Contacts of the helix formed by residues 156 - 164 (chain B) in PDB entry 6R7Y
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 SER 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLU* 3.3 25.5 + - - -
135B LEU 3.9 6.5 - - - -
136B ARG* 4.7 6.2 - - - +
154B GLY 4.0 1.8 + - - -
155B LYS* 1.3 84.9 - - - +
157B LEU* 1.3 65.1 + - - +
158B LEU* 3.3 6.6 + - - +
159B ARG* 3.2 33.2 + - - +
160B ARG* 3.6 15.1 + - - +
283B GLU* 4.5 15.7 + - - -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 3.6 32.8 - - + -
35B LEU* 5.8 4.5 - - + -
38B ARG* 4.3 26.0 - - + +
135B LEU* 3.0 44.0 + - + +
136B ARG 4.8 0.7 - - - -
137B ALA* 3.9 16.8 - - + +
143B ILE* 5.4 3.0 - - + +
151B LEU* 3.8 35.7 - - + -
155B LYS 4.6 0.2 - - - +
156B SER* 1.3 71.9 + - - +
158B LEU* 1.3 65.0 + - - +
160B ARG* 3.4 4.8 + - - +
161B LEU* 3.1 33.0 + - + +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 5.3 5.6 - - + -
35B LEU* 6.0 4.0 - - + -
129B LYS* 4.0 27.6 - - + -
132B LEU* 3.7 45.6 + - + +
133B GLU* 4.9 2.7 - - - +
135B LEU* 6.0 0.9 - - + +
156B SER* 3.3 3.8 + - - +
157B LEU* 1.3 77.3 - - - +
159B ARG* 1.3 59.1 + - - +
161B LEU* 3.3 8.6 + - + +
162B LEU* 3.0 39.6 + - + +
167B VAL* 4.5 18.6 - - + -
170B VAL* 4.3 24.5 - - + -
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 5.1 13.5 + - - +
155B LYS* 6.1 0.9 - - + -
156B SER* 3.2 25.6 + - - +
158B LEU* 1.3 79.4 - - - +
160B ARG* 1.3 57.8 + - - +
162B LEU* 3.2 14.3 + - - +
163B THR* 2.9 35.0 + - - +
283B GLU* 4.2 25.6 + - - +
284B PRO 3.1 25.8 + - - +
285B ARG* 4.2 0.2 - - - +
286B PRO* 3.3 45.9 - - + +
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Residues in contact with ARG 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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143B ILE* 5.2 5.0 - - + +
148B GLN* 3.3 26.0 + - - +
149B ALA* 4.3 12.6 - - + +
150B LYS* 3.6 18.9 + - - +
151B LEU* 4.4 13.2 - - + -
155B LYS* 3.1 40.2 - - + +
156B SER 3.6 12.5 + - - +
157B LEU 3.4 4.9 + - - +
158B LEU 3.4 0.4 - - - -
159B ARG* 1.3 75.0 - - - +
161B LEU* 1.3 65.6 + - - +
163B THR* 4.5 11.5 - - - +
164B SER* 3.2 54.0 + - - +
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Residues in contact with LEU 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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31B THR* 5.1 8.5 - - + -
34B TRP* 5.0 7.9 - - + -
35B LEU* 4.2 26.9 - - + -
143B ILE* 3.9 18.8 - - + -
157B LEU* 3.1 27.8 + - + +
158B LEU* 3.7 10.8 - - + +
159B ARG 3.2 0.2 - - - -
160B ARG* 1.3 78.2 - - - +
162B LEU* 1.3 60.2 + - - +
164B SER* 4.3 0.9 - - - -
165B GLY 3.5 1.2 + - - -
166B ILE* 3.0 66.4 + - + -
167B VAL* 3.1 29.1 + - + -
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Residues in contact with LEU 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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129B LYS* 5.9 5.2 - - - +
158B LEU* 3.0 35.5 + - + +
159B ARG* 3.2 16.1 + - - +
161B LEU* 1.3 76.6 - - - +
163B THR* 1.3 65.0 + - - +
165B GLY* 3.4 10.9 + - - -
167B VAL* 3.3 34.2 - - + +
168B ILE 3.7 15.0 - - - +
169B GLN* 4.7 4.3 - - - -
170B VAL* 5.2 4.9 - - + +
286B PRO* 6.4 1.8 - - + -
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Residues in contact with THR 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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159B ARG* 2.9 23.3 + - - +
160B ARG* 4.5 15.7 - - - +
162B LEU* 1.3 78.7 - - - +
164B SER* 1.3 61.0 + - - +
165B GLY* 3.2 1.5 + - - -
286B PRO* 4.9 11.6 - - - +
287B GLY* 5.1 13.4 + - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 5.7 0.5 - - - +
146B TYR* 5.5 3.3 - - - -
148B GLN* 6.1 2.0 - - - -
149B ALA* 5.4 9.1 - - - +
160B ARG* 3.2 37.6 + - - +
161B LEU* 4.0 1.0 + - - +
163B THR* 1.3 75.8 - - - +
165B GLY* 1.3 60.6 + - - +
166B ILE* 3.4 27.4 - - - +
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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