Contacts of the strand formed by residues 229 - 236 (chain C) in PDB entry 2PWP
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 CYS 229 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B SER* 4.3 9.6 - - - +
193C SER* 3.3 38.8 + - - -
194C LEU* 4.4 7.6 - - - -
195C TRP* 3.9 23.6 - - - -
219C ASN* 3.3 23.6 - - - +
220C ILE 3.0 19.7 - - - +
221C SER* 4.5 1.3 - - - -
222C ILE* 3.7 6.8 + - - +
225C TYR* 4.2 5.0 + - - +
226C PRO 3.5 5.5 - - - +
227C CYS 4.1 3.8 - - - -
228C GLY* 1.3 79.1 - - - +
230C ILE* 1.3 62.5 + - - +
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Residues in contact with ILE 230 (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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63C TYR* 3.9 26.9 - - + -
190C GLN* 3.5 30.7 - - + +
191C CYS 3.1 22.2 - - - +
192C GLU* 3.7 14.4 - - - +
193C SER* 4.5 0.7 - - - +
219C ASN* 4.0 4.9 - - - -
220C ILE* 2.9 35.6 + - + +
222C ILE* 4.2 6.7 - - + -
225C TYR* 3.9 30.3 - - + -
226C PRO* 6.2 0.2 - - + -
229C CYS* 1.3 76.4 - - - +
231C GLY* 1.3 59.4 + - - +
401C SPD 3.9 17.3 - - - -
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Residues in contact with GLY 231 (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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67C MET* 5.0 1.2 - - - +
190C GLN* 3.7 4.2 - - - +
191C CYS* 2.8 32.3 + - - +
192C GLU 2.8 14.0 + - - -
217C TYR* 3.2 20.8 + - - -
218C ALA 3.2 9.9 - - - -
219C ASN* 4.5 0.4 - - - -
230C ILE* 1.3 79.0 - - - +
232C ILE* 1.3 62.0 + - - +
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Residues in contact with ILE 232 (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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66C MET* 3.9 27.8 - - + +
67C MET* 4.0 16.4 - - - +
70C VAL* 4.4 9.0 - - + -
188C VAL* 3.6 25.6 - - + -
189C ALA 3.6 4.0 - - - +
217C TYR* 3.4 9.9 - - - -
218C ALA* 2.8 46.6 + - + +
220C ILE* 3.7 35.7 - - + -
231C GLY* 1.3 72.1 - - - -
233C LEU* 1.3 62.1 + - - +
234C CYS* 3.4 23.3 + - - -
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Residues in contact with LEU 233 (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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174C TYR* 3.6 37.9 - - + +
187C CYS 3.8 1.0 - - - +
188C VAL* 3.1 6.9 - - - +
189C ALA* 2.8 44.0 + - + +
191C CYS* 3.7 17.7 - - + +
204C MET* 4.1 25.8 - - + +
205C ILE* 3.7 35.7 - - + +
208C ALA* 4.3 0.9 - - + -
215C VAL* 3.8 20.2 - - + -
216C GLU 3.9 3.4 - - - +
217C TYR* 4.7 2.9 - - + -
232C ILE* 1.3 70.7 - - - +
234C CYS* 1.3 58.4 + - - +
235C CYS* 3.9 11.5 - - - -
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Residues in contact with CYS 234 (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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70C VAL* 4.4 6.3 - - - -
187C CYS 3.8 2.7 - - - -
188C VAL* 3.9 8.5 - - - -
214C LYS 3.7 1.6 - - - +
215C VAL* 3.4 5.1 - - - +
216C GLU* 2.8 50.5 + - + +
232C ILE* 3.5 35.2 - - - -
233C LEU* 1.3 71.3 - - - +
235C CYS* 1.3 62.4 + - - +
236C SER* 5.0 0.2 + - - -
242C LEU* 3.6 17.4 - - + +
269C PHE* 3.7 31.9 - - + -
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Residues in contact with CYS 235 (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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174C TYR* 4.4 8.1 - - - -
186C TYR* 3.5 7.3 - - - +
187C CYS* 2.7 42.9 + - + +
208C ALA* 3.8 28.5 - - - -
212C PHE* 3.6 34.0 - - + -
214C LYS 3.7 3.4 - - - -
215C VAL* 4.8 2.0 - - - +
233C LEU* 3.9 21.5 - - - -
234C CYS* 1.3 75.7 - - - +
236C SER* 1.3 63.0 + - - +
242C LEU* 3.8 2.2 - - - +
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Residues in contact with SER 236 (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 GLY 4.5 0.2 - - - -
186C TYR* 3.3 29.4 - - - -
212C PHE* 3.3 7.8 - - - +
213C LYS 3.3 6.4 + - - -
214C LYS 2.8 35.4 + - - -
216C GLU* 4.6 1.0 + - - -
234C CYS 5.0 0.2 + - - -
235C CYS* 1.3 73.0 - - - +
237C LYS* 1.3 59.9 + - - +
238C THR* 3.8 10.3 - - - -
241C GLY* 3.3 29.8 - - - -
242C LEU* 3.4 11.4 + - - +
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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