Contacts of the strand formed by residues 189 - 195 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145M GLY 4.2 8.1 - - - -
146M ALA* 4.3 4.0 - - - -
149M ALA* 3.5 15.3 - - + -
161M CYS* 3.6 4.0 - - - -
163M THR* 3.6 19.3 - - - -
182M ALA* 4.8 1.1 - - + -
187M LEU* 2.9 16.6 + - + +
188M PRO* 1.3 74.3 - - - +
190M ILE* 1.3 65.6 + - - +
191M PHE* 3.6 41.0 + - + -
244M CYS* 3.8 2.5 - - - -
250M PRO* 3.2 28.0 - - + +
251M ILE 3.3 4.7 + - - -
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Residues in contact with ILE 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M VAL* 4.1 11.7 - - + -
161M CYS 2.8 16.1 + - - +
162M LEU* 3.6 25.8 - - + -
163M THR 2.9 23.2 + - - -
189M CYS* 1.3 77.0 - - - +
191M PHE* 1.3 63.1 + - - +
192M ILE* 3.2 25.0 + - + +
237M THR* 5.0 4.9 - - + +
240M ALA* 3.9 22.9 - - + -
241M ALA* 4.0 13.7 - - + +
244M CYS* 3.9 13.9 - - - -
251M ILE* 3.6 21.1 - - + +
253M MET* 4.5 9.6 - - + -
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Residues in contact with PHE 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142M VAL* 3.6 36.8 - - + -
146M ALA* 4.5 3.4 - - + -
163M THR* 3.5 9.0 - - + -
165M TYR* 4.3 6.7 - + + -
178M ALA* 3.6 27.4 - - + -
179M TYR* 3.8 30.5 - + + -
182M ALA* 3.5 23.6 - - + -
189M CYS* 3.6 25.8 - - - -
190M ILE* 1.3 70.3 - - - +
192M ILE* 1.3 61.5 + - - +
220M ILE* 4.1 5.8 - - + -
250M PRO* 3.9 15.0 - - + -
251M ILE 3.0 11.6 + - - +
252M LEU* 3.3 16.0 - - + +
253M MET 2.9 24.4 + - - -
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Residues in contact with ILE 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M LEU* 4.2 4.7 - - + -
162M LEU* 3.6 37.0 - - + -
163M THR 2.7 10.7 + - - +
164M LEU* 3.1 29.8 - - + -
165M TYR* 2.9 31.5 + - - +
190M ILE* 3.3 21.5 - - + +
191M PHE* 1.3 74.0 - - - +
193M CYS* 1.3 64.8 + - - +
194M GLU* 3.7 1.9 + - + +
253M MET* 3.3 31.2 - - + +
255M LEU* 3.8 24.2 - - + -
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Residues in contact with CYS 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M TYR* 3.4 31.2 + - + +
166M GLY 4.1 2.0 - - - -
167M ASP* 4.0 21.1 - - - -
191M PHE 4.0 1.6 + - - -
192M ILE* 1.3 72.6 - - - +
194M GLU* 1.3 54.2 + - - +
195M ASN* 3.2 9.5 + - - -
213M TYR* 3.7 40.2 - - + -
252M LEU* 5.2 3.8 - - + +
253M MET 2.8 12.5 + - - +
254M GLU* 3.4 4.3 - - - +
255M LEU 2.8 30.4 + - - -
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Residues in contact with GLU 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M GLN* 3.5 24.2 - - - +
71M CYS* 4.3 12.0 - - - +
87M THR* 4.4 7.4 + - - -
88M ALA* 6.1 0.7 - - - +
90M ARG* 5.1 14.2 - - - +
94M PHE* 3.5 24.3 - - - -
164M LEU* 3.7 28.2 - - + +
165M TYR 2.8 16.1 + - - +
166M GLY* 3.4 5.2 - - - -
167M ASP 3.2 13.7 + - - -
192M ILE* 3.7 3.7 + - + -
193M CYS* 1.3 66.1 - - - +
195M ASN* 1.3 61.2 + - - +
196M ASN* 3.2 17.8 + - - +
255M LEU* 3.9 15.7 - - + -
257M THR* 4.6 2.9 - - + -
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Residues in contact with ASN 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M ASP* 4.2 10.4 - - - +
193M CYS* 3.2 3.7 + - - +
194M GLU* 1.3 71.8 - - - +
196M ASN* 1.3 54.7 + - - +
197M ARG* 2.5 38.0 + - - +
211M THR 5.6 0.6 + - - -
213M TYR* 3.7 29.7 - - + -
254M GLU* 3.1 32.2 + - + +
255M LEU 3.1 12.7 + - - +
256M GLN* 3.8 5.5 - - - +
257M THR* 3.0 25.1 + - - +
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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