Contacts of the strand formed by residues 183 - 189 (chain B) in PDB entry 3K72
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 ARG 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B GLY* 4.9 0.4 - - - -
148B SER* 3.3 22.2 + - - -
177B GLN* 3.8 21.2 - - - +
178B PRO* 5.6 4.2 - - - +
180B PHE* 4.2 19.2 - - + -
182B PHE* 1.3 74.8 - - - +
184B HIS* 1.3 63.4 + - - +
185B VAL* 2.8 22.0 + - + +
201B LYS* 6.3 1.0 - - - +
202B GLN* 3.0 34.9 - - - +
268B ASP 5.8 0.2 - - - +
269B ASN* 3.6 10.3 - - + +
270B LEU* 4.1 24.9 - - + +
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Residues in contact with HIS 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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108B TYR* 2.9 35.1 + + - +
182B PHE* 4.1 16.9 - - + -
183B ARG* 1.3 68.5 - - - +
185B VAL* 1.3 62.1 + - - +
186B LEU 3.1 28.0 + - - -
187B LYS* 3.4 22.1 - - + +
188B LEU* 5.2 0.9 - - + -
227B GLU 5.3 0.9 + - - -
228B ILE* 3.4 44.6 + - + +
266B LEU* 5.4 0.7 - - + -
269B ASN* 3.0 52.6 + - + +
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Residues in contact with VAL 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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146B PHE* 3.7 29.3 + - + -
148B SER* 4.7 0.9 - - - -
183B ARG* 2.8 21.2 + - + +
184B HIS* 1.3 75.1 - - - +
186B LEU* 1.3 75.1 + - + +
198B GLU* 3.4 33.6 - - - +
199B VAL* 5.0 1.6 - - - -
201B LYS* 5.8 1.3 - - + -
202B GLN* 3.1 42.2 - - + +
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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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145B GLY* 4.0 0.9 - - - -
146B PHE* 3.2 25.2 + - + +
184B HIS* 3.1 19.0 - - - -
185B VAL* 1.3 87.0 - - + +
187B LYS* 1.3 62.7 + - - +
189B THR* 5.5 4.7 - - + +
194B GLN* 4.4 4.7 - - + +
195B PHE* 3.0 65.5 - - + +
198B GLU* 3.4 33.7 - - + -
199B VAL* 3.6 17.9 - - + -
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Residues in contact with LYS 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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143B ARG* 5.8 2.0 - - - +
144B ILE 3.3 9.3 - - - +
145B GLY* 4.2 0.8 - - - -
184B HIS* 3.4 15.1 + - + +
186B LEU* 1.3 79.1 - - - +
188B LEU* 1.3 90.2 + - - +
189B THR* 3.0 21.3 + - + +
227B GLU 5.3 4.0 - - - +
228B ILE* 3.3 31.5 + - - +
229B GLY* 3.8 15.0 - - - -
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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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106B ASP* 3.1 42.0 - - - +
107B LEU 3.7 16.8 - - - +
108B TYR* 4.2 13.5 - - + -
143B ARG* 4.1 25.1 + - + +
144B ILE 3.5 4.7 - - - -
145B GLY* 3.8 13.0 - - - +
184B HIS* 6.1 0.4 - - + -
187B LYS* 1.3 88.0 + - + +
189B THR* 1.3 63.9 + - - +
228B ILE* 4.8 2.0 - - + +
229B GLY 3.1 28.5 - - - +
230B TRP* 3.5 22.2 - - + -
231B ARG 4.0 1.1 - - - +
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Residues in contact with THR 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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143B ARG* 3.8 7.5 - - - +
144B ILE* 3.2 27.6 + - - +
186B LEU* 5.5 3.8 - - + +
187B LYS* 3.0 25.3 + - + +
188B LEU* 1.3 77.2 - - - +
190B ASN* 1.3 67.3 + - - +
191B ASN* 2.7 34.1 + - - +
195B PHE* 4.4 7.8 - - - -
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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