Contacts of the helix formed by residues 217 - 233 (chain A) in PDB entry 1B3U
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLU 3.7 3.0 + - - +
216A GLN* 1.3 70.9 - - - +
218A SER* 1.3 63.6 + - - +
219A VAL 3.0 1.6 + - - -
220A ARG* 2.8 40.9 + - - +
221A LEU* 3.1 26.9 + - - +
255A SER* 3.7 21.4 - - - +
257A ARG* 4.9 16.1 - - + +
258A VAL* 4.6 1.9 - - + +
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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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178A PRO* 5.4 0.2 - - - +
182A ARG* 3.3 38.7 + - - -
216A GLN* 4.1 14.9 - - - +
217A ASP* 1.3 78.7 - - - +
219A VAL* 1.3 60.2 + - - +
221A LEU* 3.8 13.4 - - - +
222A LEU* 3.7 14.0 - - - +
257A ARG* 4.9 15.8 - - - +
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Residues in contact with VAL 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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178A PRO* 4.2 8.7 - - + +
181A ARG* 4.2 18.4 - - + +
182A ARG* 3.6 25.1 - - + -
185A ALA* 4.8 4.8 - - + +
211A LEU* 3.9 26.7 - - + +
214A ASP* 3.6 29.2 - - + +
216A GLN* 2.8 25.5 + - + +
218A SER* 1.3 78.3 + - - +
220A ARG* 1.3 66.7 + - - +
221A LEU 3.2 0.4 - - - -
222A LEU* 3.2 20.1 + - - +
223A ALA* 3.9 3.1 + - - +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU 3.7 8.7 - - - -
212A ALA* 3.3 23.0 - - - +
213A SER* 3.9 3.6 - - - +
214A ASP 2.9 47.5 + - - +
215A GLU* 3.8 7.5 + - - +
216A GLN 3.1 7.1 + - - +
217A ASP* 2.8 43.2 + - - +
219A VAL* 1.3 77.2 - - - +
221A LEU* 1.3 61.8 + - - +
223A ALA* 3.0 21.4 + - - +
224A VAL* 4.2 1.9 + - - +
253A ASP* 2.7 39.5 + - - +
254A LYS* 5.4 2.2 - - - +
255A SER* 3.6 9.3 - - - +
258A VAL* 4.2 13.8 - - + +
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Residues in contact with LEU 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 ASP 3.1 14.6 + - - +
218A SER* 3.8 9.9 - - - +
219A VAL 3.2 0.4 - - - -
220A ARG* 1.3 77.0 - - - +
222A LEU* 1.3 89.9 + - + +
223A ALA 3.1 0.9 + - - -
224A VAL* 3.5 18.6 + - - +
225A GLU 4.7 0.7 + - - -
257A ARG* 4.0 39.7 - - + +
258A VAL* 4.1 21.7 - - + +
261A MET* 3.6 37.3 - - + +
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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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182A ARG* 3.4 48.0 - - + +
185A ALA* 4.1 20.5 - - + +
186A SER* 4.7 11.2 - - - +
218A SER 3.7 9.6 - - - +
219A VAL 3.2 9.2 + - - +
221A LEU* 1.3 99.0 - - + +
223A ALA* 1.3 61.6 + - - +
224A VAL 3.3 1.0 + - - -
225A GLU* 3.7 16.1 + - + +
226A ALA* 3.7 9.4 + - - +
261A MET* 6.2 2.2 - - + -
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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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185A ALA* 5.3 2.9 - - - +
208A PHE* 3.5 16.0 - - + +
211A LEU* 4.6 6.5 - - + -
212A ALA* 3.9 34.8 - - + +
219A VAL 3.9 2.3 + - - +
220A ARG 3.0 17.4 + - - +
222A LEU* 1.3 78.2 - - - +
224A VAL* 1.3 57.6 + - - +
226A ALA* 3.2 9.1 + - - +
227A CYS* 2.9 24.7 + - - +
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Residues in contact with VAL 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 ARG 4.9 1.1 - - - +
221A LEU 3.8 15.7 - - - +
222A LEU 3.3 0.6 - - - -
223A ALA* 1.3 77.4 - - + +
225A GLU* 1.3 62.2 + - - +
227A CYS* 3.0 22.3 - - + +
228A VAL* 3.2 9.2 + - - +
247A LEU* 5.7 2.5 - - + -
250A ALA* 4.5 13.0 - - + -
258A VAL* 4.1 9.9 - - + +
261A MET* 3.7 37.9 - - + +
262A VAL* 4.0 24.2 - - + -
265A LYS* 4.1 15.3 - - + -
269A LEU* 4.7 9.8 - - + +
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Residues in contact with GLU 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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186A SER 6.2 0.4 - - - +
221A LEU 4.7 0.6 + - - +
222A LEU* 3.7 13.5 + - + +
223A ALA 3.3 0.2 - - - -
224A VAL* 1.3 75.7 - - - +
