Contacts of the helix formed by residues 212 - 223 (chain C) in PDB entry 1XPU
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 ARG 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337B GLY 2.8 36.1 + - - +
338B THR* 3.4 12.1 - - - +
339B GLY 4.5 1.8 - - - -
340B ASN* 4.9 0.8 - - - +
366B ARG* 3.3 35.8 - - - +
210C ASP 5.4 0.7 - - - +
211C GLU* 1.3 80.4 - - - +
213C PRO* 1.3 72.9 - - + +
214C GLU* 3.3 28.8 + - - +
215C GLU* 3.0 38.8 + - + +
216C VAL* 3.0 22.9 + - - +
231C THR* 4.1 1.6 - - - -
232C PHE* 3.7 16.2 - - + -
3600C AGS 3.5 13.7 + - - -
3701C FPD 3.2 32.1 + - + +
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Residues in contact with PRO 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B THR* 3.2 20.2 + - - +
173B ARG* 3.7 11.0 - - - +
302B GLY 4.3 4.0 - - - +
305B ARG* 3.9 26.5 - - + +
212C ARG* 1.3 87.2 - - + +
214C GLU* 1.3 58.6 + - - +
216C VAL* 3.5 16.3 + - + +
217C THR* 3.7 5.0 + - - +
231C THR* 3.8 20.6 - - + -
232C PHE* 3.6 15.9 - - + -
233C ASP* 3.4 24.0 - - - +
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Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 3.5 13.4 - - - +
138B PRO* 3.9 20.6 - - - +
139B LEU* 3.7 31.8 + - + +
140B HIS* 4.9 3.8 + - + +
171B GLY 4.9 1.9 - - - +
173B ARG* 2.7 33.7 + - - -
304B ALA 4.2 5.9 - - - +
305B ARG* 5.1 6.0 - - + +
340B ASN* 3.2 25.6 + - - +
212C ARG* 3.4 23.4 + - - +
213C PRO* 1.3 79.1 - - - +
215C GLU* 1.3 63.8 + - - +
217C THR* 3.3 14.4 + - - -
218C GLU* 3.7 11.4 + - - +
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.1 16.0 - - - +
366B ARG* 4.9 3.8 - - - -
367B LYS* 4.9 3.5 - - - +
185C THR* 4.0 20.0 - - + +
211C GLU* 3.5 28.7 - - + +
212C ARG* 3.0 47.6 + - + +
214C GLU* 1.3 79.7 - - - +
216C VAL* 1.3 63.2 + - - +
218C GLU* 3.1 30.3 - - - +
219C MET* 3.4 23.4 + - - +
3600C AGS 4.5 7.5 + - - -
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Residues in contact with VAL 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 4.3 7.4 - - + -
211C GLU* 4.2 15.0 - - + -
212C ARG 3.0 16.9 + - - +
213C PRO* 3.5 12.1 - - + +
214C GLU 3.2 0.2 - - - -
215C GLU* 1.3 78.1 - - - +
217C THR* 1.3 59.2 + - + +
219C MET* 3.5 3.6 + - - +
220C GLN* 2.7 48.0 + - - +
227C VAL* 4.6 2.9 - - + +
229C ALA* 3.6 35.7 - - + -
230C SER 4.9 0.4 - - - +
231C THR* 4.2 17.9 - - + -
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Residues in contact with THR 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 5.3 10.8 - - + -
137B THR* 2.6 53.0 + - - +
138B PRO* 4.3 1.9 - - - +
213C PRO 3.7 3.5 + - - +
214C GLU 3.3 4.5 + - - -
216C VAL* 1.3 76.7 - - + +
218C GLU* 1.3 59.1 + - - +
220C GLN* 3.3 19.4 - - - +
221C ARG* 2.8 53.5 + - - +
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Residues in contact with GLU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 3.1 31.0 - - + +
367B LYS* 3.4 20.1 + - - -
185C THR* 4.0 3.6 - - - +
189C GLN* 2.8 28.2 + - - +
214C GLU 3.7 13.1 + - - +
215C GLU* 3.1 26.0 - - - +
217C THR* 1.3 82.7 + - - +
219C MET* 1.3 63.3 + - - +
221C ARG* 3.5 5.3 + - - +
222C LEU* 3.3 31.8 + - + +
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Residues in contact with MET 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C THR* 4.8 7.0 - - + +
188C LEU* 4.0 31.2 - - + +
189C GLN* 3.4 35.7 - - + +
206C VAL* 3.7 26.7 - - + -
208C LEU* 4.1 28.3 - - + -
211C GLU* 5.5 1.1 - - - +
215C GLU 3.4 17.7 + - - +
216C VAL 3.6 3.6 - - - +
217C THR 3.2 0.2 - - - -
218C GLU* 1.3 77.5 - - - +
220C GLN* 1.3 66.9 + - - +
222C LEU* 3.4 1.7 + - - -
223C VAL* 3.1 47.0 + - + +
227C VAL* 4.6 2.7 - - + -
263C LEU* 6.0 0.4 - - + -
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Residues in contact with GLN 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 6.1 1.4 - - - +
69C ASP 4.8 11.1 + - - -
71C SER* 5.5 2.2 + - - -
216C VAL* 2.7 34.0 + - - +
217C THR* 3.3 20.8 - - - +
219C MET* 1.3 74.5 - - - +
221C ARG* 1.3 62.3 + - + +
223C VAL 3.8 12.3 - - - +
225C GLY 5.5 0.3 - - - +
227C VAL* 3.9 38.4 + - + +
229C ALA* 5.5 2.8 - - - +
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Residues in contact with ARG 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 3.5 21.1 - - - +
138B PRO* 5.6 7.9 - - - +
308B GLU* 2.8 38.6 + - - -
217C THR* 2.8 29.2 + - - +
218C GLU* 4.0 5.2 - - - +
220C GLN* 1.3 83.0 - - + +
222C LEU* 1.3 64.7 + - + +
223C VAL 3.6 1.5 - - - +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 3.8 35.4 - - + +
193C GLN* 4.5 27.6 - - + +
218C GLU* 3.3 25.3 + - + +
219C MET* 4.2 2.2 - - - +
221C ARG* 1.3 80.6 - - + +
223C VAL* 1.3 65.5 + - + +
224C LYS* 3.3 11.1 + - - +
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Residues in contact with VAL 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLN* 5.3 2.7 - - - -
192C ALA* 3.9 22.0 - - + -
193C GLN* 6.4 0.4 - - - -
204C LEU* 4.1 13.7 - - + -
206C VAL* 3.7 27.8 - - + -
219C MET* 3.1 40.9 + - + +
220C GLN 3.8 12.0 - - - +
221C ARG 4.7 1.4 - - - +
222C LEU* 1.3 76.1 - - + +
224C LYS* 1.3 68.7 + - - +
225C GLY* 3.2 16.5 + - - +
226C GLU 5.0 0.2 - - - +
227C VAL* 3.8 14.3 - - + +
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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