Contacts of the strand formed by residues 169 - 176 (chain G) in PDB entry 3Q3G
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 THR 169 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G ASP 5.0 2.4 + - - -
133G SER* 3.3 17.4 + - - +
135G ILE* 3.9 20.4 - - + -
164G LEU 3.5 18.4 - - - +
165G LYS* 5.9 0.2 - - - -
166G LYS* 3.3 45.1 + - + +
167G SER 3.6 0.4 - - - -
168G LYS* 1.4 76.7 - - - +
170G LEU* 1.4 63.0 + - - +
171G PHE* 3.6 23.6 - - + -
189G PHE* 3.8 14.7 - - - -
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Residues in contact with LEU 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G SER 2.9 5.7 + - - +
134G ASP* 3.6 8.0 - - - +
135G ILE* 2.8 32.2 + - - +
169G THR* 1.4 75.5 - - - +
171G PHE* 1.3 59.4 + - - +
186G PHE* 3.6 31.6 - - + +
189G PHE* 3.6 22.9 - - + -
190G GLN* 3.7 30.5 - - + +
228G GLY 3.8 14.4 - - - +
230G ARG* 3.3 40.6 - - - +
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Residues in contact with PHE 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G ILE* 3.1 43.1 - - + +
137G PHE* 3.7 20.2 - + + -
161G MET* 3.6 57.4 - - + -
164G LEU* 3.7 22.2 - - + -
165G LYS* 4.8 3.6 - - + -
169G THR* 3.6 27.6 - - + -
170G LEU* 1.3 75.5 - - - +
172G SER* 1.3 61.0 + - - +
184G PHE* 3.6 5.3 - - + -
186G PHE* 3.5 10.4 - - - -
189G PHE* 3.3 49.1 - + + +
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Residues in contact with SER 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G ILE 3.1 5.1 + - - -
136G ALA* 3.3 1.6 - - - -
137G PHE* 2.8 30.3 + - - -
171G PHE* 1.3 74.1 - - - +
173G LEU* 1.3 59.8 + - - +
184G PHE* 2.8 25.1 + - - -
185G THR* 3.5 8.1 - - - -
186G PHE* 3.6 31.4 + - - -
222G LEU* 3.1 30.4 - - - +
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Residues in contact with LEU 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137G PHE* 3.4 18.2 - - + +
139G ILE* 3.9 21.8 - - + -
157G VAL* 3.6 31.6 - - + -
172G SER* 1.3 75.4 - - - +
174G MET* 1.3 71.1 + - - +
182G ILE* 3.6 4.7 - - - +
183G HIS* 2.9 50.1 + - + -
184G PHE* 3.1 35.9 + - + +
199G VAL* 4.9 1.1 - - + -
202G ILE* 3.8 23.3 - - + -
222G LEU* 4.2 3.8 - - - -
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Residues in contact with MET 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G PHE 2.9 6.3 + - - +
138G LEU* 3.2 20.7 - - + +
139G ILE* 2.9 25.3 + - - +
173G LEU* 1.3 78.0 - - - +
175G GLN* 1.3 63.3 + - - +
180G PHE* 3.7 36.1 - - + -
181G ARG 3.4 24.2 - - - +
182G ILE* 4.0 15.5 - - + -
214G GLY* 3.5 20.4 - - - +
217G LYS* 3.8 20.9 - - + +
218G VAL* 4.1 15.9 - - + -
221G GLU* 5.7 0.2 - - - +
222G LEU* 3.9 15.9 - - + -
703G GOL 4.7 2.5 - - - -
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Residues in contact with GLN 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G ILE* 3.3 27.1 - - + +
141G GLY* 3.1 20.8 - - - -
150G PHE* 3.6 11.8 - - - -
174G MET* 1.3 75.5 - - - +
176G TYR* 1.3 64.7 + - - +
180G PHE* 3.5 2.6 - - - -
181G ARG 2.9 32.3 + - - +
183G HIS* 3.1 29.4 + - + +
202G ILE* 4.0 1.2 - - - +
203G THR 2.7 27.5 + - - -
204G GLN* 3.4 3.6 - - - -
205G LEU* 2.8 41.1 + - + +
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Residues in contact with TYR 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G LEU* 3.5 37.5 - - + -
139G ILE 2.9 19.8 + - - -
140G ASP* 3.5 26.4 - - + +
141G GLY 2.8 28.1 + - - -
174G MET* 4.2 0.4 - - + -
175G GLN* 1.3 75.3 - - - +
177G SER* 1.3 64.2 + - - +
179G GLU 3.4 6.3 - - - -
180G PHE* 3.4 20.6 - - + -
205G LEU* 4.1 2.9 - - - -
209G THR* 3.7 14.0 - - + +
210G HIS 3.5 18.8 - - - -
211G THR* 2.8 44.9 + - + +
214G GLY* 4.4 1.8 - - - -
239G VAL* 4.9 2.6 - - + +
240G ILE 4.7 1.1 - - - -
241G THR* 3.2 26.7 + - - -
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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