Contacts of the strand formed by residues 179 - 189 (chain A) in PDB entry 1K4C
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 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LYS 5.7 0.2 - - - +
122A THR* 4.1 15.3 - - + +
149A GLY* 3.7 38.1 - - - +
150A TYR 3.7 6.7 - - - +
151A PHE* 4.1 9.0 - - + -
174A VAL 3.7 0.9 - - - +
175A LEU* 3.5 7.9 - - - +
176A GLN* 3.0 33.3 + - - +
177A SER* 3.1 10.6 - - - +
178A ASP* 1.3 90.4 - - + +
180A TYR* 1.3 62.4 + - - +
181A THR* 4.9 1.5 + - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 5.7 3.9 - - + +
148A LYS* 3.6 1.4 - - - -
149A GLY 2.9 23.9 + - - -
150A TYR* 2.8 54.8 + + + +
151A PHE* 3.5 30.7 - + - -
152A PRO* 4.4 0.2 - - + -
153A GLU* 3.8 34.9 - - + +
173A ALA* 3.9 19.1 - - + -
174A VAL 3.4 10.5 - - - -
175A LEU* 3.7 35.2 - - + +
179A LEU* 1.3 72.2 - - - +
181A THR* 1.3 63.0 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.9 17.7 - - + -
147A VAL 3.2 6.7 - - - +
148A LYS* 2.9 46.9 + - + +
149A GLY 3.6 1.4 + - - -
150A TYR* 4.4 0.4 - - - -
172A PRO 4.4 0.5 - - - +
173A ALA* 3.3 3.3 - - - -
174A VAL* 3.0 44.3 + - + +
179A LEU* 4.9 1.6 + - - +
180A TYR* 1.3 79.8 + - - +
182A LEU* 1.3 65.9 + - - +
160B LEU* 6.2 0.4 - - - -
178B THR* 5.7 7.9 - - + +
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.9 3.2 - - - +
147A VAL* 2.7 51.8 + - + +
150A TYR* 3.3 29.6 - - + +
153A GLU* 5.0 1.3 - - - +
155A VAL* 3.6 15.5 - - + +
157A VAL* 4.3 9.0 - - + -
170A THR* 4.2 17.5 - - + -
171A PHE* 3.5 22.9 - - - +
172A PRO 4.3 2.2 - - - +
173A ALA* 3.9 11.4 - - + +
181A THR* 1.3 77.5 - - - +
183A SER* 1.3 74.2 + - - +
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A LEU* 4.2 5.0 - - - +
145A CYS 3.2 9.6 - - - -
146A LEU* 3.2 30.1 - - - +
170A THR* 3.8 0.5 - - - -
171A PHE* 3.1 36.3 + - - +
182A LEU* 1.3 79.3 - - - +
184A SER* 1.3 60.6 + - - +
133B VAL* 4.2 7.5 - - - +
135B PHE* 3.8 26.2 - - - -
176B SER* 5.3 3.6 - - - -
178B THR* 4.9 2.8 + - - -
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLY* 3.1 25.3 - - - -
145A CYS* 3.1 17.1 + - - -
157A VAL* 3.7 24.8 - - - +
159A TRP* 3.1 22.8 + - - -
168A VAL* 4.0 2.3 - - - +
169A HIS 3.2 5.1 + - - -
170A THR* 3.0 25.3 + - - +
171A PHE* 4.8 0.4 - - - -
182A LEU* 4.6 0.4 - - - +
183A SER* 1.3 74.4 - - - +
185A SER* 1.3 60.9 + - - +
135B PHE* 3.8 5.5 - - - -
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 3.6 12.0 - - - +
143A LEU 3.6 4.7 - - - -
159A TRP* 4.6 0.7 - - - -
167A GLY 4.0 1.2 + - - -
168A VAL* 3.1 9.7 - - - +
169A HIS* 2.5 53.1 + - - -
171A PHE* 4.2 5.1 - - - -
184A SER* 1.3 75.2 + - - +
186A VAL* 1.3 64.5 + - - +
187A THR* 4.6 1.7 + - - -
135B PHE* 3.7 16.1 - - - -
137B ASN* 2.9 25.1 + - - -
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL 3.8 0.3 - - - +
142A THR* 3.4 2.6 - - - +
143A LEU* 2.8 54.0 + - + +
159A TRP* 3.7 39.9 - - + +
164A LEU* 3.8 29.6 - - + -
166A SER 4.9 0.9 - - - +
167A GLY 3.1 4.7 - - - +
168A VAL* 4.0 15.9 - - + -
185A SER* 1.3 75.6 + - - +
187A THR* 1.3 66.2 + - - +
188A VAL* 4.4 9.3 + - + +
198A VAL* 4.2 6.3 - - + -
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.4 39.0 - - + +
141A VAL 3.3 11.9 - - - +
142A THR* 3.1 24.2 + - - +
164A LEU* 5.7 0.2 - - - +
166A SER 4.3 4.9 - - - +
167A GLY* 2.9 28.2 + - - -
169A HIS* 6.0 1.7 - - - -
185A SER* 4.6 2.8 + - - -
186A VAL* 1.3 74.7 - - - +
188A VAL* 1.3 66.9 + - - +
137B ASN* 5.0 2.4 + - - +
138B ASN* 5.6 4.2 + - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.3 8.9 - - - +
141A VAL* 2.9 40.7 + - + +
143A LEU* 4.9 4.9 - - + -
164A LEU* 4.0 35.2 - - + -
186A VAL* 4.4 6.3 - - + +
187A THR* 1.3 78.4 - - - +
189A PRO* 1.3 84.7 - - + +
192A SER* 3.8 9.0 - - - +
193A TRP* 4.2 12.3 - - + -
198A VAL* 4.6 14.8 - - + -
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Residues in contact with PRO 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER 3.5 12.1 - - - +
140A MET* 3.5 15.5 - - + -
188A VAL* 1.3 91.7 - - + +
190A SER* 1.3 65.1 + - - +
191A SER* 3.1 12.6 - - - +
192A SER* 2.8 34.8 + - - +
193A TRP 3.8 1.2 + - - -
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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