.3 82.9 + - + +
217A ILE* 3.1 13.5 + - - +
218A ILE* 3.0 32.9 + - + +
264A ASN* 4.2 7.0 - - + +
267A GLU* 3.7 21.5 - - - +
268A ALA* 3.9 18.8 - - + +
271A ASN* 3.0 45.7 - - + +
275A ALA* 4.8 7.2 - - + +
330A PRO* 3.6 30.3 - - + -
331A ASP 3.5 20.9 - - - -
332A MET* 3.2 35.0 - - + +
333A ILE 4.6 2.4 + - - -
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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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183A LEU* 3.7 25.8 - - + -
185A LEU* 3.9 21.1 - - + -
196A PHE* 3.7 27.6 - - + -
213A PRO 3.1 0.8 - - - -
214A TRP* 1.3 97.7 - - + +
216A VAL* 1.3 55.8 + - - +
218A ILE* 2.7 7.5 + - - +
219A ALA 2.6 32.9 + - - -
329A ILE* 4.9 3.4 - - + -
332A MET* 3.7 27.1 - - + -
342A LEU* 4.0 13.5 - - + -
346A TYR* 3.6 21.8 - - + +
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Residues in contact with VAL 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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195A HIS* 4.7 6.5 - - - +
196A PHE* 4.2 21.3 - - + +
199A TYR* 3.3 57.0 - - + +
212A THR* 4.1 6.7 - - + -
213A PRO* 3.4 25.3 + - + +
215A ILE* 1.3 74.9 - - - +
217A ILE* 1.3 54.9 + - + +
219A ALA* 3.4 8.5 - - - +
220A LYS* 2.7 42.2 + - + +
342A LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 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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209A HIS* 4.9 3.8 - - + +
212A THR* 3.6 31.6 - - + +
213A PRO 3.2 14.6 - - - +
214A TRP* 3.1 12.1 - - - +
215A ILE 2.9 0.4 + - - -
216A VAL* 1.3 79.2 - - + +
218A ILE* 1.3 60.8 + - - +
220A LYS* 3.6 3.0 + - - +
221A TYR* 3.2 29.2 + - + +
247A ILE* 4.2 17.0 - - + -
264A ASN* 4.4 4.3 - - - +
265A PHE* 3.5 41.1 - - + -
268A ALA* 3.9 18.6 - - + -
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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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185A LEU* 3.9 19.3 - - + -
214A TRP* 3.0 25.7 + - + +
215A ILE* 2.7 11.7 + - - +
217A ILE* 1.3 70.9 - - - +
219A ALA* 1.3 58.9 + - - +
221A TYR* 3.7 0.9 - - - -
222A LEU* 2.8 36.3 + - + +
243A PHE* 3.7 18.6 - - + -
247A ILE* 4.2 7.0 - - + -
268A ALA* 3.1 38.4 - - + +
271A ASN* 4.0 0.2 - - + -
272A VAL* 3.6 22.7 - - + +
275A ALA* 4.0 15.0 - - + -
276A LEU* 4.8 7.9 - - + -
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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* 3.8 12.1 - - + +
196A PHE* 3.7 47.6 - - + -
215A ILE 2.6 16.2 + - - +
216A VAL 3.4 7.2 - - - +
218A ILE* 1.3 73.6 - - - +
220A LYS* 1.3 57.1 + - + +
222A LEU* 3.4 9.0 + - - +
223A ALA* 2.9 28.4 + - - +
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Residues in contact with LYS 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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196A PHE* 2.7 37.4 + - + +
197A GLN* 3.8 9.3 + - - +
199A TYR* 3.9 29.2 - - + -
216A VAL* 2.7 24.3 + - + +
217A ILE* 3.8 6.1 - - - +
219A ALA* 1.3 69.6 - - - +
221A TYR* 1.3 69.9 + - + +
222A LEU 2.9 4.0 - - - -
223A ALA* 2.9 25.6 + - + +
224A GLN* 3.0 13.4 + - - +
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Residues in contact with TYR 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 ILE* 3.2 22.2 + - + +
