Contacts of the strand formed by residues 189 - 195 (chain Y) in PDB entry 3EXG
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 CYS 189 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145Y GLY 4.5 1.3 - - - -
146Y ALA* 4.2 11.7 - - - -
149Y ALA* 3.5 15.9 - - + -
161Y CYS* 3.5 3.8 - - - -
163Y THR* 3.6 18.6 - - - -
187Y LEU* 2.8 17.5 + - + +
188Y PRO* 1.3 74.0 - - - +
190Y ILE* 1.3 67.6 + - - +
191Y PHE* 3.5 44.9 + - + -
244Y CYS* 3.9 2.3 - - - -
250Y PRO* 3.3 22.3 - - + +
251Y ILE 3.3 5.4 + - - -
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Residues in contact with ILE 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Y VAL* 4.7 5.4 - - + -
161Y CYS 2.6 18.8 + - - +
162Y LEU* 3.5 23.8 - - + -
163Y THR 2.8 25.7 + - - -
189Y CYS* 1.3 78.2 - - - +
191Y PHE* 1.3 60.3 + - - +
192Y ILE* 3.1 25.1 + - + +
237Y THR* 5.1 2.9 - - + +
240Y ALA* 3.9 14.8 - - + +
241Y ALA* 3.8 32.8 - - + +
244Y CYS* 3.8 14.6 - - + -
251Y ILE* 3.7 16.8 - - + +
253Y MET* 4.5 10.8 - - + -
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Residues in contact with PHE 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y VAL* 3.7 35.2 - - + -
146Y ALA* 4.4 2.2 - - + -
163Y THR* 3.5 10.1 - - + -
165Y TYR* 4.4 8.5 - + + -
178Y ALA* 3.7 18.8 - - + -
179Y TYR* 3.9 25.8 - + + -
182Y ALA* 3.5 31.4 - - + -
189Y CYS* 3.5 26.7 - - - -
190Y ILE* 1.3 69.1 - - - +
192Y ILE* 1.3 60.3 + - - +
193Y CYS 3.9 0.7 + - - -
220Y ILE* 4.2 5.8 - - + -
250Y PRO* 3.9 16.6 - - + -
251Y ILE 3.0 14.4 + - - +
252Y LEU* 3.2 18.0 - - + +
253Y MET 2.9 23.8 + - - -
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Residues in contact with ILE 192 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75Y LEU* 4.2 4.7 - - + -
162Y LEU* 3.4 42.8 - - + -
163Y THR 2.8 9.5 + - - +
164Y LEU* 3.2 28.8 - - + -
165Y TYR* 3.1 28.1 + - - -
190Y ILE* 3.5 14.6 - - + +
191Y PHE* 1.3 74.2 - - - +
193Y CYS* 1.3 67.9 + - - +
194Y GLU* 3.7 2.0 + - + +
253Y MET* 3.2 31.9 - - + +
255Y LEU* 3.8 26.2 - - + -
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Residues in contact with CYS 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Y TYR* 3.6 31.2 - - + +
167Y ASP* 4.1 20.4 - - - -
191Y PHE 3.9 1.0 + - - -
192Y ILE* 1.3 72.4 - - - +
194Y GLU* 1.3 59.8 + - - +
195Y ASN* 3.1 9.6 + - - -
213Y TYR* 3.7 41.1 - - + +
252Y LEU* 5.5 1.3 - - + -
253Y MET 2.9 11.3 + - - +
254Y GLU* 3.6 9.1 - - + +
255Y LEU 3.0 24.9 + - - -
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Y GLN* 3.6 24.3 - - - +
71Y CYS* 3.9 20.2 - - - +
87Y THR* 4.6 5.2 + - - -
90Y ARG* 4.9 13.7 - - - +
94Y PHE* 3.9 19.1 - - - -
164Y LEU* 3.8 30.9 - - + +
165Y TYR 2.8 18.6 + - - +
166Y GLY* 3.5 4.9 - - - -
167Y ASP* 3.2 20.1 + - - +
192Y ILE* 3.7 5.1 + - + -
193Y CYS* 1.3 67.7 - - - +
195Y ASN* 1.3 62.1 + - - +
196Y ASN* 3.5 7.7 + - - +
255Y LEU* 4.0 12.1 - - + -
257Y THR* 4.7 5.8 - - + -
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Residues in contact with ASN 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Y ASP* 4.1 9.0 - - + -
193Y CYS* 3.1 9.0 + - - +
194Y GLU* 1.3 71.5 - - - +
196Y ASN* 1.3 53.9 + - - +
197Y ARG* 2.6 32.1 + - - +
211Y THR 5.6 0.2 + - - -
213Y TYR* 3.3 36.4 - - + -
254Y GLU* 3.3 22.3 + - + +
255Y LEU 3.0 15.3 + - - +
256Y GLN* 3.8 6.6 - - - +
257Y THR* 2.8 29.1 + - - +
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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