Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 1M9L
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 ALA 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TYR* 3.2 52.8 - - + +
157A LYS* 3.1 12.3 + - + +
160A ASN* 1.3 79.4 - - - +
162A THR* 1.3 58.4 + - - +
163A SER 3.6 0.7 - - - -
164A GLU* 3.5 17.4 - - - +
165A TYR* 2.9 22.5 + - - +
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Residues in contact with THR 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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153A TYR* 3.7 25.9 - - + +
157A LYS 3.4 2.1 + - - -
158A GLU* 3.0 36.0 - - - +
159A ASN* 3.2 4.9 + - - -
160A ASN 4.6 2.5 - - - -
161A ALA* 1.3 69.5 - - - +
163A SER* 1.3 66.3 + - - +
164A GLU 3.1 0.9 - - - -
165A TYR* 2.9 13.1 + - - +
166A ARG 3.1 10.6 + - - -
182A MET* 4.0 12.8 - - + -
183A PRO* 3.1 40.9 - - + +
185A ASP* 4.5 6.7 - - - +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASN 4.8 5.9 + - - -
161A ALA 3.6 0.2 - - - -
162A THR* 1.3 77.8 - - - +
164A GLU* 1.3 56.4 + - - +
167A ILE* 3.0 33.7 + - - +
183A PRO* 3.4 15.9 + - - +
185A ASP* 4.0 9.2 + - - -
187A ASP* 3.8 20.0 + - - +
188A GLU* 2.7 34.6 + - - +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 2.9 38.4 + - - -
160A ASN 4.4 4.6 + - - +
161A ALA* 3.5 21.6 + - - +
162A THR 3.1 0.2 - - - -
163A SER* 1.3 77.3 - - - +
165A TYR* 1.3 70.8 + - - +
167A ILE* 3.9 7.8 - - - +
168A GLU* 2.9 43.4 + - + +
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Residues in contact with TYR 165 (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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130A TRP* 4.3 3.5 + - - -
134A ASP* 3.4 21.8 + - - -
139A LEU* 5.6 9.2 - - + +
153A TYR* 3.4 40.4 - + - +
156A TYR* 3.1 62.0 - + + +
161A ALA 2.9 10.0 + - - +
162A THR 2.9 8.7 + - - +
164A GLU* 1.3 78.2 + - - +
166A ARG* 1.3 57.5 + - - +
168A GLU* 3.3 5.0 + - + +
169A VAL* 2.9 32.0 + - - +
179A LEU* 3.3 33.1 - - + +
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Residues in contact with ARG 166 (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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162A THR 3.1 7.5 + - - -
165A TYR* 1.3 73.9 - - - +
167A ILE* 1.3 58.3 + - - +
169A VAL* 2.8 46.1 + - + +
170A VAL* 2.9 42.5 + - - +
177A LYS* 3.2 31.9 + - - +
178A LYS* 5.0 16.3 - - - +
179A LEU* 5.0 6.3 - - + +
183A PRO* 3.2 30.7 - - + +
184A VAL* 5.6 0.4 - - + +
188A GLU* 3.2 30.1 - - + -
189A ARG* 3.9 25.2 - - - +
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Residues in contact with ILE 167 (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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163A SER* 3.0 36.3 + - - +
164A GLU* 3.9 7.2 - - - +
166A ARG* 1.3 73.3 - - - +
168A GLU* 1.3 56.7 + - - +
170A VAL* 3.5 6.3 - - - +
171A LYS* 3.0 60.9 + - - +
187A ASP* 4.1 4.3 - - - +
188A GLU* 3.1 20.7 + - - +
191A GLN* 3.6 41.7 - - + +
192A ALA* 4.1 18.6 - - + +
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Residues in contact with GLU 168 (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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164A GLU* 2.9 33.1 + - + +
165A TYR* 3.5 6.3 - - + +
167A ILE* 1.3 76.8 - - - +
169A VAL* 1.3 59.7 + - - +
171A LYS* 4.6 9.7 - - - +
172A ARG* 2.8 67.5 + - + +
173A LEU* 3.5 9.0 + - + +
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Residues in contact with VAL 169 (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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165A TYR 2.9 18.0 + - - +
166A ARG* 2.8 25.1 + - - +
168A GLU* 1.3 72.6 - - + +
170A VAL* 1.3 66.5 + - - +
173A LEU* 2.8 46.8 + - + +
176A LEU* 3.0 43.7 - - + +
177A LYS 4.4 3.1 - - - +
179A LEU* 3.4 35.0 - - + -
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Residues in contact with VAL 170 (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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166A ARG* 2.9 40.9 + - - +
167A ILE* 3.5 10.8 - - - +
169A VAL* 1.3 75.1 - - - +
171A LYS* 1.3 67.7 + - + +
173A LEU 4.4 5.4 - - - +
189A ARG* 6.3 0.4 - - - +
192A ALA* 3.7 29.8 - - + +
196A ARG* 3.8 34.2 - - + +
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Residues in contact with LYS 171 (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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167A ILE* 3.0 41.3 + - - +
168A GLU* 4.3 10.1 - - - +
170A VAL* 1.3 82.6 - - + +
172A ARG* 1.3 58.5 + - + +
191A GLN* 5.3 5.5 - - - +
195A ALA* 3.6 36.3 - - + +
196A ARG* 5.7 6.1 - - + +
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Residues in contact with ARG 172 (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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168A GLU* 2.8 47.8 + - - +
170A VAL 4.9 0.2 - - - -
171A LYS* 1.3 75.2 - - + +
173A LEU* 1.3 69.7 + - + +
174A PRO* 4.0 3.3 - - - +
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Residues in contact with LEU 173 (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 LEU* 5.1 3.8 - - + -
140A ASP* 3.4 41.3 - - + +
168A GLU* 3.9 17.7 - - + +
169A VAL* 2.8 40.8 + - + +
170A VAL* 4.4 4.7 - - - +
172A ARG* 1.3 88.2 - - + +
174A PRO* 1.3 68.5 - - + +
176A LEU* 4.0 24.1 - - + +
179A LEU* 5.8 0.7 - - + -
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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