Contacts of the strand formed by residues 194 - 205 (chain B) in PDB entry 6D6Q
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 GLN 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A MET* 3.0 41.0 + - + +
242A LEU 3.5 5.6 - - - +
243A LEU* 3.7 19.3 - - + +
188B LEU* 3.2 3.7 - - - +
189B LEU* 2.7 38.4 + - + +
192B SER* 3.2 30.5 + - - +
193B GLY* 1.3 78.6 - - - +
195B ILE* 1.3 59.4 + - - +
196B ALA 3.7 0.2 + - - -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE 3.0 16.8 - - - +
241A MET* 3.2 10.8 - - - -
242A LEU* 3.0 25.7 + - + +
243A LEU* 4.5 21.1 - - - +
244A LYS* 5.1 2.7 - - + +
247A VAL* 5.9 1.1 - - + -
186B LEU* 4.1 19.7 - - + -
187B ALA 3.6 4.5 - - - +
188B LEU* 3.7 15.3 - - + -
193B GLY 5.0 2.9 - - - +
194B GLN* 1.3 73.5 - - - +
196B ALA* 1.3 58.9 + - - +
197B LEU 3.0 34.8 - - - +
198B LEU* 4.3 14.4 - - + -
213B LEU* 4.8 15.5 - - + -
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Residues in contact with ALA 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 4.5 2.2 + - - -
239A GLY* 5.0 0.2 - - - -
240A ILE 3.9 15.0 + - - +
241A MET* 5.0 2.0 - - + -
242A LEU* 5.7 0.7 - - - -
104B GLN* 3.5 19.6 + - - +
105B THR* 4.0 20.5 - - + +
108B ALA* 5.1 6.7 - - + -
109B ALA* 6.2 0.7 - - + -
156B VAL* 4.0 22.9 - - + -
187B ALA 2.6 15.1 + - - +
189B LEU* 4.8 13.5 - - + -
194B GLN 3.7 2.4 + - - -
195B ILE* 1.3 74.5 - - - +
197B LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.5 13.9 - - - +
101B GLN* 4.2 10.8 - - + +
104B GLN* 3.3 18.6 - - - +
105B THR* 3.7 13.5 - - + -
134B TYR* 2.8 48.9 - - + +
185B ALA 6.0 0.4 - - - -
186B LEU* 3.1 4.7 - - - -
187B ALA* 2.9 34.6 + - + +
195B ILE* 3.0 12.3 - - - +
196B ALA* 1.3 80.2 - - - +
198B LEU* 1.3 68.0 + - - +
199B GLU* 3.5 31.9 - - + +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.8 8.1 - - + -
234A ILE* 3.2 37.0 - - + +
235A GLN* 3.4 1.4 - - - -
236A SER* 2.9 30.6 + - - +
242A LEU* 5.3 3.1 - - + -
247A VAL* 4.3 25.4 - - + -
184B LEU* 3.7 32.5 - - + -
185B ALA 3.6 1.8 - - - -
186B LEU* 3.9 12.3 - - + -
195B ILE* 4.3 13.5 - - + -
197B LEU* 1.3 76.6 - - - +
199B GLU* 1.3 60.9 + - - +
213B LEU* 4.0 20.9 - - + -
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 2.8 29.5 + - - +
234A ILE 3.8 1.1 - - - -
235A GLN* 3.2 30.2 + - - +
236A SER 4.1 1.0 - - - +
101B GLN* 3.0 39.3 + - - +
134B TYR* 5.7 2.5 - - + -
184B LEU* 3.5 3.5 - - - +
185B ALA* 2.7 42.7 + - + +
197B LEU* 3.5 25.8 - - + +
198B LEU* 1.3 75.2 - - - +
200B MET* 1.3 65.3 + - - +
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Residues in contact with MET 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.7 16.6 + - - +
231A ILE* 3.4 18.2 - - + -
233A THR* 3.7 12.2 - - - -
234A ILE* 3.2 41.9 + - + +
182B PRO* 5.1 4.3 - - + -
183B GLN 3.4 13.2 - - - +
184B LEU* 3.5 26.7 - - + -
199B GLU* 1.3 82.1 + - - +
201B ASP* 1.3 69.3 + - - +
202B ALA 4.5 5.2 - - - +
204B LEU* 3.2 37.7 - - + -
209B LEU* 4.2 14.6 - - + -
212B VAL* 5.6 1.3 - - + -
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.6 29.5 - - + +
112A ASN* 5.0 12.7 + - + +
232A CYS 4.1 5.2 - - - -
233A THR* 4.5 0.9 - - - -
181B GLY 4.2 1.2 - - - +
183B GLN* 2.8 50.4 + - - +
200B MET* 1.3 78.7 - - - +
202B ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASN* 5.1 14.4 - - + +
113A SER* 5.7 0.4 - - - -
231A ILE 3.0 11.3 - - - +
232A CYS* 3.3 17.4 + - - +
180B GLY 3.5 17.0 - - - +
181B GLY 3.6 0.4 - - - +
182B PRO* 3.3 33.6 - - + +
183B GLN 4.7 0.2 - - - +
200B MET* 4.2 3.9 - - - +
201B ASP* 1.3 77.3 - - - +
203B ARG* 1.3 63.9 + - - +
204B LEU* 3.6 9.7 - - - +
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Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASN 5.1 1.4 + - - +
113A SER* 4.0 24.0 + - - +
114A LYS* 4.4 8.3 + - - +
188A HIS* 5.4 2.4 - - - +
189A HIS* 3.3 37.5 + - - -
226A ASN* 4.8 0.2 - - - +
230A GLU* 3.2 38.5 + - + +
231A ILE 3.1 6.7 - - - +
232A CYS* 4.3 6.3 - - - +
182B PRO* 3.9 13.9 - - - +
202B ALA* 1.3 75.8 - - - +
204B LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU* 3.0 7.1 - - - -
231A ILE* 2.7 45.5 + - + +
163B PHE* 4.8 15.0 - - + -
182B PRO* 4.0 24.9 - - + -
200B MET* 3.2 34.3 - - + -
202B ALA 3.6 12.3 - - - +
203B ARG* 1.3 79.5 - - - +
205B HIS* 1.3 67.3 + - - +
208B HIS* 3.7 28.3 - - + +
209B LEU* 5.1 2.0 - - + +
212B VAL* 5.0 7.0 - - + -
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Residues in contact with HIS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A HIS 4.1 8.4 + - - -
229A ARG* 3.2 33.8 + - + +
230A GLU* 4.2 6.8 - - + +
231A ILE* 4.3 3.6 - - - +
204B LEU* 1.3 96.1 - - - +
206B GLU* 1.3 75.7 + - + +
207B ASP* 3.1 41.9 + - + +
208B HIS* 3.6 29.1 + + + +
209B LEU* 4.4 0.7 + - - +
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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