Contacts of the helix formed by residues 213 - 229 (chain A) in PDB entry 6PUO
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 GLY 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLY 3.7 2.5 - - - -
177A ALA 3.4 14.1 - - - -
178A LYS 3.4 16.6 - - - -
179A ASN* 4.1 13.7 - - - +
180A PHE* 4.4 6.1 - - - -
212A THR* 1.3 75.7 + - - +
214A VAL* 1.3 60.0 + - - -
216A LYS* 2.9 26.9 + - - +
217A GLN* 3.5 9.4 + - - +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A VAL* 4.2 21.5 - - + -
174A THR 4.4 4.7 - - - +
175A GLY* 3.7 8.7 - - - +
176A GLY 3.3 35.3 + - - +
180A PHE* 3.6 21.0 - - + -
190A PHE* 6.0 0.4 - - + -
213A GLY* 1.3 70.3 - - - -
215A MET* 1.3 59.5 + - + +
217A GLN* 2.9 25.5 + - + +
218A VAL* 3.2 16.1 + - + +
330A LEU* 3.7 32.5 - - + -
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Residues in contact with MET 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLY 5.8 1.1 - - - +
176A GLY 4.5 3.8 - - - +
177A ALA* 4.0 29.4 - - + -
207A THR* 3.5 13.7 - - - +
208A GLY* 3.2 39.3 - - - +
210A SER* 3.0 34.5 - - - +
212A THR* 3.5 18.6 - - + +
213A GLY 3.2 0.4 - - - -
214A VAL* 1.3 77.7 - - + +
216A LYS* 1.3 62.2 + - - +
218A VAL* 3.6 17.8 - - - +
219A GLY 3.9 1.6 + - - -
278A ASP* 3.4 9.9 - - - +
281A HIS* 3.7 9.4 + - - -
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 3.5 35.6 + - - +
191A ARG* 6.1 0.2 - - - +
210A SER 4.3 0.2 + - - -
211A HIS* 3.3 45.1 - - + +
212A THR 3.4 3.7 + - - -
213A GLY 2.9 12.0 + - - +
215A MET* 1.3 78.7 - - - +
217A GLN* 1.3 77.4 + - - +
219A GLY* 3.0 13.9 + - - -
220A GLU* 3.1 32.0 + - - +
278A ASP* 3.7 11.5 - - - +
280A ASN* 4.9 0.7 + - - -
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Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASN* 5.1 2.0 + - - +
180A PHE* 3.4 53.5 + - - -
181A ASN* 4.9 0.8 - - - +
182A MET* 3.4 26.3 - - - +
187A LYS* 4.3 11.2 - - - +
190A PHE* 5.3 11.9 - - + -
191A ARG* 4.5 14.4 + - + +
213A GLY 3.7 12.7 + - - +
214A VAL* 2.9 10.8 + - + +
216A LYS* 1.3 87.5 - - - +
218A VAL* 1.3 64.1 + - - +
220A GLU* 3.0 27.8 + - - +
221A ALA* 3.1 6.9 + - - +
330A LEU* 5.6 3.3 - - + +
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Residues in contact with VAL 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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173A VAL* 4.8 14.4 - - + -
190A PHE* 5.2 9.3 - - + -
194A LEU* 3.8 27.1 - - + -
205A ILE* 4.6 19.3 - - + -
207A THR* 4.7 6.7 - - + -
214A VAL* 3.2 19.3 + - + +
215A MET* 3.6 16.6 - - - +
217A GLN* 1.3 76.9 - - - +
219A GLY* 1.3 66.0 + - - +
221A ALA* 3.0 18.4 + - - +
222A VAL* 3.1 19.4 + - + +
238A THR* 5.9 0.9 - - + -
281A HIS* 4.6 13.0 - - + -
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Residues in contact with GLY 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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215A MET 3.9 4.4 + - - -
216A LYS 3.0 9.4 + - - -
218A VAL* 1.3 82.8 - - - +
220A GLU* 1.3 62.6 + - - +
222A VAL* 3.0 10.5 + - - +
223A ARG 2.9 17.8 + - - -
278A ASP* 4.8 2.7 - - - -
280A ASN* 3.1 32.5 + - - +
281A HIS* 5.2 7.6 - - - -
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Residues in contact with GLU 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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191A ARG* 3.8 26.6 + - - +
211A HIS* 6.2 0.2 - - - -
216A LYS* 3.1 32.5 + - - +
217A GLN* 3.0 18.5 + - - +
219A GLY* 1.3 75.9 - - - +
221A ALA* 1.3 59.8 - - - +
223A ARG* 3.0 38.7 + - - +
224A ASP* 2.9 28.0 + - - +
280A ASN* 3.7 8.3 + - - +
