Contacts of the strand formed by residues 189 - 196 (chain C) in PDB entry 3U1K
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 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C ASN* 3.5 7.0 - - - -
188C VAL* 1.3 75.9 - - - +
190C ALA* 1.3 60.5 + - - -
219C ALA* 3.3 2.3 - - - -
220C GLY 2.8 33.4 + - - -
252C THR* 3.0 22.2 - - - +
255C ILE* 3.9 14.1 - - - -
256C ILE* 3.7 3.6 - - - +
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Residues in contact with ALA 190 (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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167C VAL* 3.9 5.9 - - + +
170C ILE* 3.5 43.5 - - + -
171C ASN* 2.8 33.1 + - - +
188C VAL* 5.1 0.2 - - + -
189C GLY* 1.3 76.4 - - - +
191C VAL* 1.3 70.0 + - - +
203C ASN* 5.0 0.3 + - - -
217C VAL* 4.9 1.8 - - + -
218C VAL 3.2 11.7 - - - +
219C ALA* 4.2 5.4 - - + -
252C THR* 4.0 0.7 - - - -
255C ILE* 3.3 5.1 - - - +
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Residues in contact with VAL 191 (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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51C LEU* 4.3 2.7 - - + -
167C VAL* 4.3 4.5 - - - -
190C ALA* 1.3 80.1 - - - +
192C ARG* 1.3 62.5 + - - +
193C ILE* 4.2 11.2 - - + -
202C VAL* 4.0 9.9 - - + -
203C ASN* 3.3 18.2 - - - +
217C VAL* 3.4 6.8 - - - +
218C VAL* 2.9 31.6 + - + +
248C GLY* 3.6 36.3 - - - +
251C TYR* 3.9 21.1 - - + -
252C THR* 4.4 3.6 - - + +
255C ILE* 3.8 16.6 - - + -
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Residues in contact with ARG 192 (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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126C LYS* 5.1 0.2 - - - +
133C ILE* 6.0 2.0 - - - +
164C GLU* 4.0 16.8 - - - +
166C ASP* 2.8 43.4 + - - -
167C VAL* 3.3 18.8 - - + +
191C VAL* 1.3 74.9 - - - +
193C ILE* 1.3 75.9 + - - +
203C ASN* 2.7 40.7 + - - +
204C PRO* 3.8 30.0 + - + -
209C MET* 3.8 18.5 - - - +
214C LEU 5.8 0.2 - - - -
215C ASN* 2.7 33.7 + - - +
216C LEU 3.0 11.2 - - - +
217C VAL* 3.7 20.8 - - + +
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Residues in contact with ILE 193 (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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191C VAL* 4.2 8.3 - - + -
192C ARG* 1.3 89.0 - - - +
194C GLY* 1.3 71.8 + - - +
200C TYR* 4.3 13.2 - - + -
201C VAL 3.4 2.5 - - - +
202C VAL* 3.9 19.1 - - + +
214C LEU* 3.6 5.7 - - + +
216C LEU* 2.6 48.8 + - + +
218C VAL* 4.8 1.1 - - + -
244C ALA* 3.7 39.7 - - + +
247C VAL* 4.0 14.8 - - + -
248C GLY* 3.7 22.4 - - - -
251C TYR* 4.3 0.7 - - + -
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Residues in contact with GLY 194 (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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193C ILE* 1.3 76.7 - - - +
195C ILE* 1.3 65.2 + - - +
196C ILE* 3.9 10.3 - - - -
200C TYR* 3.5 4.9 - - - -
201C VAL 2.8 33.1 + - - -
204C PRO* 4.2 9.8 - - - +
212C SER* 3.3 13.5 - - - -
214C LEU* 3.4 5.8 - - - -
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Residues in contact with ILE 195 (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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194C GLY* 1.3 77.0 - - - +
196C ILE* 1.3 60.6 + - - +
197C ASP 4.1 1.0 + - - -
198C GLY* 3.6 35.4 - - - +
199C GLU 3.3 3.6 - - - +
200C TYR* 3.6 34.3 - - + -
211C SER 4.0 1.0 - - - +
212C SER* 2.8 11.2 + - - -
213C THR* 2.9 44.3 + - + +
214C LEU* 4.0 25.8 - - + +
236C ILE* 4.0 19.7 - - + -
240C ASP* 4.5 11.4 - - + +
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Residues in contact with ILE 196 (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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194C GLY* 3.9 2.9 - - - -
195C ILE* 1.3 87.4 - - - +
197C ASP* 1.3 84.6 + - - +
199C GLU* 2.8 47.9 + - - +
201C VAL* 3.6 30.1 - - + -
204C PRO* 4.7 1.8 - - + -
208C GLU* 3.5 34.8 - - + +
211C SER* 4.2 20.4 - - - +
212C SER* 3.8 13.9 - - - +
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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