Contacts of the strand formed by residues 173 - 183 (chain R) in PDB entry 2D2I
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 ILE 173 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164R ALA* 4.4 5.2 - - + +
167R LEU* 3.8 12.6 - - + -
168R HIS* 3.0 43.6 + - + +
172R GLY* 1.3 72.2 - - - -
174R ILE* 1.3 56.1 + - - +
175R LYS* 3.6 24.9 - - - +
226R LEU* 3.6 21.1 - - + -
229R LYS* 2.7 34.3 + - + -
230R LEU* 4.4 9.2 - - + -
247R LEU* 6.2 0.2 - - + -
249R VAL* 3.6 36.6 - - + -
250R GLN 3.9 2.2 - - - -
251R VAL* 4.2 5.6 - - + -
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Residues in contact with ILE 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306Q ASP* 4.6 6.0 - - - +
172R GLY 4.3 0.2 - - - +
173R ILE* 1.3 76.7 - - - +
175R LYS* 1.3 70.7 - - + +
229R LYS* 3.2 30.4 - - - +
250R GLN* 3.0 42.9 + - + +
251R VAL 3.3 28.5 - - - +
252R GLU* 3.8 21.8 - - + +
308R ASP* 5.8 0.4 - - - +
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Residues in contact with LYS 175 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q MET* 3.8 23.3 - - + +
306Q ASP* 2.8 44.4 + - + +
308Q ASP* 2.4 35.0 + - - -
309Q LEU* 3.9 17.5 - - + -
173R ILE* 3.6 10.6 - - - +
174R ILE* 1.3 80.9 - - - +
176R GLY* 1.3 60.9 + - - +
229R LYS* 3.3 12.1 - - - -
249R VAL* 3.6 0.3 - - - -
250R GLN* 2.8 63.0 + - + +
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Residues in contact with GLY 176 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q MET* 3.8 10.4 - - - +
309Q LEU* 4.9 5.6 - - - -
175R LYS* 1.3 80.3 - - - +
177R THR* 1.3 61.2 + - - -
229R LYS 2.9 10.4 + - - +
230R LEU* 3.8 15.9 - - - -
231R ASN 3.2 19.2 + - - -
248R VAL 3.1 13.9 - - - -
249R VAL* 3.8 2.0 - - - -
250R GLN 4.8 0.2 - - - -
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Residues in contact with THR 177 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248Q VAL* 3.7 27.4 - - + -
303Q LEU* 4.2 12.5 - - - +
305Q MET* 4.8 0.2 - - - -
309Q LEU* 4.3 12.1 - - + +
311Q LYS* 3.4 34.3 + - + +
176R GLY* 1.3 75.6 - - - -
178R MET* 1.3 71.3 + - - +
230R LEU* 5.6 0.4 - - - -
231R ASN 3.2 14.9 + - - -
232R GLY* 4.4 0.9 - - - -
247R LEU* 3.2 4.1 - - - +
248R VAL* 2.8 41.4 + - + +
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Residues in contact with MET 178 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311Q LYS* 3.8 5.4 + - - +
156R THR* 4.4 13.5 - - + -
160R LEU* 3.8 31.0 - - + -
177R THR* 1.3 80.1 + - - +
179R THR* 1.3 75.1 + - - +
180R THR* 3.9 8.5 - - + +
213R THR* 3.7 16.4 - - + -
216R ALA* 4.4 7.6 - - + +
230R LEU* 6.2 1.1 - - + -
231R ASN 2.9 13.6 + - - +
232R GLY* 2.9 26.1 - - - -
233R ILE 3.0 31.0 + - - +
245R VAL* 4.4 7.9 - - + -
246R ASP 3.1 14.1 - - - +
247R LEU* 3.8 15.7 - - + -
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Residues in contact with THR 179 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246Q ASP* 2.5 29.4 + - + +
311Q LYS* 3.0 18.2 + - - -
178R MET* 1.3 75.7 + - - +
180R THR* 1.3 66.1 + - - +
181R THR* 4.0 5.1 + - - +
233R ILE* 3.2 22.0 - - + +
235R LEU* 4.0 27.8 - - + -
244R VAL 3.9 0.7 - - - +
245R VAL* 3.5 0.3 - - - -
246R ASP* 2.7 46.2 + - - +
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Residues in contact with THR 180 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R THR* 4.1 15.0 - - + +
178R MET* 3.9 8.0 - - + +
179R THR* 1.3 74.3 - - - +
181R THR* 1.3 61.7 + - - +
182R HIS* 3.3 15.6 + - + -
213R THR* 4.9 4.5 - - + -
233R ILE 3.1 5.9 + - - +
234R ALA* 3.4 26.0 - - + +
235R LEU 2.9 26.2 + - - -
244R VAL 3.3 7.9 + - - -
245R VAL* 4.0 10.8 - - - +
316R TYR* 2.6 28.7 + - - -
6339R SO4 5.2 1.3 - - - +
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Residues in contact with THR 181 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Q THR* 4.0 14.2 + - + -
208Q ILE* 4.4 12.1 - - + +
235Q LEU* 3.8 16.0 - - + +
237Q VAL* 4.4 12.3 - - + -
179R THR* 4.0 5.3 + - - +
180R THR* 1.3 69.8 - - - +
182R HIS* 1.3 59.3 - - - +
235R LEU* 3.4 12.2 - - + +
237R VAL* 3.8 34.1 - - + -
243R SER* 3.5 3.6 - - - -
244R VAL* 2.8 47.6 + - + +
246R ASP* 6.0 1.2 - - - +
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Residues in contact with HIS 182 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155R CYS* 3.6 25.6 - - - -
156R THR* 3.9 6.7 - - - -
180R THR* 3.3 14.1 + - + +
181R THR* 1.3 74.2 - - - +
183R SER* 1.3 80.5 + - - +
185R THR* 4.0 13.2 - - + -
234R ALA* 5.3 0.7 - - + -
235R LEU 2.9 7.9 + - - +
236R ARG* 3.3 31.2 + - - +
237R VAL* 2.7 37.3 + - - +
242R VAL 4.8 0.4 - - - -
243R SER* 3.3 15.8 + - - -
316R TYR* 3.3 24.4 + - - -
318R ASN* 3.8 22.9 - - + +
6339R SO4 5.9 1.6 - - - -
6340R SO4 5.6 0.7 - - - -
6341R NAP 5.1 0.4 - - - -
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Residues in contact with SER 183 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182R HIS* 1.3 94.7 + - - +
184R TYR* 1.3 65.7 + - - +
236R ARG* 3.4 4.9 + - - -
237R VAL 3.8 0.4 - - - -
239R THR* 3.0 30.9 + - - -
240R PRO 3.8 2.0 - - - -
241R ASN* 2.9 28.7 - - - -
242R VAL 2.6 27.6 + - - -
243R SER* 3.3 9.0 + - - -
318R ASN* 4.3 4.7 - - - -
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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