226A ALA* 1.3 66.4 + - - +
228A VAL* 2.9 22.7 + - - +
229A ASN* 3.1 34.4 + - - +
261A MET* 5.8 1.3 - - + +
265A LYS* 2.7 44.3 + - - +
268A GLU* 5.1 3.8 - - - +
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Residues in contact with ALA 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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185A ALA* 4.6 10.1 - - + +
188A LEU* 4.2 28.7 - - + -
189A GLY 5.0 4.0 - - - +
208A PHE* 4.3 6.5 - - + -
222A LEU 3.7 6.7 + - - +
223A ALA* 3.2 16.2 + - - +
225A GLU* 1.3 77.9 - - - +
227A CYS* 1.3 57.9 - - - +
229A ASN* 3.3 11.1 + - - +
230A ILE* 2.8 38.3 + - + +
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Residues in contact with CYS 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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208A PHE* 3.6 21.5 - - + -
223A ALA 2.9 13.2 + - - +
224A VAL* 3.0 17.5 - - - +
225A GLU 3.0 0.2 - - - -
226A ALA* 1.3 75.5 - - - +
228A VAL* 1.3 63.0 + - - +
230A ILE* 4.0 2.7 - - - +
231A ALA* 3.1 23.5 + - - +
243A VAL* 3.7 26.1 - - - +
247A LEU* 4.1 29.2 - - + -
269A LEU* 4.2 9.6 - - + +
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Residues in contact with VAL 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 VAL 3.6 12.1 - - - +
225A GLU* 2.9 16.6 + - - +
227A CYS* 1.3 77.8 - - - +
229A ASN* 1.3 64.9 + - - +
231A ALA* 3.4 4.3 + - - +
232A GLN* 3.0 49.9 + - + +
265A LYS* 4.5 18.2 - - + -
268A GLU* 4.0 34.1 - - + +
269A LEU* 3.7 28.7 - - + -
272A ALA* 4.3 1.5 - - + +
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Residues in contact with ASN 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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189A GLY* 3.7 32.1 - - - +
190A GLU 5.0 0.3 + - - -
225A GLU* 3.1 35.6 + - - +
226A ALA* 3.5 7.7 - - - +
228A VAL* 1.3 79.7 - - - +
230A ILE* 1.3 62.4 + - + +
232A GLN* 3.3 27.4 + - - +
233A LEU* 3.4 21.7 + - + +
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Residues in contact with ILE 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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188A LEU* 4.5 7.4 - - + -
189A GLY* 5.6 1.6 - - - -
192A ALA* 5.0 7.9 - - + -
200A VAL* 4.7 9.6 - - + -
204A ILE* 3.6 28.5 - - + -
205A ILE* 4.0 15.7 - - + -
208A PHE* 3.6 35.0 - - + -
226A ALA* 2.8 26.4 + - + +
227A CYS* 4.1 4.0 - - - +
229A ASN* 1.3 75.3 - - + +
231A ALA* 1.3 62.0 + - - +
233A LEU* 3.3 14.2 + - - +
234A LEU* 3.3 35.4 + - + +
243A VAL* 4.3 7.9 - - + -
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Residues in contact with ALA 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 CYS* 3.1 19.0 + - - +
228A VAL* 3.8 4.7 - - - +
230A ILE* 1.3 77.1 - - - +
232A GLN* 1.3 63.3 + - - +
233A LEU 3.3 0.5 + - - -
234A LEU 3.4 16.6 + - - +
239A LEU* 4.0 27.4 - - + +
243A VAL* 4.7 12.7 - - + +
269A LEU* 6.1 2.2 - - + -
272A ALA* 4.0 28.0 - - + +
273A VAL* 5.2 2.2 - - + +
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Residues in contact with GLN 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 VAL* 3.0 34.8 + - - +
229A ASN* 3.6 24.6 + - - +
230A ILE 3.2 0.2 - - - -
231A ALA* 1.3 76.9 - - - +
233A LEU* 1.3 61.6 + - + +
234A LEU 3.5 2.6 + - - +
268A GLU* 5.4 3.8 + - - +
272A ALA* 4.0 18.1 - - + +
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Residues in contact with LEU 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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189A GLY 4.7 2.2 - - - +
192A ALA* 3.9 38.6 - - + +
193A LYS* 3.2 48.7 - - + +
197A LEU* 3.5 27.9 - - + +
200A VAL* 5.2 7.6 - - + -
229A ASN* 3.6 17.3 - - + +
230A ILE* 3.3 10.0 + - - +
231A ALA 3.2 0.8 - - - -
232A GLN* 1.3 81.6 - - + +
234A LEU* 1.3 62.9 + - + +
235A PRO* 4.5 0.9 - - - +
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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