Contacts of the helix formed by residues 139 - 152 (chain A) in PDB entry 4OE4
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 TYR 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 2.8 29.2 + - + +
135A ILE* 3.7 9.6 - - + -
138A LYS* 1.3 103.9 + - + +
140A ARG* 1.3 64.9 + - - +
141A TYR 3.3 2.5 - - - -
142A ASP* 3.4 21.6 + - + +
143A MET* 2.9 23.9 + - - +
245A LEU* 4.5 10.1 - - + -
249A VAL* 3.5 30.5 - - + -
252A GLU* 2.3 43.8 + - - -
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Residues in contact with ARG 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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135A ILE 3.1 15.0 + - - +
136A SER* 2.7 35.2 + - - +
137A THR* 3.1 16.8 + - - +
138A LYS 3.4 0.6 - - - -
139A TYR* 1.3 77.8 - - - +
141A TYR* 1.3 83.1 + - + +
143A MET* 3.9 1.2 - - - +
144A LEU* 3.0 43.4 + - + +
159A GLU* 2.6 38.0 + - - +
163A ILE* 3.8 30.7 - - + +
164A THR* 5.8 0.6 + - - -
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Residues in contact with TYR 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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43A ASP* 3.3 36.5 - - + +
46A LEU* 3.6 36.9 - - + +
47A LEU* 3.7 22.9 - - + +
50A SER* 3.2 25.1 - - - +
137A THR 5.1 4.7 - - - -
138A LYS 5.2 2.6 + - - -
139A TYR 3.3 0.6 - - - -
140A ARG* 1.3 101.3 - - + +
142A ASP* 1.3 58.2 + - - +
144A LEU* 3.5 15.5 + - + +
145A ALA* 3.0 23.4 + - - +
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Residues in contact with ASP 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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50A SER* 2.9 18.0 + - - -
53A LYS* 3.0 31.7 + - - -
54A PHE* 3.3 23.0 - - + -
138A LYS 5.2 0.9 - - - +
139A TYR* 3.4 26.4 + - + +
140A ARG 3.4 0.4 - - - -
141A TYR* 1.3 78.4 - - - +
143A MET* 1.3 57.5 + - - +
145A ALA 3.3 0.2 + - - -
146A ALA* 2.9 27.7 + - - +
245A LEU* 4.3 14.1 - - + -
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Residues in contact with MET 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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135A ILE* 4.1 30.5 - - + -
139A TYR 2.9 18.1 + - - +
140A ARG 3.9 2.5 - - - +
142A ASP* 1.3 75.1 - - - +
144A LEU* 1.3 65.8 + - - +
146A ALA* 3.3 1.2 + - - +
147A THR* 3.0 34.0 + - - -
162A CYS* 3.5 26.0 - - + +
163A ILE* 4.5 1.1 - - + -
166A LEU* 4.8 1.6 - - + -
214A THR* 4.0 13.9 - - + -
242A SER* 3.7 28.5 - - - +
245A LEU* 3.8 23.5 - - + +
246A LEU* 3.8 19.5 - - + +
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Residues in contact with LEU 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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47A LEU* 3.9 14.4 - - + -
140A ARG* 3.0 41.6 + - + +
141A TYR* 3.7 21.8 - - + +
143A MET* 1.3 76.0 - - - +
145A ALA* 1.3 58.4 + - - +
147A THR* 3.7 1.6 - - - -
148A MET* 2.8 38.9 + - - +
155A VAL* 4.2 13.9 - - + +
158A ALA* 3.8 7.6 - - + -
159A GLU* 3.5 44.4 - - + +
162A CYS* 4.1 4.0 - - - -
163A ILE* 3.8 14.1 - - + -
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Residues in contact with ALA 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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47A LEU* 4.3 1.3 - - + +
50A SER* 3.7 15.5 - - - -
51A LEU* 3.7 27.4 - - + -
54A PHE* 3.6 22.9 - - + -
141A TYR 3.0 17.7 + - - +
142A ASP 3.7 0.7 - - - +
144A LEU* 1.3 74.7 - - - +
146A ALA* 1.3 60.9 + - - +
148A MET* 4.4 0.9 - - - -
149A LEU* 2.9 36.4 + - + +
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Residues in contact with ALA 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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54A PHE* 3.8 9.1 - - + -
