Contacts of the strand formed by residues 189 - 196 (chain B) in PDB entry 3AIH
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 GLU 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ASN* 4.4 3.6 - - - +
186A ARG* 2.9 52.9 + - - -
214A LEU* 3.6 17.8 - - + +
215A SER 5.0 0.5 - - - +
217A SER* 3.2 12.7 + - - -
145B LEU 3.3 7.0 - - - -
175B TYR 3.4 10.8 - - - +
176B GLY* 4.5 5.4 - - - -
177B ASN 5.2 0.2 - - - +
186B ARG* 3.3 11.6 + - - +
187B PRO 4.8 0.2 - - - +
188B ARG* 1.3 76.6 - - - +
190B ALA* 1.3 62.6 + - - +
191B GLU* 6.0 0.3 - - - +
216B CYS 3.3 3.6 + - - -
217B SER* 3.3 14.6 + - - +
218B TYR* 2.9 28.6 + - - -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 4.2 1.1 - - - -
128B ILE* 3.8 28.5 - - + -
145B LEU* 3.9 11.0 + - + +
174B THR* 3.5 3.3 - - - -
175B TYR* 2.8 38.2 + - + +
189B GLU* 1.3 77.2 - - - +
191B GLU* 1.3 67.6 + - - +
218B TYR* 3.1 20.4 - - + +
220B LEU* 5.0 2.2 - - + -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.5 27.1 - - + +
215A SER* 2.8 34.3 + - - -
172B SER* 5.1 5.2 + - - +
173B GLN 3.5 5.6 - - - +
174B THR* 4.0 22.7 - - + +
189B GLU* 6.0 0.2 - - - +
190B ALA* 1.3 80.7 - - - +
192B VAL* 1.3 64.2 + - - +
193B ARG* 2.4 43.5 + - - +
218B TYR 2.9 8.1 + - - +
219B VAL* 3.2 7.1 - - + +
220B LEU* 2.9 24.8 + - - +
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 4.0 9.0 - - + -
128B ILE* 3.8 16.8 - - + -
172B SER* 3.3 9.7 + - - -
173B GLN* 2.8 36.1 + - + +
175B TYR* 3.6 32.5 - - + -
191B GLU* 1.3 80.2 - - - +
193B ARG* 1.3 64.3 + - - +
194B PHE* 3.5 29.4 - - + -
220B LEU* 3.3 14.1 - - + +
222B ILE* 3.6 24.0 - - + -
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PRO* 3.0 28.0 + - - +
170B TYR* 5.9 7.0 - - + +
171B HIS 4.2 4.0 - - - +
172B SER* 5.1 6.9 + - - +
191B GLU* 2.4 41.0 + - - +
192B VAL* 1.3 76.1 - - - +
194B PHE* 1.3 56.5 + - - +
195B LEU* 4.2 11.0 - - + -
219B VAL* 3.7 27.4 - - - +
220B LEU 2.8 11.2 + - - +
221B THR* 3.3 16.6 - - + +
222B ILE* 2.8 34.3 + - - +
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B PHE* 3.8 12.8 - + - -
124B TYR* 3.5 26.5 - + - -
170B TYR* 5.4 0.7 - - - -
171B HIS* 3.3 49.3 + + + +
173B GLN* 3.8 25.1 - - + -
192B VAL* 3.5 27.8 - - + -
193B ARG* 1.3 74.5 - - - +
195B LEU* 1.3 70.7 + - - +
222B ILE* 3.4 28.0 - - + +
224B THR* 4.5 4.7 - - + -
226B ARG* 4.3 13.9 - - - -
227B LEU* 3.0 32.7 - - + +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B TYR* 6.6 0.2 - - + -
193B ARG* 4.9 10.8 - - + -
194B PHE* 1.3 87.3 - - - +
196B CYS* 1.3 58.3 + - - +
221B THR* 3.9 22.0 - - + -
222B ILE 2.6 13.1 + - - +
223B ARG* 3.2 42.7 - - - +
224B THR* 2.8 32.6 + - - +
227B LEU* 4.1 5.4 - - - -
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Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 1.3 70.8 - - - +
197B ASP* 1.3 68.7 + - - +
223B ARG* 2.8 25.2 + - - +
224B THR 3.5 4.3 - - - -
227B LEU* 3.6 21.9 - - - +
228B CYS* 2.0 50.3 - - - -
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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