Contacts of the strand formed by residues 186 - 193 (chain A) in PDB entry 2IBS
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 LYS 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A GLY* 1.3 72.8 - - - -
187A THR* 1.3 62.6 + - - +
207A ARG* 3.8 5.5 - - - +
208A PHE* 3.5 5.2 - - - -
209A GLN* 2.8 68.1 + - + +
211A SER* 3.1 29.9 + - - +
212A GLY* 4.0 10.9 - - - +
213A LYS 3.6 22.0 - - - +
214A GLY 3.7 5.2 - - - +
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Residues in contact with THR 187 (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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168A TRP* 4.5 4.7 - - + -
181A LEU* 3.9 9.4 + - + +
185A GLY 4.6 0.2 + - - -
186A LYS* 1.3 76.7 - - - +
188A SER* 1.3 63.7 + - - +
189A VAL* 4.1 15.9 - - + -
206A ILE* 3.7 34.1 - - + -
207A ARG 3.5 2.7 - - - +
208A PHE* 3.7 14.3 - - + +
214A GLY 3.0 9.0 + - - +
215A LEU* 3.3 8.4 - - + +
216A SER* 2.9 25.1 + - - -
238A TRP* 3.8 26.0 - - + -
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Residues in contact with SER 188 (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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187A THR* 1.3 72.2 - - - +
189A VAL* 1.3 62.0 + - - +
190A TYR* 3.6 28.3 + - - -
205A VAL 3.7 0.5 - - - +
206A ILE* 3.4 5.0 - - - +
207A ARG* 2.7 52.1 + - - +
216A SER* 3.3 12.9 + - - -
218A TRP* 3.6 16.0 + - - -
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Residues in contact with VAL 189 (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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168A TRP* 3.8 27.6 - - + -
169A LEU* 3.9 21.8 - - + -
187A THR* 4.1 4.0 - - + -
188A SER* 1.3 77.7 - - - +
190A TYR* 1.3 60.8 + - - +
191A TYR* 4.8 0.7 - - + +
204A VAL* 4.2 22.0 - - + -
205A VAL 3.4 3.6 - - - +
206A ILE* 4.9 0.9 - - + -
215A LEU* 3.8 21.1 - - + -
216A SER 2.8 10.2 + - - +
217A LEU* 3.9 22.6 - - + +
218A TRP* 2.7 35.3 + - - +
243A ILE* 4.5 0.7 - - + -
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Residues in contact with TYR 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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30A PHE* 3.8 24.2 - + + -
34A LEU* 3.5 34.6 - - + +
188A SER* 3.6 32.9 + - - -
189A VAL* 1.3 72.9 - - - +
191A TYR* 1.3 64.6 + - - +
192A LEU* 3.4 2.3 + - + +
204A VAL* 3.3 4.1 - - - -
205A VAL* 2.7 63.8 + - + +
207A ARG* 3.8 16.3 - - + -
218A TRP* 3.5 46.2 + + + -
220A THR* 4.4 5.2 - - + -
229A PRO* 4.0 14.1 - - + -
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Residues in contact with TYR 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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189A VAL* 4.1 1.8 - - + +
190A TYR* 1.3 69.0 - - - +
192A LEU* 1.3 58.7 + - - +
193A GLY* 3.6 20.3 - - - -
202A SER* 3.7 9.9 - - - -
204A VAL* 3.8 17.9 - - + +
217A LEU* 5.8 0.4 - - + -
218A TRP 3.0 10.9 + - - +
219A ASP* 3.9 5.6 - - - +
220A THR* 2.6 32.2 + - - +
245A PHE* 3.6 24.2 - + + -
385A ARG* 5.3 1.2 + - - -
389A ARG* 3.2 36.4 - - - +
390A ASP* 2.5 38.4 + - - -
391A PHE* 3.6 30.1 - + - -
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Residues in contact with LEU 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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27A VAL* 4.0 19.1 - - + -
30A PHE* 4.3 11.7 - - + -
163A VAL* 4.4 8.5 - - + -
190A TYR 3.4 7.8 + - - +
191A TYR* 1.3 81.7 - - - +
193A GLY* 1.3 63.1 + - - +
195A VAL* 3.5 37.5 - - + +
203A ALA* 3.0 13.4 + - + +
205A VAL* 3.6 24.9 - - + +
220A THR* 3.9 19.1 + - + +
227A PHE* 3.7 38.6 - - + -
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Residues in contact with GLY 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 TYR* 3.6 27.5 - - - -
192A LEU* 1.3 79.3 - - - +
194A GLU* 1.3 60.5 + - - -
195A VAL* 2.9 15.0 + - - +
201A VAL 3.9 0.2 - - - +
202A SER* 3.7 9.2 - - - -
203A ALA* 2.8 28.9 + - - +
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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