Contacts of the helix formed by residues 156 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU* 3.3 25.4 + - - -
135A LEU 3.9 6.5 - - - -
136A ARG* 4.7 6.4 - - - +
154A GLY 4.1 1.6 + - - -
155A LYS* 1.3 84.5 - - - +
157A LEU* 1.3 65.0 + - - +
158A LEU* 3.3 6.8 + - - +
159A ARG* 3.2 34.5 + - - +
160A ARG* 3.6 15.2 + - - +
283A GLU* 4.5 15.1 + - - -
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Residues in contact with LEU 157 (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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34A TRP* 3.6 32.5 - - + -
35A LEU* 5.8 4.5 - - + -
38A ARG* 4.3 24.9 - - + +
135A LEU* 3.0 43.8 + - + +
136A ARG 4.8 0.7 - - - -
137A ALA* 3.9 16.8 - - + +
143A ILE* 5.4 2.3 - - + +
151A LEU* 3.8 35.2 - - + -
156A SER* 1.3 72.3 + - - +
158A LEU* 1.3 65.6 + - - +
160A ARG* 3.4 5.1 + - - +
161A LEU* 3.1 33.0 + - + +
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Residues in contact with LEU 158 (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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21A ILE* 5.3 5.6 - - + -
35A LEU* 6.0 3.8 - - + -
129A LYS* 4.0 26.9 - - + -
132A LEU* 3.7 47.4 + - + +
133A GLU* 4.9 2.2 - - - +
135A LEU* 5.6 0.6 - - + +
156A SER* 3.3 3.8 + - - +
157A LEU* 1.3 76.4 - - - +
159A ARG* 1.3 60.0 + - - +
161A LEU* 3.3 8.7 + - + +
162A LEU* 3.0 40.4 + - + +
167A VAL* 4.5 19.1 - - + -
170A VAL* 4.3 24.0 - - + -
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Residues in contact with ARG 159 (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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133A GLU* 5.1 13.3 - - - +
155A LYS* 6.1 1.3 - - + -
156A SER* 3.2 25.1 + - - +
158A LEU* 1.3 79.0 - - - +
160A ARG* 1.3 57.2 + - - +
162A LEU* 3.2 15.5 + - - +
163A THR* 2.9 34.7 + - - +
283A GLU* 4.2 25.6 + - - +
284A PRO 3.1 25.7 + - - -
285A ARG* 4.2 0.2 - - - +
286A PRO* 3.3 45.0 - - + +
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Residues in contact with ARG 160 (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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143A ILE* 5.2 5.0 - - + +
148A GLN* 3.3 26.6 + - - +
149A ALA* 4.3 12.2 - - + +
150A LYS* 3.6 18.0 + - - +
151A LEU* 4.4 13.9 - - + -
155A LYS* 3.1 39.6 - - + +
156A SER 3.6 12.5 + - - +
157A LEU 3.4 4.6 + - - +
158A LEU 3.4 0.2 - - - -
159A ARG* 1.3 78.0 - - - +
161A LEU* 1.3 63.5 + - - +
163A THR* 4.5 10.9 - - - +
164A SER* 3.2 54.2 + - - +
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Residues in contact with LEU 161 (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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31A THR* 5.1 8.5 - - + -
34A TRP* 5.0 7.9 - - + -
35A LEU* 4.2 26.7 - - + -
143A ILE* 3.9 18.2 - - + -
157A LEU* 3.1 29.1 + - + +
158A LEU* 3.7 11.2 - - + +
159A ARG 3.2 0.2 - - - -
160A ARG* 1.3 77.9 - - - +
162A LEU* 1.3 58.4 + - - +
164A SER* 4.3 1.6 - - - -
165A GLY 3.5 1.2 + - - -
166A ILE* 3.0 65.1 + - + -
167A VAL* 3.1 30.1 + - + -
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Residues in contact with LEU 162 (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 LYS* 5.9 4.9 - - - +
158A LEU* 3.0 34.2 + - + +
159A ARG* 3.2 15.9 + - - +
161A LEU* 1.3 77.0 - - - +
163A THR* 1.3 65.2 + - - +
165A GLY* 3.4 11.1 + - - -
167A VAL* 3.3 33.8 - - + +
168A ILE 3.7 15.7 - - - +
169A GLN* 4.7 4.0 - - - -
170A VAL* 5.2 6.1 - - + +
286A PRO* 6.4 1.6 - - + -
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Residues in contact with THR 163 (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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159A ARG* 2.9 23.1 + - - +
160A ARG* 4.5 14.7 - - - +
162A LEU* 1.3 78.8 - - - +
164A SER* 1.3 60.3 + - - +
165A GLY* 3.2 1.5 + - - -
286A PRO* 4.9 12.0 - - - +
287A GLY* 5.1 13.9 + - - +
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Residues in contact with SER 164 (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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143A ILE* 5.7 0.5 - - - +
146A TYR* 5.5 3.5 - - - -
148A GLN* 6.1 2.2 - - - -
149A ALA* 5.4 9.4 - - - +
160A ARG* 3.2 37.4 + - - +
161A LEU 4.0 0.9 + - - -
163A THR* 1.3 77.7 - - - +
165A GLY* 1.3 60.5 + - - +
166A ILE* 3.4 27.7 - - - +
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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