Contacts of the helix formed by residues 209 - 231 (chain A) in PDB entry 3P1Q
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 SER 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A THR 4.0 1.2 + - - -
208A LEU* 1.3 75.0 - - - +
210A GLU* 1.3 65.4 + - - +
211A ASP* 3.5 8.1 + - - +
212A SER* 3.1 24.7 + - - -
213A TYR* 2.8 22.5 + - - +
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Residues in contact with GLU 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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208A LEU 4.1 0.2 + - - -
209A SER* 1.3 72.2 - - - +
211A ASP* 1.3 57.3 + - - +
213A TYR* 3.4 9.3 + - - +
214A LYS* 3.0 27.2 + - - +
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A SER* 3.2 7.1 + - - +
210A GLU* 1.3 75.2 - - - +
212A SER* 1.3 66.1 + - - +
214A LYS* 3.3 15.2 + - - +
215A ASP* 3.1 19.6 + - - +
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Residues in contact with SER 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 6.0 0.3 - - - +
208A LEU* 3.6 32.6 - - - +
209A SER* 3.1 16.3 + - - -
211A ASP* 1.3 76.5 - - - +
213A TYR* 1.3 64.3 + - - +
215A ASP* 3.0 2.9 + - - +
216A SER* 2.9 28.7 + - - -
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Residues in contact with TYR 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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202A MET* 6.1 0.2 - - - +
205A LEU* 3.6 55.6 - - + +
208A LEU* 3.8 12.9 - - + +
209A SER 2.8 21.7 + - - +
210A GLU* 3.4 9.6 - - - +
212A SER* 1.3 72.0 - - - +
214A LYS* 1.3 58.0 + - - +
216A SER* 3.9 0.9 - - - -
217A THR* 2.8 51.7 + - + +
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Residues in contact with LYS 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 GLU 3.0 13.3 + - - +
211A ASP* 3.6 14.2 + - - +
213A TYR* 1.3 79.9 - - + +
215A ASP* 1.4 79.5 + - - +
217A THR* 2.8 19.6 + - - +
218A LEU* 3.1 14.6 + - + +
249A FSC 4.0 36.2 + - - +
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Residues in contact with ASP 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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167A PRO* 4.5 16.4 - - + +
211A ASP 3.1 10.0 + - - +
212A SER* 3.0 7.1 + - - -
214A LYS* 1.4 84.3 - - - +
216A SER* 1.3 67.4 + - - +
218A LEU* 3.8 6.9 + - + +
219A ILE* 3.6 17.3 - - - +
249A FSC 3.9 35.6 - - + +
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Residues in contact with SER 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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165A THR* 2.7 41.2 + - - -
167A PRO* 4.7 5.5 - - - +
170A LEU* 3.6 15.1 - - - +
205A LEU* 4.1 12.8 - - - -
208A LEU* 3.6 4.4 - - - +
212A SER* 2.9 19.1 + - - -
213A TYR 3.9 2.2 - - - -
215A ASP* 1.3 76.8 - - - +
217A THR* 1.4 66.2 + - - +
218A LEU 3.1 1.2 + - - -
219A ILE 3.2 4.2 + - - -
220A MET* 2.9 25.2 + - - +
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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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205A LEU* 4.0 28.9 - - + -
213A TYR* 2.8 46.7 + - + +
214A LYS* 2.8 17.8 + - - +
216A SER* 1.4 78.4 - - - +
218A LEU* 1.3 56.2 + - - +
220A MET* 3.5 12.3 - - + +
221A GLN* 2.9 28.9 + - - +
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Residues in contact with LEU 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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214A LYS* 3.1 17.0 + - + +
215A ASP* 3.9 8.7 - - + +
216A SER 3.1 1.0 + - - -
217A THR* 1.3 78.0 + - - +
219A ILE* 1.3 66.6 + - + +
221A GLN* 3.3 15.1 + - - +
222A LEU* 3.3 24.7 + - + +
249A FSC 3.0 58.6 - - + -
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Residues in contact with ILE 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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167A PRO* 4.6 9.6 - - + +
170A LEU* 3.6 36.8 - - + +
171A GLY* 3.7 16.2 - - - +
174A LEU* 4.7 4.5 - - + -
215A ASP 3.6 17.3 - - - +
216A SER 3.7 4.0 - - - +
218A LEU* 1.3 75.9 - - + +
220A MET* 1.3 66.5 + - - +
222A LEU* 3.0 21.0 + - + +
223A LEU* 3.0 14.4 + - + +
249A FSC 3.3 43.3 - - + -
374P VAL* 4.5 13.2 - - + -
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Residues in contact with MET 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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170A LEU* 4.0 9.9 - - + -
198A PHE* 3.4 29.0 - - + +
201A ALA* 3.7 21.3 - - + -
202A MET* 3.4 55.4 - - + +
205A LEU* 4.0 20.2 - - + -
216A SER* 2.9 20.8 + - - +
217A THR* 3.5 20.6 - - + +
218A LEU 3.2 0.2 - - - -
219A ILE* 1.3 78.1 - - - +
221A GLN* 1.3 56.7 + - - +
223A LEU* 3.2 13.9 + - + +
224A ARG 2.9 22.5 + - - -
