Contacts of the helix formed by residues 155 - 163 (chain B) in PDB entry 2KRI
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 GLY 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A TRP* 5.7 2.2 - - - -
150B PRO* 5.3 8.5 - - - -
152B CYS 2.9 17.6 + - - -
153B GLU 3.3 0.6 + - - -
154B ASP* 1.3 79.2 + - - +
156B SER* 1.3 60.2 + - - +
157B ASP* 3.1 13.0 - - - -
158B GLU* 3.1 19.1 + - - +
159B TRP* 3.5 9.8 + - - +
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Residues in contact with SER 156 (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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132B PHE* 4.2 6.0 - - - -
134B CYS* 3.2 11.3 - - - +
135B ASN* 2.9 34.9 + - - -
152B CYS* 3.9 0.8 - - - +
154B ASP* 2.6 33.3 + - - -
155B GLY* 1.3 75.4 - - - +
157B ASP* 1.3 59.2 + - - +
158B GLU 3.1 1.9 + - - -
159B TRP* 3.5 27.0 + - - +
162B ARG* 4.0 21.7 - - - +
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Residues in contact with ASP 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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132B PHE* 3.7 15.3 - - + -
140B ILE* 3.6 10.5 - - + -
144B TRP 2.7 3.0 - - - +
145B ALA* 4.0 1.3 - - - -
146B CYS* 2.7 38.5 + - - -
149B ASP 3.1 0.5 - - - +
150B PRO 3.9 0.2 - - - -
151B ASP* 2.6 21.5 + - - +
152B CYS* 2.8 38.4 + - - +
155B GLY* 3.1 5.0 - - - -
156B SER* 1.3 80.1 + - - +
158B GLU* 1.3 63.9 + - - +
159B TRP 3.5 0.4 - - - -
166B CA 1.8 36.9 - - - -
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Residues in contact with GLU 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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144B TRP 3.2 0.7 - - - +
146B CYS* 3.6 5.2 - - - +
147B ASP* 2.6 16.7 + - - +
148B ASN* 2.7 25.3 + - - -
149B ASP 3.1 30.1 - - - +
150B PRO* 3.8 8.5 - - + -
155B GLY* 3.1 11.4 + - - +
156B SER 3.1 0.2 - - - -
157B ASP* 1.3 88.1 - - - +
159B TRP* 1.3 57.3 + - - +
160B PRO* 3.4 10.8 - - - +
163B CYS* 4.7 3.6 - - - -
166B CA 1.8 32.7 - - - -
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Residues in contact with TRP 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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135B ASN* 4.6 14.8 - - + -
154B ASP* 6.1 0.2 - - - -
155B GLY 3.5 7.6 + - - +
156B SER* 3.5 24.4 + - - +
157B ASP 3.5 1.0 + - - -
158B GLU* 1.3 76.6 - - - +
160B PRO* 1.3 68.6 - - + +
161B GLN* 3.1 32.3 - - + +
162B ARG* 2.7 49.2 + - + -
163B CYS* 3.3 11.0 + - - -
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Residues in contact with PRO 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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158B GLU 3.4 9.9 - - - +
159B TRP* 1.3 94.6 - - + +
161B GLN* 1.3 65.3 + - + +
162B ARG 3.1 4.3 + - - -
163B CYS* 3.3 24.2 + - + +
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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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159B TRP* 3.0 37.1 + - + +
160B PRO* 1.3 82.3 - - + +
162B ARG* 1.3 65.1 + - + +
163B CYS 3.7 0.4 - - - -
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Residues in contact with ARG 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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132B PHE* 3.2 41.3 - - - -
133B GLN 2.8 22.6 + - - -
134B CYS 3.8 0.6 - - - -
135B ASN* 2.7 57.7 + - - +
146B CYS* 4.1 5.6 - - - -
156B SER* 4.0 16.4 - - - +
159B TRP* 2.7 28.4 + - + +
161B GLN* 1.3 85.7 - - + +
163B CYS* 1.3 60.2 + - - +
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Residues in contact with CYS 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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146B CYS* 2.0 50.9 - - + -
157B ASP 4.5 0.9 - - - -
158B GLU 4.7 2.7 - - - -
159B TRP 3.5 19.7 - - - -
160B PRO* 3.3 18.7 + - + +
161B GLN 3.7 0.6 - - - -
162B ARG* 1.3 80.2 - - - +
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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