Contacts of the strand formed by residues 189 - 195 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146U ALA* 4.3 7.2 - - - -
149U ALA* 3.5 20.2 - - + -
161U CYS* 3.9 2.7 - - - -
163U THR* 3.6 24.0 - - - -
182U ALA* 4.6 1.8 - - + -
187U LEU* 2.7 17.8 + - + +
188U PRO* 1.3 76.1 - - - +
190U ILE* 1.3 64.0 + - - +
191U PHE* 3.6 38.2 + - + -
244U CYS* 4.0 2.1 - - - -
250U PRO* 3.2 6.4 - - + +
251U ILE 3.0 25.5 + - - +
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Residues in contact with ILE 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160U VAL* 4.2 12.6 - - + -
161U CYS 3.0 12.4 + - - +
162U LEU* 3.6 30.1 - - + -
163U THR* 2.8 28.9 + - - -
188U PRO 5.1 0.2 - - - +
189U CYS* 1.3 75.7 - - - +
191U PHE* 1.3 64.8 + - - +
192U ILE* 3.3 20.4 + - + +
237U THR* 5.2 2.2 - - + +
240U ALA* 4.1 11.0 - - + -
241U ALA* 4.0 25.4 - - + +
244U CYS* 3.7 17.3 - - + -
251U ILE* 3.4 22.4 - - + +
253U MET* 4.3 9.9 - - + -
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Residues in contact with PHE 191 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142U VAL* 4.0 31.9 - - + -
146U ALA* 4.7 2.9 - - + -
163U THR* 3.4 9.6 - - + -
165U TYR* 4.2 8.5 + + + +
178U ALA* 4.2 14.1 - - + -
179U TYR* 3.8 37.9 - + + -
182U ALA* 3.5 32.8 - - + -
189U CYS* 3.6 24.2 - - - -
190U ILE* 1.3 70.8 - - - +
192U ILE* 1.3 62.4 + - - +
193U CYS 4.0 0.5 + - - -
220U ILE* 4.1 7.2 - - + -
250U PRO* 3.9 13.2 - - + -
251U ILE 3.0 16.3 + - - +
252U LEU* 3.4 9.5 - - + +
253U MET 2.9 24.3 + - - +
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Residues in contact with ILE 192 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U LEU* 4.1 3.8 - - + -
162U LEU* 3.6 36.8 - - + -
163U THR 2.6 10.9 + - - -
164U LEU* 3.1 33.9 - - + -
165U TYR* 2.8 31.5 + - - +
190U ILE* 4.0 12.3 - - + +
191U PHE* 1.3 76.9 - - - +
193U CYS* 1.3 67.4 + - - +
194U GLU* 3.8 1.7 + - - +
253U MET* 3.3 36.1 - - + +
255U LEU* 4.1 23.3 - - + -
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Residues in contact with CYS 193 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165U TYR* 3.3 32.3 + - + +
167U ASP* 4.1 18.8 - - - -
191U PHE 4.0 1.2 + - - -
192U ILE* 1.3 74.6 - - - +
194U GLU* 1.3 55.2 + - - +
195U ASN* 3.3 13.9 + - - -
213U TYR* 3.8 39.0 - - + +
252U LEU* 5.7 1.8 - - + -
253U MET 3.0 7.7 + - - -
254U GLU* 3.4 7.0 - - - -
255U LEU 2.8 30.6 + - - -
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Residues in contact with GLU 194 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U GLN* 3.5 23.2 + - - +
71U CYS* 5.4 6.9 - - - +
87U THR* 4.7 4.7 + - - -
90U ARG* 4.5 15.3 - - - +
94U PHE* 3.5 27.2 - - - -
164U LEU* 3.6 22.1 - - + +
165U TYR 3.0 15.3 + - - +
166U GLY* 3.4 9.7 + - - -
167U ASP* 3.3 20.4 + - - +
192U ILE* 3.8 2.3 + - + +
193U CYS* 1.3 68.9 - - - +
195U ASN* 1.3 60.8 + - - +
196U ASN* 3.5 7.3 + - - +
255U LEU* 3.8 16.2 - - + +
257U THR* 4.7 10.1 - - + -
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Residues in contact with ASN 195 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U ASP* 3.6 18.2 - - + +
193U CYS* 3.3 14.6 + - - -
194U GLU* 1.3 70.8 - - - +
196U ASN* 1.3 58.9 + - - +
197U ARG* 3.1 23.6 + - - +
211U THR 5.4 0.8 + - - -
213U TYR* 4.1 16.2 - - + -
254U GLU* 2.9 29.9 + - + +
255U LEU 3.1 8.9 + - - +
256U GLN* 3.7 18.4 - - - +
257U THR* 3.0 25.6 + - - +
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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