Contacts of the strand formed by residues 183 - 189 (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 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B SER* 5.9 5.4 - - - -
161B ALA 3.3 9.4 - - - +
172B LEU* 3.9 17.1 - - + +
177B GLU* 3.1 52.0 + - - +
181B GLY 3.2 5.6 + - - +
182B PRO* 1.3 75.1 - - - +
184B LEU* 1.3 60.4 + - - +
185B ALA 4.1 0.8 + - - -
200B MET* 3.4 3.4 - - - +
201B ASP* 2.8 65.9 + - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.9 0.9 - - + -
159B CYS 4.3 0.2 - - - +
160B SER* 3.5 2.6 - - - -
161B ALA* 2.9 38.2 + - + +
162B GLY* 5.0 0.2 - - - -
182B PRO 4.3 0.4 - - - -
183B GLN* 1.3 71.4 - - - +
185B ALA* 1.3 63.4 + - - +
186B LEU* 4.2 2.6 + - + -
198B LEU* 3.7 29.8 - - + -
199B GLU 3.5 12.6 - - - +
200B MET* 3.5 31.9 - - + +
209B LEU* 4.3 6.7 - - + -
212B VAL* 4.3 24.5 - - + +
213B LEU* 4.3 17.0 - - + -
216B ALA* 4.2 19.1 - - + +
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Residues in contact with ALA 185 (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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134B TYR* 5.1 18.6 - - + -
135B ALA* 6.1 2.5 - - + +
159B CYS 3.6 8.1 - - - +
160B SER* 4.0 11.7 - - - +
183B GLN 4.1 2.0 + - - -
184B LEU* 1.3 74.4 - - - +
186B LEU* 1.3 64.3 + - - +
197B LEU* 6.0 0.4 - - - -
198B LEU* 3.6 0.9 - - - -
199B GLU* 2.7 44.6 + - + +
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Residues in contact with LEU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 5.9 2.5 - - - -
158B ALA* 3.1 5.1 - - - +
159B CYS 2.9 44.1 + - - +
184B LEU* 4.3 3.1 - - + -
185B ALA* 1.3 77.3 - - - +
187B ALA* 1.3 64.1 - - - +
188B LEU* 5.0 8.5 - - + -
195B ILE* 4.1 29.8 - - + -
197B LEU* 3.1 18.6 - - - +
198B LEU* 3.9 15.3 - - + -
199B GLU 4.8 0.2 - - - +
213B LEU* 4.8 7.2 - - + +
216B ALA* 3.2 42.6 - - + +
217B ALA* 4.7 13.0 - - + +
220B ALA* 5.3 2.2 - - + -
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Residues in contact with ALA 187 (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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105B THR* 5.1 2.9 - - + -
134B TYR* 5.3 0.2 - - + -
138B VAL* 4.4 8.3 - - + -
156B VAL* 4.4 14.6 - - + -
157B CYS 3.4 7.9 - - - +
158B ALA* 3.4 18.6 - - + -
186B LEU* 1.3 75.2 - - - +
188B LEU* 1.3 53.5 + - - +
195B ILE* 3.6 1.1 - - - +
196B ALA* 2.6 33.1 + - + -
197B LEU* 2.9 33.3 + - + +
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Residues in contact with LEU 188 (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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156B VAL* 3.6 2.6 - - - -
157B CYS* 2.9 37.7 + - + +
186B LEU* 5.0 7.4 - - + -
187B ALA* 1.3 76.1 - - - +
189B LEU* 1.3 71.9 + - - +
190B PRO* 3.6 7.9 - - + +
193B GLY* 4.6 17.0 - - - +
194B GLN 3.2 14.8 - - - +
195B ILE* 3.7 17.5 - - + -
196B ALA 3.8 1.1 - - - +
217B ALA* 4.6 16.8 - - + +
220B ALA* 3.2 35.9 - - + -
221B ARG* 4.1 23.8 - - - +
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Residues in contact with LEU 189 (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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241A MET* 3.9 38.6 - - + -
109B ALA* 4.4 11.4 - - + -
153B ARG* 5.2 12.1 - - + -
154B ASP* 3.8 25.4 - - + +
155B PHE 4.0 0.4 - - - +
156B VAL* 3.6 36.8 - - + -
188B LEU* 1.3 73.6 - - - +
190B PRO* 1.3 69.9 - - + +
191B ALA* 3.4 2.6 + - + +
192B SER* 3.4 13.5 + - - +
193B GLY* 3.0 17.8 + - - -
194B GLN* 2.7 18.0 + - - +
196B ALA* 4.8 5.8 - - + -
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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