Contacts of the strand formed by residues 185 - 192 (chain A) in PDB entry 1JUV
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 4.9 4.7 - - + -
148A ILE* 4.2 8.3 - - + -
149A VAL 3.4 5.4 - - - +
150A LYS* 2.7 43.3 + - + +
180A LYS* 3.8 0.3 - - - -
181A ILE* 2.9 42.4 + - + -
182A ASP* 2.8 31.0 + - - +
184A VAL* 1.3 84.2 + - - +
186A THR* 1.3 75.4 + - - +
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Residues in contact with THR 186 (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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147A ARG 4.5 0.2 - - - -
148A ILE* 3.5 7.3 - - - +
149A VAL* 2.9 54.1 + - + +
178A TRP* 3.6 35.1 + - + +
179A TYR 3.2 10.8 - - - +
180A LYS* 4.6 5.4 - - + -
181A ILE* 4.1 2.7 - - - -
182A ASP 5.5 0.2 - - - +
185A THR* 1.3 80.2 - - - +
187A LEU* 1.3 62.0 + - - +
188A THR* 5.3 1.0 + - - -
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Residues in contact with LEU 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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33A VAL* 4.9 1.8 - - + -
35A LYS* 3.4 33.9 - - + -
36A ASP* 3.7 24.7 - - + +
39A ASN* 3.9 8.7 - - - +
146A SER* 4.0 16.4 - - - +
147A ARG 3.5 3.1 - - - +
148A ILE* 3.4 37.2 - - + -
177A HIS 3.6 1.0 - - - +
178A TRP* 3.3 2.8 - - - -
179A TYR* 2.8 41.6 + - + +
181A ILE* 3.9 16.6 - - + -
186A THR* 1.3 76.7 - - - +
188A THR* 1.3 68.7 + - - +
189A GLU 5.0 0.4 - - - +
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Residues in contact with THR 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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145A VAL 3.8 1.6 - - - +
146A SER* 3.1 4.4 - - - -
147A ARG* 2.8 53.1 + - + +
149A VAL* 5.9 1.4 - - - +
176A THR* 3.6 20.6 - - - +
177A HIS 3.0 11.2 - - - +
178A TRP* 3.3 26.3 - - + -
186A THR* 5.3 1.6 + - - -
187A LEU* 1.3 75.0 - - - +
189A GLU* 1.3 63.1 + - - +
190A SER* 4.8 3.8 - - - +
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Residues in contact with GLU 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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39A ASN* 3.5 37.0 + - - +
43A ARG* 2.9 56.8 + - - +
144A VAL* 3.7 13.3 - - + +
145A VAL 3.7 2.7 - - - -
146A SER* 3.7 18.2 + - - +
176A THR* 3.3 1.9 - - - -
177A HIS* 2.7 59.8 + - + +
179A TYR* 5.2 1.6 + - + -
187A LEU* 4.2 1.7 - - + +
188A THR* 1.3 72.4 - - - +
190A SER* 1.3 61.4 + - - +
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Residues in contact with SER 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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143A VAL 3.5 1.6 - - - +
144A VAL* 3.4 4.3 - - - +
145A VAL* 2.9 39.8 + - - +
173A MET* 3.2 20.0 - - - +
175A GLU 3.3 6.1 - - - -
176A THR* 3.9 11.2 - - - -
188A THR* 4.1 4.9 - - - -
189A GLU* 1.3 75.6 - - - +
191A VAL* 1.3 63.4 + - - +
192A TYR* 2.9 29.3 - - - -
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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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43A ARG* 3.6 36.6 - - - +
142A GLU* 3.4 32.5 - - + +
143A VAL 3.4 2.2 - - - +
144A VAL* 4.4 8.3 - - + -
173A MET* 3.5 4.0 - - - +
174A VAL* 2.9 40.9 + - + +
175A GLU* 2.8 34.9 + - + +
177A HIS* 5.3 0.7 - - + -
189A GLU* 5.2 0.9 - - + +
190A SER* 1.3 77.6 + - - +
192A TYR* 1.3 63.6 + - - +
193A LYS* 4.1 5.8 - - - +
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Residues in contact with TYR 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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142A GLU* 3.4 5.5 - - - +
143A VAL* 2.8 45.1 + - + +
145A VAL* 3.4 26.9 - - + +
168A ILE* 3.6 37.0 - - + -
169A SER* 4.2 14.8 - - - -
171A ARG* 3.8 27.8 - - + -
172A GLU 3.3 4.3 - - - +
173A MET* 3.7 29.1 - - + -
190A SER* 2.9 27.0 + - - -
191A VAL* 1.3 73.7 - - - +
193A LYS* 1.3 64.8 + - - +
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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