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Residues in contact with ALA 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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190A PHE* 5.8 1.1 - - + -
191A ARG* 3.7 43.4 - - + +
194A LEU* 5.1 9.9 - - + -
195A VAL* 4.7 10.8 - - + +
217A GLN 3.1 5.1 + - - +
218A VAL* 3.0 14.1 + - - +
220A GLU* 1.3 76.9 - - - +
222A VAL* 1.3 64.5 + - + +
224A ASP* 3.0 19.8 + - - +
225A PHE* 3.2 10.6 + - - +
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 6.4 0.4 - - + -
205A ILE* 5.7 4.0 - - + -
218A VAL* 3.4 20.2 - - + +
219A GLY* 3.0 12.7 + - - +
221A ALA* 1.3 76.1 - - + +
223A ARG* 1.3 63.4 + - - +
225A PHE* 3.0 16.2 + - - +
226A SER* 3.1 9.9 + - - -
236A LEU* 4.3 32.5 - - + +
238A THR* 4.1 24.5 - - + +
280A ASN* 4.2 19.7 - - + +
281A HIS* 6.3 0.7 - - + +
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Residues in contact with ARG 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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191A ARG* 5.9 0.6 - - - +
219A GLY 2.9 11.7 + - - +
220A GLU* 3.0 37.6 + - - +
222A VAL* 1.3 78.7 - - - +
224A ASP* 1.3 71.3 + - - +
226A SER* 2.3 34.7 + - - +
227A LEU* 2.9 15.4 + - - +
280A ASN* 4.0 22.1 - - - +
505B GLU 4.2 17.0 + - - -
506B ASN* 5.0 10.1 - - - +
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Residues in contact with ASP 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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191A ARG* 3.8 30.9 + - + +
195A VAL* 6.3 1.8 - - + -
220A GLU 2.9 15.2 + - - +
221A ALA* 3.0 10.5 + - - +
223A ARG* 1.3 93.7 + - - +
225A PHE* 1.3 55.5 + - - +
227A LEU* 3.0 23.7 + - - +
228A SER* 3.0 12.5 + - - -
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Residues in contact with PHE 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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195A VAL* 3.6 23.5 - - + +
199A GLN* 3.8 31.2 - - + -
221A ALA 3.2 5.0 + - - +
222A VAL 3.0 10.1 + - - +
224A ASP* 1.3 76.2 - - - +
226A SER* 1.3 56.0 + - - +
228A SER* 2.9 13.7 + - - +
229A SER* 2.6 40.0 + - - -
230A SER* 4.8 11.7 - - - -
231A TYR 4.4 13.0 - - - -
232A LYS 4.3 13.2 - - - -
233A GLU* 4.5 15.5 - - + -
236A LEU* 3.6 31.9 - - + -
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Residues in contact with SER 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 VAL 3.1 8.1 + - - -
223A ARG* 2.3 41.8 + - - +
225A PHE* 1.3 75.1 - - - +
227A LEU* 1.3 63.6 + - - +
229A SER* 4.0 14.6 - - - +
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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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223A ARG* 2.9 12.6 + - - +
224A ASP* 3.0 18.1 + - - +
226A SER* 1.3 78.7 + - - +
228A SER* 1.3 60.7 + - - +
505B GLU* 5.9 12.1 - - + +
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Residues in contact with SER 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 ASP 3.0 10.2 + - - -
225A PHE* 2.9 19.8 + - - -
227A LEU* 1.3 78.9 - - - +
229A SER* 1.3 69.7 + - - +
230A SER* 3.4 10.2 + - - -
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Residues in contact with SER 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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225A PHE* 2.6 30.6 + - - -
226A SER* 4.0 14.6 - - - -
228A SER* 1.3 74.4 - - - +
230A SER* 1.3 66.0 + - - +
231A TYR* 3.6 2.9 - - - -
233A GLU* 4.8 17.7 - - - +
1134B GLN* 3.7 10.9 + - - +
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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