Contacts of the helix formed by residues 155 - 166 (chain A) in PDB entry 1ORI
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 MET 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A VAL* 4.0 20.6 - - + +
78A GLY* 4.6 3.1 - - - +
143A SER* 4.1 3.1 - - - +
144A GLU 2.9 32.5 - - - +
145A TRP* 3.3 14.3 + - + -
153A GLU 4.8 1.1 - - - +
154A SER* 1.3 78.0 - - - +
156A LEU* 1.3 66.1 + - - +
157A ASN* 3.1 4.6 + - - +
158A THR* 3.2 15.0 + - - +
159A VAL* 3.0 23.5 + - + +
354A SAH 3.3 57.7 - - + +
700A UNL 3.8 18.4 - - - +
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Residues in contact with LEU 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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145A TRP* 3.9 34.3 - - + +
151A PHE* 4.0 14.8 - - + -
154A SER* 3.3 14.8 + - - +
155A MET* 1.3 77.7 - - - +
157A ASN* 1.3 57.0 + - - +
159A VAL* 3.5 8.9 + - + +
160A LEU* 2.9 49.8 + - + +
237A VAL* 4.1 14.4 - - + -
239A ILE* 4.1 26.2 - - + -
242A VAL* 4.6 3.1 - - + -
247A LEU* 3.9 34.3 - - + -
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Residues in contact with ASN 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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154A SER* 5.0 1.3 + - - +
155A MET* 3.1 1.9 - - - -
156A LEU* 1.3 74.7 - - - +
158A THR* 1.3 68.6 + - - +
160A LEU* 2.9 18.4 + - - +
161A HIS* 3.0 26.5 + - + -
244A VAL* 3.7 23.8 - - - +
247A LEU* 3.3 25.7 - - - +
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Residues in contact with THR 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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77A VAL* 4.0 7.2 - - + -
128A VAL* 3.2 43.6 - - + +
129A GLU* 4.1 7.1 + - - +
155A MET* 3.2 21.8 + - - +
157A ASN* 1.3 78.9 - - - +
159A VAL* 1.3 58.1 + - - +
161A HIS* 3.1 13.0 + - - +
162A ALA* 2.9 26.6 + - - +
354A SAH 3.8 21.0 + - + +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.2 11.2 - - + -
141A ILE* 5.1 8.2 - - + +
143A SER* 3.3 35.9 - - - +
145A TRP* 4.1 17.3 - - + -
155A MET* 3.0 21.5 + - + +
156A LEU* 3.7 10.5 - - + +
158A THR* 1.3 72.1 - - - +
160A LEU* 1.3 66.1 + - - +
162A ALA* 3.4 6.8 + - - +
163A ARG* 3.0 24.1 + - + +
173A ILE* 4.9 8.5 - - + -
239A ILE* 4.5 21.8 - - + -
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Residues in contact with LEU 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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156A LEU* 2.9 34.6 + - + +
157A ASN* 2.9 12.5 + - - +
159A VAL* 1.3 77.6 - - - +
161A HIS* 1.3 64.5 + - + +
163A ARG* 3.4 20.4 + - - +
164A ASP* 3.1 31.3 + - - +
239A ILE* 4.4 6.5 - - + +
242A VAL* 3.3 38.6 - - + +
243A LYS* 3.8 8.3 - - - +
244A VAL* 3.6 42.4 - - + +
247A LEU* 5.0 2.2 - - + -
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Residues in contact with HIS 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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128A VAL* 4.7 5.6 - - + -
129A GLU* 2.5 38.7 + - + +
157A ASN* 3.0 26.5 + - + -
158A THR* 3.3 8.7 - - - +
160A LEU* 1.3 77.9 - - + +
162A ALA* 1.3 59.8 + - - +
164A ASP* 3.1 12.4 + - + +
165A LYS* 2.8 33.6 + - + +
244A VAL* 5.4 7.5 - - - +
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Residues in contact with ALA 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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75A LEU* 4.3 4.3 - - + -
77A VAL* 3.9 25.8 - - + -
128A VAL* 4.0 6.5 - - + +
141A ILE* 4.1 5.9 - - + +
158A THR 2.9 14.8 + - - +
159A VAL 3.8 4.5 - - - +
161A HIS* 1.3 76.0 - - - +
163A ARG* 1.3 57.1 + - - +
165A LYS* 4.7 0.2 - - - -
166A TRP* 2.9 60.7 + - + +
167A LEU 3.8 0.9 + - - -
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Residues in contact with ARG 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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141A ILE* 3.8 13.1 - - + +
159A VAL* 3.0 17.1 + - + +
160A LEU* 3.6 20.8 + - - +
162A ALA* 1.3 75.6 - - - +
164A ASP* 1.3 90.2 + - - +
167A LEU* 3.2 47.4 + - + +
173A ILE* 3.9 16.6 - - + -
239A ILE* 2.6 38.3 + - - -
240A TYR* 3.2 26.3 + - - +
241A THR* 3.5 2.6 + - - +
242A VAL 3.1 27.9 + - - -
243A LYS* 5.1 3.2 - - - +
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Residues in contact with ASP 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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137A LYS* 4.5 6.1 + - - -
160A LEU* 3.1 17.1 + - - +
161A HIS* 3.1 15.5 + - + +
163A ARG* 1.3 105.3 + - - +
165A LYS* 1.3 58.6 + - + +
166A TRP 3.8 0.2 + - - -
167A LEU 5.6 0.2 - - - +
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Residues in contact with LYS 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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128A VAL 5.2 2.9 + - - +
129A GLU* 5.2 14.5 + - - +
130A GLU* 6.0 1.0 - - - +
131A VAL 4.7 10.3 + - - -
136A GLU 4.4 0.9 - - - +
137A LYS* 3.5 11.7 + - - -
161A HIS 2.8 17.1 + - - +
164A ASP* 1.3 78.4 - - + +
166A TRP* 1.3 102.9 + - + +
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Residues in contact with TRP 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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75A LEU* 3.7 18.8 - - + -
99A ILE* 4.1 13.9 - - + -
128A VAL* 3.4 41.5 - - + -
131A VAL* 3.9 27.1 - - + -
133A LEU* 3.7 36.7 - - + +
135A VAL 4.6 0.6 + - - -
136A GLU 3.5 17.9 - - - +
137A LYS* 3.2 15.7 - - - +
138A VAL* 2.8 37.7 + - + +
141A ILE* 5.5 0.7 - - + -
162A ALA* 2.9 27.5 + - + +
164A ASP 3.5 0.8 + - - -
165A LYS* 1.3 119.9 - - + +
167A LEU* 1.3 66.7 + - - +
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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