Contacts of the helix formed by residues 133 - 148 (chain A) in PDB entry 2O7R
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 PRO 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG 4.2 0.9 - - - +
132A LEU* 1.3 84.0 - - + +
134A ALA* 1.3 65.5 + - - +
135A ALA 3.2 2.9 - - - -
136A TYR* 3.0 34.4 + - + +
137A ASP* 3.0 26.7 + - - +
181A ARG* 5.0 2.5 - - - +
236A PRO* 5.2 2.2 - - + -
245A TYR* 3.3 27.6 - - + +
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Residues in contact with ALA 134 (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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125A ARG* 3.1 38.3 + - + +
130A HIS* 3.7 24.2 - - + +
131A ARG 3.0 18.8 + - - +
132A LEU* 3.4 0.4 - - - +
133A PRO* 1.3 75.6 - - - +
135A ALA* 1.3 62.6 + - - +
137A ASP* 3.1 6.5 + - - -
138A ASP* 2.9 21.3 + - - -
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Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE* 5.2 1.6 - - + -
124A TYR* 3.7 22.5 - - + +
125A ARG 4.0 6.6 + - - +
130A HIS 5.1 1.2 + - - +
132A LEU* 4.1 13.9 - - + +
133A PRO 3.2 0.6 - - - -
134A ALA* 1.3 77.8 - - - +
136A TYR* 1.4 58.9 + - - +
138A ASP* 3.2 11.3 + - - +
139A ALA* 2.9 27.2 + - - +
174A ILE* 3.6 34.2 - - + +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.6 23.9 - - + +
133A PRO* 3.0 24.0 + - + +
135A ALA* 1.4 72.8 - - - +
137A ASP* 1.3 65.3 + - - +
139A ALA* 3.1 9.0 + - - +
140A MET* 3.0 26.5 + - - +
173A ASN* 2.7 29.2 + - - -
174A ILE* 3.8 22.2 - - + -
177A HIS* 3.4 34.5 - + + -
178A ALA* 5.4 3.2 - - - +
181A ARG* 3.6 20.0 - - - +
245A TYR* 3.3 53.8 + + - +
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A HIS* 5.8 0.4 - - + -
125A ARG* 4.0 11.0 + - - +
133A PRO* 3.0 29.4 + - - +
134A ALA* 3.5 9.3 - - - +
136A TYR* 1.3 75.3 - - - +
138A ASP* 1.3 58.2 + - - +
140A MET* 3.3 2.9 + - - +
141A GLU* 2.9 37.0 + - + +
181A ARG* 2.9 33.4 + - - +
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Residues in contact with ASP 138 (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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60A LEU* 4.2 4.8 - - + +
64A HIS* 3.1 27.4 + - - -
66A THR* 3.9 13.9 + - + +
122A VAL* 4.4 5.9 - - + +
124A TYR* 4.0 14.9 - - + +
125A ARG* 2.9 48.4 + - - +
134A ALA 2.9 10.6 + - - +
135A ALA 3.5 7.4 - - - +
137A ASP* 1.3 74.4 - - - +
139A ALA* 1.3 62.2 + - - +
141A GLU* 3.3 10.2 + - - +
142A ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 139 (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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89A PHE* 3.4 37.3 - - + -
135A ALA 2.9 12.6 + - - +
136A TYR* 3.1 8.7 + - - +
138A ASP* 1.3 76.5 - - - +
140A MET* 1.4 63.4 + - - +
142A ALA* 3.2 5.7 + - - +
143A LEU* 3.1 25.4 + - - +
174A ILE* 3.9 7.9 - - + -
178A ALA* 3.8 20.0 - - + -
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Residues in contact with MET 140 (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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136A TYR 3.0 11.0 + - - +
137A ASP 3.7 5.8 - - - +
138A ASP 3.3 0.2 - - - -
139A ALA* 1.4 72.0 - - - +
141A GLU* 1.3 66.5 + - - +
143A LEU* 3.2 22.2 + - + +
144A GLN* 3.0 36.7 + - + +
178A ALA* 3.7 26.5 - - - +
181A ARG* 3.5 49.1 - - + +
182A ALA* 3.8 27.8 - - + +
185A VAL* 4.5 10.8 - - + -
189A LEU* 5.1 2.0 - - + -
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Residues in contact with GLU 141 (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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60A LEU* 4.1 12.3 - - + +
61A ASN* 3.0 35.2 + - - +
64A HIS* 3.4 27.2 + - - -
66A THR* 4.9 0.3 + - - -
137A ASP* 2.9 23.7 + - + +
