Contacts of the strand formed by residues 169 - 176 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I ASP 5.3 1.6 + - - -
133I SER* 3.5 17.4 + - - -
135I ILE* 3.7 31.4 - - + -
164I LEU 3.6 17.0 - - - +
166I LYS* 3.4 46.1 + - - +
167I SER 5.2 0.2 - - - -
168I LYS* 1.4 76.9 - - - +
170I LEU* 1.4 67.7 + - - +
171I PHE* 3.9 13.8 - - + -
189I PHE* 4.0 11.5 - - - -
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Residues in contact with LEU 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I SER 3.0 6.9 + - - -
134I ASP* 3.7 11.8 - - - +
135I ILE* 3.0 27.4 + - - +
167I SER 5.5 2.5 - - - +
168I LYS* 4.4 2.7 - - - -
169I THR* 1.4 79.5 - - - +
171I PHE* 1.4 65.2 + - - +
186I PHE* 3.2 47.9 - - + +
189I PHE* 3.5 19.7 - - + -
190I GLN* 3.8 25.4 - - + +
228I GLY 5.3 0.9 - - - +
230I ARG* 3.3 35.0 - - - +
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Residues in contact with PHE 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I ILE* 3.4 46.9 - - + -
137I PHE* 4.0 25.8 - + + -
160I VAL 4.3 0.2 - - - -
161I MET* 3.5 58.8 - - + -
164I LEU* 4.1 16.2 - - + -
165I LYS* 5.2 2.0 - - - -
169I THR* 3.9 14.6 - - + -
170I LEU* 1.4 76.1 - - - +
172I SER* 1.4 59.4 + - - +
184I PHE* 3.7 5.2 - - + -
185I THR 3.6 2.3 - - - +
186I PHE* 3.4 14.5 - - - -
189I PHE* 3.2 55.0 - + + +
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Residues in contact with SER 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I ILE 3.2 6.4 + - - +
136I ALA* 3.1 3.8 - - - -
137I PHE* 2.8 34.3 + - - +
171I PHE* 1.4 71.0 - - - +
173I LEU* 1.4 55.3 + - - +
184I PHE* 3.4 8.2 + - - -
185I THR* 3.2 8.5 - - - -
186I PHE* 2.9 52.1 + - - -
222I LEU* 3.9 22.8 + - - +
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Residues in contact with LEU 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I PHE* 3.6 25.6 - - + +
139I ILE* 3.7 31.2 - - + -
157I VAL* 3.8 25.4 - - + -
172I SER* 1.4 74.6 - - - +
174I MET* 1.3 64.6 + - - +
182I ILE* 3.6 5.4 - - - +
183I HIS* 2.9 51.1 + - + -
184I PHE* 3.1 35.6 + - + +
202I ILE* 3.8 17.9 - - + -
222I LEU* 4.2 2.9 - - - -
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Residues in contact with MET 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I PHE 2.9 17.6 + - - +
138I LEU* 3.4 18.1 - - + +
139I ILE* 3.2 17.2 + - - +
173I LEU* 1.3 78.1 - - - +
175I GLN* 1.3 63.5 + - - +
176I TYR* 4.2 0.2 - - + -
180I PHE* 3.7 36.6 - - + -
181I ARG 3.3 23.1 - - - +
182I ILE* 3.9 15.7 - - + -
214I GLY* 3.5 21.5 - - - +
217I LYS* 3.8 21.8 - - + +
218I VAL* 4.1 13.0 - - + -
221I GLU* 5.7 1.1 - - - +
222I LEU* 3.9 16.5 - - + +
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Residues in contact with GLN 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I ILE* 3.6 25.1 - - + +
141I GLY* 3.1 20.9 - - - -
150I PHE* 3.6 12.3 - - + -
174I MET* 1.3 75.7 - - - +
176I TYR* 1.3 63.7 + - - +
180I PHE* 3.4 2.6 - - - -
181I ARG 2.9 32.4 + - - +
183I HIS* 3.1 28.4 + - + +
202I ILE* 4.0 0.6 - - - +
203I THR 2.7 27.3 + - - -
204I GLN* 3.4 3.3 - - - -
205I LEU* 2.8 40.9 + - + +
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Residues in contact with TYR 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.6 39.0 - - + -
139I ILE 3.1 24.5 + - - -
140I ASP* 3.7 27.0 - - + +
141I GLY 2.7 32.1 + - - -
174I MET* 4.2 0.2 - - + -
175I GLN* 1.3 74.3 - - - +
177I SER* 1.3 63.1 + - - +
179I GLU 3.4 6.1 - - - -
180I PHE* 3.4 20.9 - - + -
205I LEU* 4.0 3.1 - - - -
209I THR* 3.7 13.0 - - + +
210I HIS 3.5 18.6 - - - -
211I THR* 3.2 40.4 + - + +
214I GLY* 4.6 1.8 - - - -
239I VAL* 4.8 2.0 - - + +
240I ILE 4.3 1.1 - - - -
241I THR* 2.7 30.7 + - - -
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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
------------------------------------------------------------
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