Contacts of the helix formed by residues 156 - 166 (chain B) in PDB entry 7KAC
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 PHE 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLU* 4.2 15.5 + - + +
65B ILE* 3.6 31.2 - - + -
66B LEU* 4.1 22.2 - - + -
69B CYS* 4.8 0.7 - - - -
74B ILE* 3.9 32.1 - - + -
75B VAL* 4.6 2.7 - - + -
128B LEU* 3.7 31.2 - - + -
133B LYS* 6.5 0.4 - - + -
134B ILE 5.3 0.4 - - - -
135B HIS* 3.5 34.1 - + + -
153B LEU* 4.3 13.2 - - + -
154B ALA* 4.6 2.0 - - - -
155B ASP* 1.3 74.4 - - - +
157B GLY* 1.3 56.9 + - - +
158B ILE 3.4 2.9 - - - -
159B SER* 3.2 18.3 + - - +
160B ALA* 2.9 29.5 + - - +
401B W9D 4.7 0.8 + - - -
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Residues in contact with GLY 157 (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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62B GLU* 3.4 21.5 - - - -
155B ASP* 3.1 17.4 + - - -
156B PHE* 1.3 77.2 - - - +
158B ILE* 1.4 56.6 + - - +
160B ALA* 3.4 2.4 + - - +
161B GLN* 3.0 40.1 + - - +
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Residues in contact with ILE 158 (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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173A ILE* 4.3 8.5 - - + +
174A GLY* 4.2 27.6 - - - +
135B HIS 4.8 0.4 - - - +
136B ARG* 3.7 28.5 - - + +
137B ASP* 3.5 35.0 - - + +
155B ASP* 4.5 4.3 + - - +
156B PHE 3.4 0.4 - - - -
157B GLY* 1.4 73.1 - - - +
159B SER* 1.3 60.6 + - - +
161B GLN* 3.3 18.2 + - - +
162B ILE* 3.0 46.9 + - + +
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Residues in contact with SER 159 (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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65B ILE* 3.5 19.1 - - - +
134B ILE 3.1 28.1 + - - -
135B HIS 3.3 14.1 + - - -
136B ARG* 4.8 1.6 - - - -
156B PHE* 3.2 24.0 + - - +
158B ILE* 1.3 80.5 - - - +
160B ALA* 1.3 51.8 + - - +
162B ILE* 3.8 8.6 - - - +
163B GLY* 2.8 30.7 + - - -
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Residues in contact with ALA 160 (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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58B THR* 3.5 26.6 - - - +
61B LYS* 4.1 7.6 - - - +
62B GLU* 3.6 23.3 - - + +
65B ILE* 4.2 6.7 - - + -
156B PHE 2.9 17.8 + - - +
157B GLY* 3.6 6.1 - - - +
158B ILE 3.2 0.2 - - - -
159B SER* 1.3 75.6 + - - +
161B GLN* 1.4 61.2 + - - +
163B GLY* 3.9 0.6 - - - +
164B ALA* 3.0 31.4 + - - +
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Residues in contact with GLN 161 (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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173A ILE* 5.2 14.1 - - + +
28B TYR* 4.2 29.6 + - - +
58B THR* 4.6 13.7 - - - -
157B GLY* 3.0 29.4 + - - +
158B ILE* 3.3 21.4 + - - +
160B ALA* 1.4 75.1 - - - +
162B ILE* 1.3 59.7 + - + +
164B ALA* 4.1 2.2 - - - +
165B THR* 2.7 33.3 + - - +
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Residues in contact with ILE 162 (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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173A ILE* 5.0 9.0 - - + -
136B ARG* 3.4 51.1 - - + +
158B ILE* 3.0 29.3 + - + +
159B SER* 3.9 5.4 - - - +
161B GLN* 1.3 74.4 - - - +
163B GLY* 1.3 61.1 + - - +
165B THR* 3.3 4.6 + - - -
166B LEU* 2.8 37.9 + - + +
189B LYS 5.3 6.1 - - - +
190B GLY* 6.2 1.8 - - - -
192B TYR* 3.5 17.3 - - + +
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Residues in contact with GLY 163 (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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61B LYS* 5.4 5.4 - - - -
159B SER 2.8 21.1 + - - -
160B ALA* 3.9 1.6 - - - -
161B GLN 3.5 0.2 - - - -
162B ILE* 1.3 75.1 - - - +
164B ALA* 1.4 56.4 + - - +
166B LEU* 3.2 9.1 - - - +
167B ALA* 3.1 24.4 - - - +
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Residues in contact with ALA 164 (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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57B SER* 3.9 38.9 - - - +
58B THR* 4.2 5.2 - - - +
61B LYS* 4.9 3.7 - - + +
160B ALA 3.0 18.3 + - - +
161B GLN* 4.2 3.4 - - - +
163B GLY* 1.4 72.7 - - - +
165B THR* 1.3 68.4 + - - +
167B ALA* 4.1 3.4 - - - +
168B ARG* 3.7 16.1 + - - +
169B ARG* 3.8 8.3 + - - +
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Residues in contact with THR 165 (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 GLN 2.7 24.7 + - - -
162B ILE* 3.3 5.1 + - - -
164B ALA* 1.3 78.2 - - - +
166B LEU* 1.3 58.8 + - + +
167B ALA 2.9 5.5 + - - -
169B ARG* 3.6 12.9 + - + +
170B LEU* 2.9 43.0 + - + +
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Residues in contact with LEU 166 (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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162B ILE* 2.8 27.0 + - + +
163B GLY* 3.2 8.1 - - - +
165B THR* 1.3 68.9 - - + +
167B ALA* 1.3 62.0 + - - +
170B LEU* 4.8 9.6 - - - -
171B SER* 4.5 4.7 - - - -
186B VAL 5.2 7.2 - - - +
187B ALA 5.1 9.2 - - - +
188B LEU 5.3 5.6 - - - +
189B LYS 5.2 11.9 - - - +
190B GLY* 5.5 2.5 - - - -
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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