138A ASP* 3.6 10.6 - - - +
139A ALA 3.3 0.2 - - - -
140A MET* 1.3 77.4 - - - +
142A ALA* 1.3 59.7 + - - +
144A GLN* 3.3 7.8 + - - +
145A TRP* 2.9 29.9 + - - +
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Residues in contact with ALA 142 (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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60A LEU* 4.0 20.4 - - + +
68A VAL* 4.8 5.2 - - + -
87A VAL* 5.1 5.2 - - + -
122A VAL* 3.7 29.6 - - + -
138A ASP 2.9 14.4 + - - +
139A ALA 3.5 8.7 - - - +
140A MET 3.2 0.2 - - - -
141A GLU* 1.3 77.9 - - - +
143A LEU* 1.3 57.2 + - - +
145A TRP* 3.3 2.3 + - - +
146A ILE* 2.9 37.6 + - + +
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Residues in contact with LEU 143 (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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87A VAL* 4.1 35.0 - - + -
89A PHE* 5.9 0.9 - - + -
139A ALA* 3.1 15.3 + - + +
140A MET* 3.2 37.0 + - + +
142A ALA* 1.3 75.3 - - - +
144A GLN* 1.3 63.1 + - - +
146A ILE* 3.3 4.9 + - + +
147A LYS* 3.0 25.3 + - - +
163A CYS* 5.1 2.0 - - - -
165A ILE* 4.1 21.5 - - + -
178A ALA* 4.6 5.2 - - + +
182A ALA* 4.0 17.5 - - + -
189A LEU* 4.3 17.4 - - + +
192A LEU* 3.9 18.2 - - + +
194A ILE* 4.9 2.2 - - + -
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Residues in contact with GLN 144 (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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140A MET* 3.0 29.9 + - + +
141A GLU* 3.8 6.5 - - - +
143A LEU* 1.3 76.2 - - - +
145A TRP* 1.3 61.7 + - - +
147A LYS* 2.5 52.3 + - - +
148A ASP* 3.4 19.4 + - - +
185A VAL* 4.7 13.9 - - - +
188A GLU* 4.5 9.6 + - - +
189A LEU* 3.9 17.7 - - + +
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Residues in contact with TRP 145 (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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58A LEU* 3.7 44.6 - - + -
59A ALA 3.8 18.1 + - - -
60A LEU* 3.5 28.3 - - + -
68A VAL* 4.0 29.8 - - + -
70A LEU* 5.2 1.3 - - + -
141A GLU 2.9 17.3 + - - +
142A ALA 3.6 4.0 - - - +
144A GLN* 1.3 75.9 - - - +
146A ILE* 1.3 102.2 + - + +
148A ASP* 3.3 7.0 + - - +
149A SER* 3.1 34.6 + - - -
154A LEU* 4.6 9.6 - - + -
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Residues in contact with ILE 146 (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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68A VAL* 5.7 0.9 - - + -
85A LEU* 3.9 14.4 - - + -
87A VAL* 3.5 36.8 - - + -
120A ALA* 4.0 18.2 - - + -
122A VAL* 6.0 0.4 - - + -
142A ALA* 2.9 25.0 + - + +
143A LEU* 3.3 6.9 + - + +
145A TRP* 1.3 100.5 - - + +
147A LYS* 1.3 63.2 + - - +
149A SER* 3.0 17.9 + - - -
154A LEU* 4.7 7.0 - - + -
160A PHE* 3.2 17.9 - - + -
192A LEU* 3.9 27.4 - - + -
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Residues in contact with LYS 147 (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 LEU 3.0 13.3 + - - +
144A GLN* 2.5 41.2 + - - +
145A TRP 3.3 0.2 - - - -
146A ILE* 1.3 79.3 - - - +
148A ASP* 1.3 81.0 + - - +
149A SER 3.6 1.4 + - - +
150A ARG* 5.3 0.3 + - - -
160A PHE* 4.0 11.4 - - - -
188A GLU 3.4 27.1 - - - +
189A LEU* 3.5 30.5 - - + +
190A LEU 3.8 8.5 - - - +
191A PRO* 3.7 22.0 - - + +
192A LEU* 4.2 8.5 - - + -
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Residues in contact with ASP 148 (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 GLN* 3.4 17.6 + - - +
145A TRP* 3.3 6.4 + - - +
146A ILE 3.1 0.6 - - - -
147A LYS* 1.3 100.9 + - - +
149A SER* 1.3 60.6 + - - +
150A ARG* 2.7 32.7 + - - +
191A PRO* 6.0 0.2 - - - +
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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