Contacts of the helix formed by residues 153 - 162 (chain A) in PDB entry 1P22
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 LEU 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.1 40.9 + - + +
149A PRO 3.9 0.2 + - - -
151A ARG* 3.6 19.1 - - + +
152A GLY* 1.3 81.0 - - - +
154A ASP* 1.3 65.7 + - - +
155A HIS* 3.7 17.5 - - - +
156A ILE* 3.8 22.3 + - + +
84B LEU* 4.4 19.7 - - + -
87B ASN* 3.5 31.0 - - - +
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Residues in contact with ASP 154 (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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149A PRO* 3.2 39.1 - - + +
152A GLY 3.6 9.5 + - - +
153A LEU* 1.3 68.1 - - - +
155A HIS* 1.3 73.5 + - + +
156A ILE 3.0 1.6 - - - -
157A ALA* 2.7 19.8 + - - +
158A GLU* 3.0 27.7 + - + +
181A ARG* 4.7 11.6 + - - -
182A VAL* 6.4 0.4 - - + -
185A ASP* 6.1 0.9 - - - +
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Residues in contact with HIS 155 (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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152A GLY 5.1 2.4 + - - -
153A LEU* 4.2 21.0 - - + +
154A ASP* 1.3 86.2 - - + +
156A ILE* 1.3 75.8 + - + +
158A GLU* 3.3 16.7 + - - +
159A ASN* 2.5 54.6 + - - +
87B ASN* 3.9 15.3 - - - -
95B LEU* 6.0 1.4 - - + +
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Residues in contact with ILE 156 (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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148A LEU* 3.7 19.7 - - + -
153A LEU* 3.9 21.3 - - + +
154A ASP 2.7 5.1 + - - -
155A HIS* 1.3 89.4 - - + +
157A ALA* 1.3 51.1 + - - +
159A ASN* 3.0 11.0 + - - +
160A ILE* 2.8 34.2 + - + +
83B ILE* 3.8 18.2 - - + -
87B ASN* 3.5 39.7 - - + +
95B LEU* 3.8 16.2 - - + -
99B CYS* 3.9 18.6 - - - -
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Residues in contact with ALA 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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145A ILE* 3.9 38.0 - - + +
148A LEU* 3.8 18.4 - - + +
149A PRO* 4.2 6.1 - - + -
153A LEU 4.0 0.4 + - - -
154A ASP 2.7 13.2 + - - +
156A ILE* 1.3 70.8 - - - +
158A GLU* 1.3 57.8 + - - +
160A ILE* 3.4 6.4 + - - +
161A LEU* 2.9 33.3 + - - +
182A VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 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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154A ASP* 3.0 24.9 + - + +
155A HIS* 3.5 19.6 - - - +
157A ALA* 1.3 75.6 - - - +
159A ASN* 1.3 57.8 + - - +
160A ILE 3.3 0.2 + - - -
161A LEU* 3.3 2.8 + - - +
162A SER* 2.9 31.3 + - - -
182A VAL* 4.2 16.1 - - + +
185A ASP* 4.0 7.8 - - - +
186A GLY* 3.6 22.8 + - - -
188A LEU* 4.0 18.4 - - + +
191A LYS* 3.2 25.7 + - + +
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Residues in contact with ASN 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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155A HIS* 2.5 50.4 + - - +
156A ILE* 3.0 11.7 + - - +
158A GLU* 1.3 72.7 - - - +
160A ILE* 1.3 60.6 + - - +
162A SER* 2.6 25.0 + - - -
163A TYR* 3.3 20.0 - - + +
95B LEU* 5.3 8.1 - - - +
99B CYS* 5.3 6.5 - - + -
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Residues in contact with ILE 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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144A PHE* 4.5 5.4 - - + -
145A ILE* 4.3 12.1 - - + -
148A LEU* 3.9 28.0 - - + -
156A ILE 2.8 12.7 + - - +
157A ALA* 3.5 8.5 - - - +
159A ASN* 1.3 74.3 - - - +
161A LEU* 1.3 69.2 + - - +
162A SER 3.2 0.5 + - - -
163A TYR* 3.3 20.3 + - - -
164A LEU* 4.5 1.2 - - - +
83B ILE* 4.2 8.3 - - + -
99B CYS* 3.6 31.4 - - + -
102B VAL* 4.1 37.0 - - + -
103B ALA* 3.8 15.9 - - - +
106B ILE* 4.3 8.5 - - + -
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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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145A ILE* 4.4 13.5 - - + -
157A ALA 2.9 17.5 + - - +
158A GLU 4.6 0.2 - - - -
160A ILE* 1.3 75.4 - - - +
162A SER* 1.3 58.4 + - - +
164A LEU* 2.8 45.6 + - + +
169A LEU* 5.0 1.9 - - + +
172A ALA* 3.8 24.2 - - + -
179A TRP* 4.6 6.3 - - + +
182A VAL* 3.9 25.4 - - + -
183A THR* 3.2 34.3 - - + +
188A LEU* 3.2 20.0 - - + +
106B ILE* 4.2 15.9 - - + -
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Residues in contact with SER 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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158A GLU 2.9 16.3 + - - -
159A ASN* 2.6 22.6 + - - -
160A ILE 3.2 0.2 - - - -
161A LEU* 1.3 75.2 - - - +
163A TYR* 1.3 52.9 + - - +
164A LEU 3.1 3.6 + - - +
188A LEU* 3.5 12.5 - - - +
191A LYS* 5.4 15.3 - - - -
192A LEU* 4.6 4.2 - - - +
195A ARG* 2.4 36.9 + - - -
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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