220A LYS* 1.3 88.2 - - + +
222A LEU* 1.3 58.6 + - - +
224A GLN* 3.9 17.0 - - - +
225A TRP* 3.4 12.5 + - - +
243A PHE* 2.9 21.6 - - + -
246A LEU* 3.3 38.6 - - + +
247A ILE* 3.4 44.4 - - + -
249A GLN 4.4 1.5 + - - -
250A GLY* 2.9 30.7 + - - -
265A PHE* 4.3 13.2 - + - -
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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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185A LEU* 4.1 33.4 - - + +
186A ASP* 5.9 0.4 - - - -
218A ILE* 2.8 20.7 + - + +
219A ALA* 3.4 10.3 - - - +
220A LYS 2.9 0.2 - - - -
221A TYR* 1.3 75.1 - - - +
223A ALA* 1.3 68.3 + - - +
224A GLN 3.1 1.6 - - - -
225A TRP* 3.1 6.7 + - + +
226A TYR* 3.0 20.7 + - + +
232A ARG* 4.5 7.6 - - - +
233A ILE* 3.4 31.4 - - + -
243A PHE* 3.5 8.3 - - + -
276A LEU* 4.2 15.0 - - + -
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Residues in contact with ALA 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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219A ALA 2.9 15.0 + - - +
220A LYS* 3.3 15.0 - - + +
222A LEU* 1.3 78.6 - - - +
224A GLN* 1.3 61.9 + - - +
226A TYR* 3.2 20.8 - - - +
227A SER* 3.6 7.3 + - - -
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Residues in contact with GLN 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 LYS 3.0 13.6 + - - +
221A TYR* 4.0 17.7 - - - +
223A ALA* 1.3 73.1 - - - +
225A TRP* 1.3 56.8 + - - +
226A TYR 2.8 10.9 + - - -
227A SER* 2.8 20.7 + - - -
228A GLU* 3.3 36.3 + - + +
246A LEU* 3.6 31.8 - - - +
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Residues in contact with TRP 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 TYR 3.4 12.7 + - - +
222A LEU* 3.1 10.2 + - + +
224A GLN* 1.3 78.8 - - - +
226A TYR* 1.3 61.0 + - - +
228A GLU* 4.2 10.9 - - - +
229A THR* 3.4 32.3 + - + -
231A GLY* 3.9 16.1 - - - -
232A ARG* 3.8 6.2 - - - +
233A ILE* 3.2 40.6 - - + +
239A GLU* 4.0 41.3 - - + -
242A ASP* 4.8 9.4 - - + -
243A PHE* 4.0 32.3 - + + -
246A LEU* 4.2 16.1 - - + +
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Residues in contact with TYR 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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222A LEU* 3.0 10.9 + - + +
223A ALA* 3.2 18.6 - - - +
224A GLN 2.8 0.6 + - - -
225A TRP* 1.3 82.3 - - - +
227A SER* 1.3 58.0 + - - +
230A ASN* 2.6 60.6 + - - +
231A GLY 3.4 15.7 - - - -
232A ARG* 6.5 0.2 - - + -
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Residues in contact with SER 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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223A ALA 3.6 6.3 + - - -
224A GLN* 2.8 11.5 + - - -
226A TYR* 1.3 78.2 - - - +
228A GLU* 1.3 56.3 + - - -
229A THR* 2.6 19.5 + - - -
230A ASN* 4.8 6.5 + - - +
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Residues in contact with GLU 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 GLN* 3.3 39.0 + - + +
225A TRP* 4.0 9.5 + - - +
227A SER* 1.3 74.3 - - - +
229A THR* 1.3 67.6 + - - +
246A LEU* 5.1 5.9 - - - +
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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