Contacts of the strand formed by residues 189 - 194 (chain F) in PDB entry 1IB1
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 THR 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159F MET* 3.3 3.1 - - - -
160F CYS 2.7 35.4 + - - -
161F GLU* 4.8 0.2 - - - +
162F ASP* 3.2 28.2 + - - +
165F VAL* 4.0 21.9 - - + +
175F PRO* 4.7 9.2 - - + -
177F GLY* 3.5 21.0 - - - +
178F PRO* 4.6 1.0 - - - +
179F CYS* 4.4 0.7 - - - -
188F PHE* 1.3 73.6 - - - +
190F GLU* 1.3 73.6 + - - +
191F MET* 4.2 7.3 - - - +
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Residues in contact with GLU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLU 4.0 0.2 - - - +
103F ARG* 3.4 21.8 + - - +
104F LEU* 3.0 44.9 + - + +
158F LEU 3.7 7.6 - - - +
159F MET* 4.4 0.7 - - - +
174F HIS 3.7 0.2 - - - +
175F PRO* 3.6 4.5 - - - +
176F ALA* 2.7 36.4 + - + -
177F GLY 2.8 16.9 + - - +
179F CYS* 3.3 31.6 - - + +
180F ALA 4.4 0.2 + - - -
188F PHE 4.1 1.4 + - - -
189F THR* 1.3 76.3 - - - +
191F MET* 1.3 59.7 + - - +
192F HIS* 2.9 32.5 + - + +
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Residues in contact with MET 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F ALA 3.9 0.2 - - - +
157F VAL* 3.4 3.1 - - - -
158F LEU* 2.8 53.2 + - + +
160F CYS* 4.0 11.2 - - - -
165F VAL* 3.5 37.9 - - + +
168F TYR* 3.4 27.8 - - + -
169F GLN* 4.1 11.7 - - + -
173F PHE* 3.7 29.7 - - + -
174F HIS 3.3 11.4 - - - +
175F PRO* 4.0 8.3 - - - -
189F THR* 4.2 2.2 - - - +
190F GLU* 1.3 82.2 - - - +
192F HIS* 1.3 69.2 + - - +
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Residues in contact with HIS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F GLU* 3.5 32.7 + - - -
103F ARG* 4.0 8.3 - - - -
155F ARG* 4.0 18.1 + - - -
156F ALA 3.5 2.5 - - - -
157F VAL* 3.3 19.9 - - + +
172F GLY 3.7 2.3 - - - +
173F PHE* 3.3 1.4 - - - -
174F HIS* 2.8 42.6 + - + +
176F ALA* 3.5 23.2 - - + +
190F GLU* 2.9 29.1 + - + +
191F MET* 1.3 86.9 - - - +
193F CYS* 1.3 60.4 + - - +
194F SER 4.2 0.4 - - - -
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Residues in contact with CYS 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E PRO* 5.9 2.0 - - - -
144F LEU* 4.5 12.6 - - - -
155F ARG* 3.2 5.5 - - - +
156F ALA* 2.7 39.7 + - + +
171F PHE 3.7 23.6 - - - -
172F GLY* 3.8 13.0 - - - -
173F PHE* 3.4 35.0 - - + -
192F HIS* 1.3 74.4 - - - +
194F SER* 1.3 74.5 - - - +
195F LEU* 3.6 4.8 + - - +
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Residues in contact with SER 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ARG* 3.4 22.4 + - - -
154F ARG 3.9 6.3 + - - -
155F ARG* 4.3 4.9 - - - +
172F GLY 4.7 2.6 + - - -
174F HIS* 5.7 2.9 - - - -
192F HIS 4.2 1.0 + - - -
193F CYS* 1.3 85.0 - - - +
195F LEU* 1.3 68.0 + - - +
196F ARG 4.5 3.1 + - - -
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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