142A ASP 2.9 17.8 + - - +
143A MET* 3.3 4.9 + - - +
145A ALA* 1.3 76.0 - - - +
147A THR* 1.3 58.4 + - - +
150A GLY* 2.9 27.0 + - - -
151A GLN* 4.1 2.3 - - - +
241A LEU* 3.6 36.4 - - + +
242A SER* 3.9 20.8 + - - -
245A LEU* 4.3 6.7 - - + -
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Residues in contact with THR 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 MET* 3.0 18.2 + - - -
144A LEU 3.8 2.9 - - - -
146A ALA* 1.3 74.5 - - - +
148A MET* 1.3 61.2 + - - +
151A GLN* 2.9 38.6 + - - +
152A GLY 3.8 0.9 + - - -
153A LYS* 3.8 26.9 + - + -
158A ALA* 4.0 11.0 - - + -
161A ASP* 4.0 8.1 - - - +
162A CYS* 3.5 15.8 - - - +
214A THR* 3.0 26.2 + - - +
242A SER* 3.4 6.6 - - - -
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Residues in contact with MET 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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47A LEU* 4.1 22.2 - - + -
51A LEU* 4.2 25.6 - - + -
83A ASN* 5.1 0.5 - - - +
144A LEU* 2.8 26.5 + - - +
145A ALA* 3.8 3.4 - - - +
147A THR* 1.3 77.4 - - - +
149A LEU* 1.3 59.2 + - + +
152A GLY* 3.0 24.8 + - - -
153A LYS* 3.1 28.8 + - - +
154A ASN* 3.9 4.0 - - - +
155A VAL* 3.7 37.0 - - + +
158A ALA* 3.5 14.8 - - + -
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Residues in contact with LEU 149 (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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51A LEU* 3.9 31.6 - - + +
54A PHE* 3.6 32.1 - - + -
55A LYS* 3.8 26.2 - - + +
83A ASN* 3.5 28.2 - - - +
84A PRO* 3.1 23.7 - - - +
91A LEU* 3.2 27.2 - - + +
145A ALA 2.9 18.3 + - - +
146A ALA* 4.5 1.8 - - - +
148A MET* 1.3 79.4 - - + +
150A GLY* 1.3 59.9 + - - +
241A LEU* 5.3 1.3 - - + -
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Residues in contact with GLY 150 (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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81A GLN* 3.5 21.7 + - - +
82A THR 4.3 2.6 - - - +
84A PRO* 3.6 12.2 - - - +
91A LEU* 3.7 11.0 - - - -
146A ALA 2.9 18.9 + - - -
149A LEU* 1.3 79.5 - - - +
151A GLN* 1.3 62.9 + - - +
152A GLY 3.5 0.4 - - - -
238A THR* 3.4 14.0 - - - +
241A LEU* 5.3 1.6 - - - -
403A ILE* 3.9 4.2 - - - +
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Residues in contact with GLN 151 (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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81A GLN* 5.5 0.2 + - - -
84A PRO* 3.9 5.2 - - - +
146A ALA 4.1 1.6 - - - +
147A THR* 2.9 24.4 + - - +
150A GLY* 1.3 76.5 - - - +
152A GLY* 1.3 62.6 + - - +
153A LYS* 3.5 8.9 - - + +
211A PHE* 2.8 29.7 + - + +
212A ASN 4.2 4.2 + - - -
213A PHE 4.1 1.0 - - - -
214A THR* 3.2 29.8 + - - +
238A THR 3.6 17.7 - - - +
239A ALA* 3.7 14.1 - - + +
242A SER* 2.9 28.4 + - - -
346A PHE* 3.4 22.6 - - + -
349A GLN* 5.0 1.6 + - - -
401A PRO 5.4 0.7 - - - +
402A VAL 6.0 0.3 - - - -
403A ILE* 4.0 15.3 - - + +
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Residues in contact with GLY 152 (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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83A ASN* 5.3 1.8 - - - -
84A PRO* 3.4 22.0 - - - +
85A ALA* 5.7 2.0 - - - -
148A MET 3.0 11.1 + - - -
151A GLN* 1.3 79.3 - - - +
153A LYS* 1.3 59.5 + - - +
154A ASN 4.2 0.2 + - - -
157A GLN* 4.3 1.2 - - - +
346A PHE* 3.7 10.1 - - - -
347A GLN* 4.2 4.9 + - - -
400A GLY* 5.0 0.9 - - - -
401A PRO* 3.7 29.7 - - - +
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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