Contacts of the strand formed by residues 173 - 183 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164Q ALA* 4.4 6.7 - - + +
167Q LEU* 3.8 12.3 - - + -
168Q HIS* 2.9 41.5 + - + +
172Q GLY* 1.3 70.8 - - - -
174Q ILE* 1.3 63.3 + - - +
175Q LYS* 3.7 26.7 - - - +
226Q LEU* 3.7 21.1 - - + -
229Q LYS* 2.8 28.2 + - + +
230Q LEU* 4.4 8.3 - - + -
249Q VAL* 3.6 37.9 - - + -
250Q GLN 4.0 2.2 - - - -
251Q VAL* 4.1 5.2 - - + -
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Residues in contact with ILE 174 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172Q GLY 4.4 0.4 - - - +
173Q ILE* 1.3 73.9 - - - +
175Q LYS* 1.3 67.8 + - + +
229Q LYS* 3.2 30.8 - - - +
250Q GLN* 2.9 46.2 + - + +
251Q VAL 3.6 26.0 - - - +
252Q GLU* 3.6 24.0 - - + +
308Q ASP* 5.6 0.7 - - - +
306R ASP* 4.5 8.7 - - - +
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Residues in contact with LYS 175 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173Q ILE* 3.6 7.4 - - - +
174Q ILE* 1.3 79.3 - - + +
176Q GLY* 1.3 59.4 + - - +
229Q LYS* 3.4 10.1 - - - -
249Q VAL* 3.5 2.1 - - - -
250Q GLN* 2.7 64.4 + - + +
305R MET* 3.5 27.6 - - + +
306R ASP* 2.6 44.7 + - + -
308R ASP* 2.4 37.5 + - - -
309R LEU* 3.8 14.5 - - + +
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Residues in contact with GLY 176 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175Q LYS* 1.3 78.0 - - - +
177Q THR* 1.3 61.4 + - - -
229Q LYS 2.9 15.9 + - - +
230Q LEU* 3.4 16.3 - - - -
231Q ASN 3.3 14.4 + - - -
248Q VAL 3.1 13.5 - - - -
249Q VAL* 3.8 2.7 - - - -
305R MET* 3.7 11.1 - - - +
309R LEU* 4.7 6.5 - - - -
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Residues in contact with THR 177 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Q GLY* 1.3 75.8 - - - -
178Q MET* 1.3 64.1 + - - +
230Q LEU* 5.5 0.4 - - - -
231Q ASN 3.2 13.1 + - - -
232Q GLY* 4.6 0.5 - - - -
247Q LEU* 3.4 3.3 - - - +
248Q VAL* 2.8 38.4 + - + +
248R VAL* 3.5 30.7 - - + -
303R LEU* 4.0 13.7 - - - +
309R LEU* 4.2 11.2 - - + +
311R LYS* 3.1 39.5 + - + +
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Residues in contact with MET 178 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Q THR* 4.4 12.8 - - + -
160Q LEU* 3.7 30.7 - - + -
177Q THR* 1.3 78.9 - - - +
179Q THR* 1.3 75.3 + - - +
180Q THR* 4.0 6.7 - - + +
213Q THR* 3.7 15.9 - - + +
216Q ALA* 4.4 9.2 - - + +
230Q LEU* 6.2 1.3 - - + -
231Q ASN 2.9 12.7 + - - +
232Q GLY* 2.8 30.5 - - - -
233Q ILE 3.1 29.1 + - - +
245Q VAL* 4.7 6.5 - - + -
246Q ASP 3.2 13.5 - - - +
247Q LEU* 3.8 17.3 - - + -
311R LYS* 3.9 4.9 + - - +
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Residues in contact with THR 179 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178Q MET* 1.3 74.6 + - - +
180Q THR* 1.3 67.3 + - - +
181Q THR* 4.0 5.1 + - - +
233Q ILE* 3.2 21.5 - - + +
235Q LEU* 4.1 27.8 - - + -
244Q VAL 3.9 0.9 - - - +
245Q VAL* 3.5 0.5 - - - -
246Q ASP* 2.7 45.8 + - - +
246R ASP* 2.4 31.2 + - + +
311R LYS* 3.2 17.0 + - - -
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Residues in contact with THR 180 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156Q THR* 4.1 20.6 - - + +
178Q MET* 4.0 8.5 - - + +
179Q THR* 1.3 75.4 - - - +
181Q THR* 1.3 55.7 + - - +
182Q HIS* 3.4 14.9 + - + +
213Q THR* 4.7 4.0 - - + -
233Q ILE 3.0 6.6 + - - +
234Q ALA* 3.1 27.8 - - + -
235Q LEU 2.6 33.5 + - - -
244Q VAL 3.4 7.7 + - - -
245Q VAL* 4.2 3.8 - - - +
316Q TYR* 2.8 26.6 + - - -
5339Q SO4 5.5 0.4 - - - +
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Residues in contact with THR 181 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Q THR* 4.0 5.1 + - - +
180Q THR* 1.3 70.3 - - - +
182Q HIS* 1.3 58.8 + - - +
235Q LEU* 3.3 12.6 - - + +
237Q VAL* 3.8 33.0 - - + -
243Q SER* 3.5 4.0 - - - -
244Q VAL* 2.9 45.9 + - + +
246Q ASP* 6.1 0.9 - - - +
181R THR* 4.0 14.5 + - + -
208R ILE* 4.2 16.3 - - + +
235R LEU* 3.9 15.3 - - + +
237R VAL* 4.2 10.5 - - + -
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Residues in contact with HIS 182 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Q CYS* 3.6 25.0 - - - -
156Q THR* 4.0 7.0 - - - -
180Q THR* 3.4 14.6 + - + +
181Q THR* 1.3 74.9 - - - +
183Q SER* 1.3 83.4 + - - +
185Q THR* 4.1 12.8 - - + -
234Q ALA* 5.1 1.6 - - + -
235Q LEU 2.8 11.1 + - - +
236Q ARG* 3.2 30.5 + - - +
237Q VAL* 2.7 35.0 + - - -
243Q SER* 3.2 14.9 + - - -
316Q TYR* 3.3 20.2 + - - -
318Q ASN* 3.6 27.6 - - + +
5340Q SO4 6.1 0.2 - - - -
5341Q NAP 4.8 0.7 - - - -
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Residues in contact with SER 183 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Q HIS* 1.3 93.4 + - - +
184Q TYR* 1.3 66.6 + - - +
236Q ARG* 3.4 3.6 + - - -
237Q VAL 3.8 0.9 - - - -
239Q THR* 2.8 30.7 + - - -
240Q PRO 3.7 2.0 - - - -
241Q ASN* 2.8 29.7 + - - -
242Q VAL 2.7 27.0 + - - -
243Q SER* 3.2 9.6 + - - -
318Q ASN* 4.2 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