Contacts of the strand formed by residues 182 - 188 (chain B) in PDB entry 1K6O
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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B GLY 5.8 0.8 + - - -
181B THR* 1.3 75.2 + - - +
183B VAL* 1.3 64.9 + - - +
199B THR* 3.0 30.0 - - - +
200B ARG* 5.4 1.0 - - - +
201B LYS* 3.4 45.0 + - + +
202B LEU* 3.6 13.1 + - + +
186C LEU* 3.8 1.4 - - + +
187C VAL* 3.7 1.9 - - - -
188C ALA* 3.3 29.4 + - + +
219C LEU* 3.3 35.0 - - + -
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Residues in contact with VAL 183 (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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172B ALA* 4.1 24.0 - - + +
175B LEU* 4.3 10.3 - - + -
176B SER* 3.8 20.2 - - - +
181B THR* 3.7 18.4 - - - +
182B GLN* 1.3 81.8 - - - +
184B LEU* 1.3 62.1 + - - +
185B LEU 4.0 0.2 - - - -
197B PHE* 3.7 13.6 - - + +
198B ALA* 3.4 19.2 - - - -
199B THR* 2.8 12.5 + - - +
202B LEU* 3.1 10.6 - - - +
168C ILE* 5.1 0.4 - - + -
185C LEU* 3.9 19.5 - - + -
186C LEU 3.2 9.4 - - - +
187C VAL* 4.0 10.1 - - + -
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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
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183B VAL* 1.3 72.5 - - - +
185B LEU* 1.3 70.0 + - - +
186B LEU* 5.1 2.2 - - + -
197B PHE 3.7 2.0 - - - +
198B ALA* 3.7 23.3 - - + -
202B LEU* 3.4 18.8 - - + +
205B MET* 3.9 31.2 - - + -
206B ILE* 4.2 19.3 - - + -
184C LEU* 3.3 30.9 - - + +
185C LEU* 3.2 8.4 - - - +
186C LEU* 2.8 51.0 + - + -
205C MET* 4.8 3.4 - - + -
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Residues in contact with LEU 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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168B ILE* 3.5 39.3 - - + +
169B MET* 3.4 36.3 - - - +
172B ALA* 4.3 13.0 - - + -
183B VAL 4.0 0.6 - - - -
184B LEU* 1.3 77.9 - - - +
186B LEU* 1.3 66.6 + - - +
187B VAL* 4.4 7.0 - - + -
196B THR* 3.6 6.1 - - - -
197B PHE* 2.9 38.1 + - + +
168C ILE* 5.6 0.2 - - + -
172C ALA* 5.4 0.7 - - + -
183C VAL* 4.4 12.6 - - + -
184C LEU 3.4 13.9 - - - +
185C LEU* 4.1 20.2 - - + -
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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
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184B LEU* 5.1 2.2 - - + -
185B LEU* 1.3 77.1 - - - +
187B VAL* 1.3 60.7 + - - +
188B ALA* 5.5 1.3 - - + +
194B VAL* 3.7 15.9 - - + -
195B TYR 3.7 1.3 - - - -
196B THR* 3.2 29.6 - - + -
206B ILE* 4.5 5.6 - - + -
215B ILE* 4.4 23.1 - - + -
219B LEU* 6.2 0.7 - - + -
182C GLN 3.8 0.5 - - - +
183C VAL* 3.1 7.1 - - - -
184C LEU* 2.8 48.1 + - + -
202C LEU* 3.7 37.7 - - + +
205C MET* 4.1 17.5 - - + -
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Residues in contact with VAL 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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161B PHE* 3.4 36.3 - - + -
165B LYS* 4.1 17.3 - - + -
168B ILE* 4.7 1.1 - - + -
169B MET* 5.2 1.3 - - - -
185B LEU* 4.4 21.1 - - + -
186B LEU* 1.3 76.4 - - - +
188B ALA* 1.3 62.8 + - - +
193B HIS 3.8 0.7 - - - +
194B VAL* 3.3 4.3 - - - -
195B TYR* 2.7 46.7 + - + +
175C LEU* 3.5 30.7 - - + -
181C THR* 4.4 4.5 - - - +
182C GLN 3.8 2.7 - - - +
183C VAL* 4.1 6.7 - - + -
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Residues in contact with ALA 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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186B LEU* 4.0 2.6 + - + +
187B VAL* 1.3 73.6 - - - +
189B SER* 1.3 69.5 + - - +
192B GLY 6.3 0.2 - - - -
193B HIS 3.6 4.5 - - - +
194B VAL* 4.4 13.9 - - + +
219B LEU* 4.9 13.0 - - + -
181C THR* 3.2 23.6 - - - -
182C GLN* 3.0 36.7 + - + +
202C LEU* 5.7 2.0 - - + -
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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