Contacts of the strand formed by residues 188 - 194 (chain C) in PDB entry 3GB9
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 GLN 188 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C LYS* 4.6 7.7 + - - +
124C PHE* 3.6 37.7 - - + -
128C ASP* 3.3 34.5 + - + +
129C ILE 3.0 18.2 + - - +
130C MET* 4.0 3.6 - - + -
131C LEU* 2.7 33.4 + - - +
185C ARG* 3.3 23.4 - - - +
186C GLU* 4.1 20.9 + - - +
187C LEU* 1.3 76.9 - - - +
189C GLU* 1.3 57.0 + - - +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ASN* 5.7 0.5 + - - -
124C PHE* 4.6 7.3 - - - -
130C MET* 4.0 3.4 - - - -
131C LEU* 3.3 32.5 - - + +
133C ARG* 3.9 20.2 + - + +
171C ARG* 3.3 31.9 + - - +
175C LEU* 3.7 23.3 - - + +
187C LEU 4.0 2.9 + - - +
188C GLN* 1.3 77.0 + - - +
190C GLY* 1.3 59.8 + - - +
215C ASP* 4.4 2.1 - - - +
293C SO4 4.7 1.6 + - - -
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C MET* 3.6 14.2 - - - +
131C LEU 3.2 7.3 + - - +
132C ILE* 3.7 6.1 - - - -
133C ARG* 3.0 32.4 + - - +
134C ASP 3.7 0.7 + - - -
189C GLU* 1.3 77.2 - - - +
191C THR* 1.3 63.5 + - - -
192C TYR 3.9 0.2 + - - -
215C ASP* 3.2 13.2 - - - -
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ALA* 3.9 13.3 - - + +
249A TYR* 4.4 3.6 + - - -
130C MET* 4.1 2.0 - - - +
133C ARG* 5.8 0.2 - - - +
134C ASP* 3.4 23.3 - - - +
135C HIS* 3.8 8.5 - - - -
136C ILE* 3.9 26.0 - - + -
190C GLY* 1.3 72.5 - - - -
192C TYR* 1.3 70.7 + - - +
193C VAL 3.9 0.2 + - - -
213C GLY 4.0 17.5 + - - -
214C ALA* 3.9 1.5 - - - -
215C ASP* 2.9 32.3 + - - +
216C ALA 3.2 8.7 + - - +
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Residues in contact with TYR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ASN* 3.3 29.9 + - - +
116C ALA 5.3 0.2 + - - -
117C ALA* 4.2 5.6 - - + -
130C MET* 4.1 10.3 - - + +
132C ILE* 4.3 13.2 - - + -
134C ASP 3.0 11.1 + - - +
135C HIS* 3.0 9.1 - - + +
136C ILE 3.0 21.5 + - - +
166C TYR* 5.7 0.9 - - - -
190C GLY 3.9 1.6 + - - -
191C THR* 1.3 73.9 - - - +
193C VAL* 1.3 67.3 + - - +
194C MET* 4.1 2.2 - - - -
216C ALA* 3.4 13.5 - - + -
217C VAL 4.1 1.6 - - - -
218C GLY* 3.0 41.7 - - - -
219C MET 3.2 0.9 + - - -
220C SER* 3.1 38.2 + - - -
221C THR* 4.3 4.3 - - + -
222C VAL* 3.7 20.4 - - + -
239C SER* 3.4 16.8 - - - -
290C SO4 4.7 0.3 + - - -
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.1 0.4 - - + -
136C ILE* 3.4 26.7 - - + +
138C LEU* 3.6 30.5 - - + -
191C THR 3.9 0.6 + - - -
192C TYR* 1.3 76.5 - - - +
194C MET* 1.3 64.5 + - - +
195C VAL* 4.7 0.7 - - + -
209C LEU* 4.0 14.4 - - + -
212C LEU* 6.1 1.3 - - + -
214C ALA* 3.3 29.2 - - + -
216C ALA 2.9 16.2 + - - +
217C VAL* 3.4 19.7 - - + +
218C GLY 3.1 22.5 + - - +
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Residues in contact with MET 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C MET* 4.6 18.6 - - + +
93C LEU* 5.9 0.2 - - - -
136C ILE 3.0 10.0 + - - +
137C ASN* 4.3 7.2 - - - +
138C LEU* 3.3 26.5 + - - +
139C PRO* 3.3 23.9 - - + +
192C TYR* 4.1 3.7 - - + -
193C VAL* 1.3 71.5 - - - +
195C VAL* 1.3 72.9 + - - +
196C ALA* 4.5 7.6 - - - +
218C GLY 3.4 2.5 - - - -
219C MET 3.3 25.1 - - - +
220C SER* 3.4 27.1 - - - +
222C VAL* 3.8 17.7 - - + -
223C PRO* 3.8 30.3 - - + -
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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