Contacts of the strand formed by residues 133 - 140 (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 SER 133 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G ASP* 1.4 76.9 + - - +
134G ASP* 1.3 61.6 + - - +
135G ILE* 3.9 17.7 - - - -
168G LYS 3.0 11.9 + - - +
169G THR* 3.3 15.9 - - - -
170G LEU 2.9 30.4 + - - +
230G ARG* 3.8 2.1 - - - +
234G PHE* 3.5 11.9 - - - +
236G ILE* 3.8 1.1 - - - +
320G GLU* 2.6 32.8 + - - +
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Residues in contact with ASP 134 (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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133G SER* 1.3 69.6 - - - +
135G ILE* 1.3 59.3 + - - +
170G LEU* 3.6 13.8 - - - +
186G PHE* 3.7 22.7 - - + -
223G PHE* 3.4 18.3 - - + -
229G ALA* 3.9 5.4 - - - +
230G ARG* 2.7 69.2 + - - +
233G ALA* 3.5 6.6 - - - +
234G PHE 2.9 13.9 + - - +
235G LYS* 5.2 1.4 - - + +
236G ILE 3.1 23.4 + - - -
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Residues in contact with ILE 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G SER* 4.1 8.3 - - - +
134G ASP* 1.3 70.1 - - - +
136G ALA* 1.3 65.4 + - - +
137G PHE* 4.2 15.6 - - + -
164G LEU* 4.4 10.5 - - + -
169G THR* 3.9 24.7 - - + -
170G LEU 2.8 9.3 + - - +
171G PHE* 3.1 55.0 - - + +
172G SER 3.1 2.9 + - - +
186G PHE* 3.7 2.4 - - - -
236G ILE* 3.6 37.2 - - + +
238G VAL* 4.7 5.8 - - + -
316G ILE* 3.7 25.8 - - + -
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Residues in contact with ALA 136 (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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134G ASP 3.7 0.8 + - - -
135G ILE* 1.3 75.2 - - - +
137G PHE* 1.3 64.8 + - - +
172G SER 3.3 6.3 - - - +
186G PHE* 4.3 6.3 - - + -
222G LEU* 4.1 19.3 - - + -
223G PHE* 3.6 29.8 - - + -
236G ILE 2.8 9.1 + - - +
237G LEU* 3.4 13.1 - - + -
238G VAL* 2.9 25.3 + - - +
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Residues in contact with PHE 137 (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* 4.2 6.7 - - + -
136G ALA* 1.3 73.4 - - - +
138G LEU* 1.3 59.6 + - - +
139G ILE* 3.9 8.3 - - + -
156G PHE* 6.2 1.1 - + - -
157G VAL* 3.7 29.4 - - + -
160G VAL* 3.7 33.0 - - + -
161G MET* 3.6 29.2 - - + -
171G PHE* 3.7 22.7 - + + -
172G SER 2.8 16.9 + - - +
173G LEU* 3.4 21.4 - - + -
174G MET* 2.9 25.6 + - - -
184G PHE* 5.2 0.4 - + - -
222G LEU* 4.2 5.0 - - - +
237G LEU* 4.2 1.8 - - - -
238G VAL* 3.3 34.8 - - + +
240G ILE* 5.4 3.4 - - + -
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Residues in contact with LEU 138 (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* 1.3 70.8 - - - +
139G ILE* 1.3 59.9 + - - +
140G ASP 4.1 0.2 + - - -
174G MET* 3.2 37.9 - - + +
176G TYR* 3.5 28.6 - - + -
211G THR* 4.4 2.9 - - + +
214G GLY* 3.7 4.3 - - - +
215G ILE* 3.6 42.8 - - + +
218G VAL* 3.7 10.8 - - + -
237G LEU* 3.7 17.9 - - + +
238G VAL 3.0 7.2 + - - +
239G VAL* 3.4 19.2 - - + +
240G ILE 3.2 22.3 + - - +
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Residues in contact with ILE 139 (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* 4.4 12.6 - - + -
138G LEU* 1.3 75.3 - - - +
140G ASP* 1.3 62.4 + - - +
150G PHE* 3.9 32.1 - - + -
153G MET* 4.0 22.7 - - + -
154G LYS* 5.2 6.1 - - + -
157G VAL* 4.0 26.7 - - + -
173G LEU* 3.9 28.0 - - + -
174G MET 2.9 11.3 + - - +
175G GLN* 3.3 16.7 - - + +
176G TYR* 2.9 28.9 + - - -
202G ILE* 4.6 5.6 - - + -
238G VAL 5.6 0.2 - - - +
240G ILE* 3.9 13.2 - - + -
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Residues in contact with ASP 140 (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* 1.3 69.8 - - - +
141G GLY* 1.3 57.5 + - - +
142G SER* 2.6 37.8 + - - -
145G ILE* 3.4 14.2 - - + +
150G PHE* 4.1 0.2 - - - -
153G MET* 3.2 24.3 - - - +
175G GLN* 4.7 0.2 - - - -
176G TYR* 3.5 25.2 - - - +
177G SER* 5.1 0.2 - - - -
209G THR* 4.3 5.9 + - - +
240G ILE 2.9 20.8 + - - +
241G THR* 2.7 27.0 + - - -
242G ASP* 3.0 20.8 + - - +
243G GLY 4.0 1.0 + - - -
500G CA 4.1 0.5 - - - -
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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