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Residues in contact with GLN 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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198A PHE* 5.4 0.2 - - - -
217A THR 2.9 13.7 + - - +
218A LEU* 3.5 12.1 - - - +
219A ILE 3.1 0.4 - - - -
220A MET* 1.3 75.8 - - - +
222A LEU* 1.3 60.7 + - + +
224A ARG* 3.2 23.0 + - - +
225A ASP* 2.7 60.4 + - - +
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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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174A LEU* 3.7 31.4 - - + -
218A LEU* 3.3 20.8 + - + +
219A ILE* 3.0 18.2 + - + +
221A GLN* 1.3 75.3 - - + +
223A LEU* 1.4 66.3 + - - +
225A ASP* 3.3 13.4 + - - +
226A ASN* 3.0 27.7 + - - +
372P LYS* 3.7 30.2 - - + +
373P SEP 4.4 4.9 - - - +
374P VAL* 4.2 20.0 - - + -
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Residues in contact with LEU 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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170A LEU* 4.1 18.2 - - + +
173A ALA 4.5 2.7 - - - +
174A LEU* 3.7 42.4 - - + +
177A SER* 5.4 0.2 - - - -
194A ALA* 4.0 32.7 - - + +
197A THR* 3.7 25.8 - - + -
198A PHE* 4.2 19.3 - - + +
219A ILE 3.0 18.2 + - - +
220A MET* 3.4 12.3 - - - +
222A LEU* 1.4 75.5 - - - +
224A ARG* 1.4 56.7 + - - +
226A ASN* 3.2 4.9 + - - +
227A LEU* 2.9 33.8 + - - +
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Residues in contact with ARG 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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198A PHE* 3.3 48.2 - - + -
199A ASP* 4.7 4.0 + - - -
220A MET 2.9 14.0 + - - +
221A GLN* 3.6 27.4 - - - +
223A LEU* 1.4 75.8 - - - +
225A ASP* 1.3 59.6 - - - +
227A LEU* 3.2 33.4 + - - +
228A THR* 2.9 45.5 + - - +
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Residues in contact with ASP 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 GLN* 2.7 50.9 + - - +
222A LEU* 3.5 17.5 - - - +
224A ARG* 1.3 73.4 - - - +
226A ASN* 1.3 58.8 + - - +
228A THR* 3.4 6.8 + - - -
229A LEU* 3.0 28.2 + - - +
372P LYS* 2.8 38.6 + - + +
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Residues in contact with ASN 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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174A LEU* 3.5 15.9 + - + +
177A SER* 5.4 0.2 + - - -
178A VAL* 3.6 15.2 - - - +
194A ALA* 5.4 1.8 - - + -
222A LEU 3.0 11.7 + - - +
223A LEU* 3.7 8.1 - - - +
224A ARG 3.2 0.2 - - - -
225A ASP* 1.3 74.1 - - - +
227A LEU* 1.3 61.5 + - - +
229A LEU* 3.1 4.8 + - - +
230A TRP* 2.8 63.6 + - + -
371P ARG* 3.4 7.1 - - - -
372P LYS* 2.8 50.0 + - - +
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Residues in contact with LEU 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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191A ILE* 3.7 39.5 - - + +
194A ALA* 4.0 14.8 - - + +
195A LYS* 3.7 36.3 - - + +
198A PHE* 4.7 4.0 - - + -
223A LEU 2.9 21.1 + - - +
224A ARG* 3.6 40.2 - - - +
226A ASN* 1.3 76.1 - - - +
228A THR* 1.3 59.8 + - - +
230A TRP* 4.7 2.7 - - + -
231A THR* 2.5 41.8 + - + +
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Residues in contact with THR 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 ARG* 2.9 30.6 + - - +
225A ASP* 3.7 7.6 - - - -
227A LEU* 1.3 78.7 - - - +
229A LEU* 1.3 62.2 + - - +
231A THR* 3.3 18.4 - - - +
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Residues in contact with LEU 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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181A TYR* 5.3 0.3 + - - -
225A ASP 3.0 17.9 + - - +
226A ASN* 3.1 5.6 + - - +
228A THR* 1.3 79.1 - - - +
230A TRP* 1.3 72.7 + - + +
231A THR* 3.6 2.3 + - - +
369P LYS* 4.0 23.6 - - - +
370P ARG 4.3 0.9 - - - -
371P ARG* 3.7 40.4 - - + +
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Residues in contact with TRP 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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177A SER* 3.1 31.9 - - - -
178A VAL* 4.0 9.0 - - + -
181A TYR* 3.4 72.9 + + + -
190A ALA* 3.8 11.0 - - + -
191A ILE* 3.9 28.8 - - + +
194A ALA* 4.7 4.0 - - + -
226A ASN* 2.8 54.1 + - + +
227A LEU* 4.2 4.3 - - - +
229A LEU* 1.3 102.3 - - + +
231A THR* 1.3 62.7 + - - +
371P ARG* 4.0 15.1 - - + +
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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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191A ILE* 3.9 33.9 - - + -
195A LYS* 4.8 8.5 - - - +
227A LEU* 2.5 28.7 + - + +
228A THR* 3.3 15.6 - - - +
229A LEU 4.3 2.4 - - - +
230A TRP* 1.3 84.9 - - + +
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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