Contacts of the strand formed by residues 189 - 194 (chain B) in PDB entry 3I8E
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 HIS 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE 3.5 0.3 - - - +
181B VAL* 3.3 4.3 - - - -
182B TYR* 2.8 70.2 + - + +
184B ASP* 3.1 30.6 + - - -
186B GLN* 3.9 18.8 - - + +
187B GLY 3.1 15.7 + - - -
188B ARG* 1.3 75.0 + - - +
190B VAL* 1.3 61.0 + - - +
209B GLN* 3.5 20.6 + - + +
210B GLU 3.4 9.4 - - - +
211B ASN* 3.2 27.5 + - - -
212B VAL* 3.7 6.6 - - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B CYS* 4.1 25.1 - - - -
180B PHE 3.2 8.7 - - - +
181B VAL* 5.1 0.7 - - - -
189B HIS* 1.3 73.1 - - - +
191B LYS* 1.3 67.0 + - - +
192B THR* 5.4 0.2 - - + -
207B TRP* 4.8 14.4 - - + +
208B LYS 4.7 0.6 - - - +
209B GLN* 3.3 7.3 - - - +
210B GLU* 2.9 51.7 + - + +
211B ASN 3.6 18.2 - - - +
212B VAL* 3.8 18.4 - - + -
231B ILE* 5.1 6.7 - - + -
240B HIS* 4.1 12.8 - - + +
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLU* 4.7 5.1 - - - +
161B GLU* 2.7 31.5 + - - +
179B CYS* 3.7 1.4 - - - -
180B PHE* 3.2 40.9 + - + -
182B TYR* 3.7 20.6 - - + -
190B VAL* 1.3 77.1 - - - +
192B THR* 1.3 76.4 + - - +
193B TYR* 2.7 34.8 + - + +
207B TRP 5.6 0.4 - - - -
209B GLN* 4.3 28.2 + - + +
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Residues in contact with THR 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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170B LEU* 4.1 15.7 - - + -
177B THR* 4.7 0.2 - - - -
178B ILE 3.4 18.4 - - - +
179B CYS* 4.4 6.5 - - + -
180B PHE* 5.1 0.2 - - - -
190B VAL* 5.4 0.7 - - + -
191B LYS* 1.3 87.1 - - - +
193B TYR* 1.3 71.4 + - - +
203B ASN 4.8 0.2 - - - +
204B LYS* 5.0 0.2 - - - -
205B GLY* 3.4 30.3 + - - -
206B PRO* 4.4 5.8 - - - -
207B TRP* 2.9 47.8 + - + +
209B GLN* 5.7 0.2 - - - +
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Residues in contact with TYR 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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159B LEU* 4.9 6.1 - - + -
160B GLU* 4.1 11.6 + - - +
161B GLU* 3.1 11.4 + - - -
177B THR* 3.3 7.7 - - - +
178B ILE* 3.1 40.8 + - + +
180B PHE* 3.4 39.0 - + - -
191B LYS* 2.7 36.2 + - + -
192B THR* 1.3 76.7 - - - +
194B GLU* 1.3 69.9 + - - +
195B VAL* 4.4 0.3 - - - +
202B PHE* 3.2 45.1 - + + -
203B ASN 3.7 12.3 - - - -
205B GLY* 4.1 3.4 - - - -
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Residues in contact with GLU 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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174B GLN* 5.6 5.7 - - - +
175B ALA* 3.3 29.1 - - + +
176B PRO 3.5 4.9 - - - -
177B THR* 4.2 9.9 - - - +
193B TYR* 1.3 74.8 - - - +
195B VAL* 1.3 63.6 + - - +
196B SER* 5.1 1.1 - - - +
202B PHE* 2.6 42.0 + - - +
203B ASN* 4.8 10.2 + - + +
204B LYS 3.7 21.4 + - - +
205B GLY* 4.1 0.2 - - - -
206B PRO* 4.4 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