Contacts of the strand formed by residues 181 - 188 (chain C) in PDB entry 3KJ4
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 LEU 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122C LYS 5.4 0.9 - - - +
124C THR* 4.2 17.7 - - + +
151C GLY* 3.4 36.3 - - - +
152C TYR 4.1 0.4 - - - +
153C PHE* 4.0 23.8 - - + -
177C LEU* 3.3 1.0 - - - -
178C GLN* 2.6 53.1 + - + +
179C SER* 3.2 5.1 - - - +
180C ASP* 1.3 84.6 - - - +
182C TYR* 1.3 63.6 + - - +
183C THR* 4.2 0.2 - - - +
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Residues in contact with TYR 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C GLY 3.1 5.7 + - - -
152C TYR* 2.9 61.6 + + + +
153C PHE* 3.9 26.9 - + - -
155C GLU* 3.3 49.0 - - + +
175C ALA* 3.5 17.3 - - + -
176C VAL* 3.2 7.0 - - - -
177C LEU* 3.4 30.7 - - + +
181C LEU* 1.3 71.0 - - - +
183C THR* 1.3 59.8 + - - +
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Residues in contact with THR 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 4.9 3.8 - - - +
149C VAL 3.1 14.2 + - - -
150C LYS* 3.4 16.1 - - - +
151C GLY* 3.6 13.0 - - - +
152C TYR* 4.0 2.0 - - - -
174C PRO 4.7 0.3 - - - +
175C ALA* 4.2 0.7 - - - -
176C VAL* 2.9 47.8 + - + +
178C GLN* 3.1 46.7 + - + +
181C LEU 4.2 0.9 - - - +
182C TYR* 1.3 76.5 - - - +
184C LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LEU* 3.4 7.0 - - - +
149C VAL* 2.7 58.4 + - + +
152C TYR* 4.0 15.7 - - - +
155C GLU* 5.1 3.6 - - - +
157C VAL* 4.3 15.5 - - + +
159C VAL* 3.6 29.2 - - + -
172C THR* 4.4 9.0 - - + -
173C PHE 3.4 19.3 - - - +
174C PRO* 4.8 2.7 - - + -
175C ALA* 3.8 22.7 - - + +
183C THR* 1.3 76.2 + - - +
185C SER* 1.3 68.6 + - - +
186C SER* 5.2 0.2 - - - -
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Residues in contact with SER 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 5.0 2.5 - - - -
140B PHE* 3.8 16.4 - - - -
181B SER* 2.6 32.5 + - - -
183B THR* 5.4 1.8 - - - -
147C CYS 3.6 7.0 - - - -
148C LEU* 3.6 17.9 - - - -
172C THR* 4.0 0.3 - - - +
173C PHE* 3.2 31.5 + - - +
174C PRO 5.4 0.2 + - - -
184C LEU* 1.3 82.0 - - - +
186C SER* 1.3 62.8 + - - +
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Residues in contact with SER 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PHE* 3.3 6.7 - - - -
146C GLY* 3.0 3.1 - - - -
147C CYS* 2.8 41.0 + - - -
159C VAL* 3.8 18.6 - - - -
161C TRP* 3.5 14.0 + - - -
170C VAL* 3.8 0.2 - - - +
171C HIS 3.4 6.4 + - - -
172C THR* 2.7 28.9 + - - -
173C PHE* 4.1 0.7 - - - -
185C SER* 1.3 78.2 - - - +
187C SER* 1.3 70.2 + - - +
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PHE* 3.4 31.5 - - - -
142B ASN* 3.6 20.5 + - - -
144C THR* 4.3 4.5 - - - -
145C LEU 3.3 8.7 - - - -
161C TRP* 3.8 2.0 + - - -
169C GLY 4.6 1.2 + - - -
170C VAL* 3.5 6.9 - - - +
171C HIS* 3.0 38.1 + - - +
173C PHE* 4.0 1.4 - - - -
186C SER* 1.3 84.8 + - - +
188C VAL* 1.3 67.3 + - - +
189C THR* 5.0 2.0 - - - +
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Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C THR* 3.6 2.4 + - - -
145C LEU* 3.0 44.3 + - + +
161C TRP* 3.4 65.5 - - + -
166C LEU* 4.3 17.0 - - + -
169C GLY 3.3 6.7 - - - -
170C VAL* 3.5 21.1 - - + -
187C SER* 1.3 70.1 - - - +
189C THR* 1.3 65.7 + - - +
190C VAL* 4.0 5.4 - - + +
200C VAL* 4.4 6.7 - - + -
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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