Contacts of the strand formed by residues 189 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 3.6 7.4 - - - -
188A VAL* 1.3 76.1 - - - +
190A ALA* 1.3 59.8 + - - -
219A ALA* 3.3 2.1 - - - -
220A GLY 2.8 34.2 + - - -
252A THR* 3.1 26.1 - - - +
255A ILE* 4.1 8.7 - - - -
256A ILE* 3.6 4.0 - - - +
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Residues in contact with ALA 190 (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 VAL* 3.4 6.3 - - + +
170A ILE* 3.6 44.2 - - + -
171A ASN* 2.9 31.7 + - - +
189A GLY* 1.3 74.7 - - - +
191A VAL* 1.3 71.1 + - - +
203A ASN* 5.1 0.7 + - - -
217A VAL* 5.0 0.4 - - + -
218A VAL 3.2 12.1 - - - +
219A ALA* 4.2 5.2 - - + -
252A THR* 3.9 1.1 - - - +
255A ILE* 3.5 5.4 - - - +
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Residues in contact with VAL 191 (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 VAL* 3.9 8.1 - - - -
190A ALA* 1.3 81.2 - - - +
192A ARG* 1.3 59.4 + - - +
193A ILE* 4.1 13.2 - - + -
202A VAL* 3.8 12.6 - - + -
203A ASN* 3.5 15.0 - - - +
216A LEU 3.9 0.2 - - - +
217A VAL* 3.4 3.2 - - - +
218A VAL* 2.9 31.4 + - + +
248A GLY* 3.6 35.4 - - - +
251A TYR* 3.8 24.7 - - + -
252A THR* 4.1 2.7 - - + +
255A ILE* 3.8 16.2 - - + -
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Residues in contact with ARG 192 (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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133A ILE* 5.9 1.8 - - - +
164A GLU* 3.9 18.6 - - - +
166A ASP* 2.7 43.8 + - - -
167A VAL* 3.5 19.0 - - + +
191A VAL* 1.3 75.1 - - - +
193A ILE* 1.3 68.2 + - - +
202A VAL* 3.5 4.3 - - - +
203A ASN* 2.7 36.4 + - - +
204A PRO* 3.8 31.1 + - + -
209A MET* 3.7 19.9 - - - +
214A LEU 5.7 0.2 - - - -
215A ASN* 2.8 31.7 + - - +
216A LEU 3.1 11.2 - - - +
217A VAL* 3.7 20.2 - - + +
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Residues in contact with ILE 193 (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 VAL* 4.1 6.5 - - + -
192A ARG* 1.3 84.1 - - - +
194A GLY* 1.3 69.8 + - - +
200A TYR* 4.4 12.8 - - + -
201A VAL 3.5 2.5 - - - +
202A VAL* 3.7 25.6 - - + +
214A LEU* 3.5 9.0 - - + +
216A LEU* 2.7 46.5 + - + -
218A VAL* 4.7 1.3 - - + -
244A ALA* 3.9 29.8 - - + +
247A VAL* 3.9 20.9 - - + -
248A GLY* 3.6 26.2 - - - -
251A TYR* 4.1 0.9 - - + -
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Residues in contact with GLY 194 (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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193A ILE* 1.3 77.7 - - - +
195A ILE* 1.3 67.3 + - - +
196A ILE* 3.9 12.1 - - - -
200A TYR* 3.4 6.2 - - - -
201A VAL 2.8 33.1 + - - -
204A PRO* 4.1 9.8 - - - +
212A SER* 3.5 3.6 - - - -
214A LEU* 3.4 12.6 - - - -
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Residues in contact with ILE 195 (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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194A GLY* 1.3 78.8 - - - +
196A ILE* 1.3 62.3 + - - +
197A ASP 4.1 0.9 + - - -
198A GLY* 4.3 21.3 - - - +
199A GLU 3.2 8.7 - - - +
200A TYR* 3.7 33.7 - - + +
211A SER 4.0 1.0 - - - +
212A SER* 3.0 10.3 + - - -
213A THR* 3.0 42.8 + - + +
214A LEU* 3.8 27.0 - - + +
236A ILE* 4.0 17.3 - - + -
240A ASP* 4.4 11.4 - - + +
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Residues in contact with ILE 196 (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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194A GLY* 3.9 9.4 - - - -
195A ILE* 1.3 84.4 - - - +
197A ASP* 1.3 81.5 + - + +
198A GLY 3.0 1.1 - - - -
199A GLU* 2.8 27.0 + - - +
201A VAL* 4.1 24.0 - - + -
204A PRO* 4.3 3.6 - - + -
208A GLU* 3.2 42.8 - - + +
211A SER* 3.9 17.5 - - - +
212A SER* 3.6 17.0 - - - -
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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