Contacts of the strand formed by residues 189 - 195 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146Q ALA* 4.1 11.4 - - - -
149Q ALA* 3.5 18.2 - - + -
161Q CYS 3.5 4.9 - - - -
163Q THR* 3.4 22.4 - - - -
182Q ALA* 4.9 0.4 - - + -
187Q LEU* 2.7 16.4 + - + +
188Q PRO* 1.3 71.9 - - - +
190Q ILE* 1.3 60.0 + - - +
191Q PHE* 3.2 46.0 + - + -
244Q CYS* 4.0 1.2 - - - -
250Q PRO* 3.2 24.9 - - + +
251Q ILE 3.2 4.0 + - - -
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Residues in contact with ILE 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Q VAL* 4.5 4.7 - - + -
161Q CYS 2.8 13.3 + - - +
162Q LEU* 3.8 24.2 - - + -
163Q THR 3.1 22.6 + - - -
189Q CYS* 1.3 71.0 - - - +
191Q PHE* 1.3 62.4 + - - +
192Q ILE* 3.3 21.9 + - + +
237Q THR* 5.0 3.6 - - + +
240Q ALA* 3.7 15.9 - - + +
241Q ALA* 3.7 33.2 - - + +
244Q CYS* 3.7 19.1 - - + -
251Q ILE* 3.5 18.6 - - + +
253Q MET* 4.6 11.4 - - + -
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Residues in contact with PHE 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Q VAL* 3.6 37.0 - - + -
146Q ALA* 4.4 2.2 - - + -
163Q THR* 3.6 8.3 - - + -
165Q TYR* 4.3 7.0 - + + -
178Q ALA* 3.8 19.5 - - + -
179Q TYR* 3.9 32.8 - + + -
182Q ALA* 3.6 30.3 - - + -
189Q CYS* 3.2 33.4 - - - -
190Q ILE* 1.3 70.1 - - - +
192Q ILE* 1.3 61.4 + - - +
193Q CYS 3.8 0.9 + - - -
220Q ILE* 4.7 2.0 - - + -
250Q PRO* 3.9 11.9 - - + -
251Q ILE 2.8 15.7 + - - +
252Q LEU* 3.2 14.3 - - + +
253Q MET 2.9 24.4 + - - -
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Residues in contact with ILE 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Q LEU* 3.8 23.8 - - + -
162Q LEU* 3.8 30.5 - - + -
163Q THR 3.0 6.3 + - - +
164Q LEU* 3.2 21.8 - - + +
165Q TYR* 3.0 27.5 + - - +
190Q ILE* 3.7 15.5 - - + +
191Q PHE* 1.3 74.1 - - - +
193Q CYS* 1.3 65.1 + - - +
194Q GLU 3.8 1.0 + - - +
253Q MET* 3.2 31.4 - - + +
255Q LEU* 3.7 27.8 - - + -
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Residues in contact with CYS 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Q TYR* 3.2 37.0 - - + +
167Q ASP* 3.9 21.3 - - - -
191Q PHE 3.8 2.2 + - - -
192Q ILE* 1.3 73.2 - - - +
194Q GLU* 1.3 64.3 + - - +
195Q ASN* 3.2 7.3 + - - -
213Q TYR* 3.8 38.1 - - + +
252Q LEU* 5.8 2.2 - - + -
253Q MET 2.9 11.2 + - - +
254Q GLU* 3.4 5.8 - - + +
255Q LEU 2.8 26.3 + - - -
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Residues in contact with GLU 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Q GLN* 3.3 27.7 - - - +
71Q CYS* 3.7 23.6 - - - +
87Q THR* 4.7 5.4 + - - -
90Q ARG* 5.2 11.1 - - - +
94Q PHE* 4.2 15.0 - - - -
164Q LEU* 4.0 29.1 - - + +
165Q TYR 2.9 14.3 + - - +
166Q GLY* 3.4 7.7 + - - -
167Q ASP* 3.3 18.9 + - - +
192Q ILE* 3.8 0.9 + - + -
193Q CYS* 1.3 68.6 - - - +
195Q ASN* 1.3 59.5 + - - +
196Q ASN* 3.4 7.5 + - + +
255Q LEU* 3.6 17.2 - - + +
257Q THR* 4.5 3.8 - - + -
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Residues in contact with ASN 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Q ASP* 3.7 14.8 - - - +
193Q CYS* 3.2 4.3 + - - +
194Q GLU* 1.3 73.1 - - - +
196Q ASN* 1.3 56.2 + - - +
197Q ARG* 3.2 25.2 + - - +
204Q VAL* 3.9 5.9 - - - +
211Q THR 4.7 2.6 + - - -
213Q TYR* 3.5 24.7 - - + -
254Q GLU* 3.2 34.6 + - + -
255Q LEU 2.6 15.8 + - - +
256Q GLN* 3.4 12.0 - - - +
257Q THR* 2.9 21.3 + - - +
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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