Contacts of the helix formed by residues 135 - 145 (chain A) in PDB entry 2P0K
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 SER 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A PHE* 4.3 1.8 - - - -
131A LEU* 3.9 24.7 - - - +
132A ASN* 2.5 31.5 + - - -
134A SER* 1.3 78.5 + - - +
136A TRP* 1.3 64.2 + - - +
137A PRO 3.5 0.7 - - - -
138A MET* 3.3 18.1 + - - +
139A PHE* 3.0 21.9 + - - +
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Residues in contact with TRP 136 (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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76A CYS* 5.1 0.2 - - + -
77A ILE* 4.4 20.2 - - + -
93A ASP 4.3 2.5 - - - -
122A MET* 6.3 2.2 - - + -
123A LEU* 3.5 28.8 + - + -
124A GLN 3.5 21.0 - - - -
125A PRO* 3.6 33.4 - - + -
126A PRO* 3.7 19.1 - - + -
129A PHE* 3.7 19.7 - + + -
132A ASN 3.6 3.8 + - - -
133A ALA 3.0 16.9 + - - +
135A SER* 1.3 76.6 - - - +
137A PRO* 1.4 74.2 - - + +
139A PHE* 3.1 31.4 + + - +
140A LEU* 2.8 56.1 + - + +
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Residues in contact with PRO 137 (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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122A MET* 6.2 4.0 - - + -
133A ALA 3.8 5.6 - - - +
134A SER* 3.6 16.8 - - - +
135A SER 3.7 0.2 - - - -
136A TRP* 1.4 102.1 - - + +
138A MET* 1.3 60.7 + - - +
140A LEU* 3.4 6.9 + - + +
141A LEU* 3.1 23.2 + - - +
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Residues in contact with MET 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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131A LEU* 4.1 21.8 - - + -
134A SER 5.2 1.1 + - - +
135A SER* 3.3 28.4 + - - +
136A TRP 3.3 0.6 - - - -
137A PRO* 1.3 73.6 - - - +
139A PHE* 1.3 74.6 + - + +
141A LEU* 3.3 3.6 + - - +
142A LYS* 3.0 41.7 + - + +
306A CL 3.5 28.8 - - + +
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Residues in contact with PHE 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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93A ASP* 3.7 26.2 - - + -
94A GLY* 3.3 26.0 - - - -
129A PHE* 3.7 15.7 - + + -
130A ARG* 3.9 11.2 - - - -
131A LEU* 4.1 16.8 - - + -
135A SER 3.0 17.3 + - - +
136A TRP* 3.1 24.9 + + - +
138A MET* 1.3 88.1 - - + +
140A LEU* 1.3 55.6 + - - +
142A LYS* 3.4 25.3 - - - +
143A THR* 2.7 51.4 + - - -
401A PO4 3.4 21.5 - - - -
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Residues in contact with LEU 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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77A ILE* 3.3 33.9 - - + -
123A LEU* 3.8 23.1 - - + +
136A TRP* 2.8 44.8 + - + +
137A PRO* 3.7 7.4 - - + +
139A PHE* 1.3 77.3 - - - +
141A LEU* 1.3 64.0 + - - +
143A THR* 3.6 4.7 - - - -
144A LEU* 3.0 43.6 + - + +
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Residues in contact with LEU 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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137A PRO 3.1 10.8 + - - +
138A MET* 3.7 7.4 - - - +
140A LEU* 1.3 81.6 - - - +
142A LYS* 1.3 59.3 + - + +
144A LEU* 3.3 4.2 + - - +
145A ASN* 3.0 32.9 + - + +
306A CL 4.1 19.1 - - + -
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Residues in contact with LYS 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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130A ARG* 5.8 0.2 - - - +
138A MET* 3.0 36.2 + - + +
139A PHE* 3.4 40.2 - - - +
141A LEU* 1.3 76.6 - - + +
143A THR* 1.3 74.5 + - - +
144A LEU 3.5 0.2 + - - -
145A ASN* 3.5 18.4 + - - +
401A PO4 4.4 7.1 + - - -
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Residues in contact with THR 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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63A LYS* 3.6 19.0 - - + +
77A ILE* 4.6 8.1 - - + -
93A ASP* 3.5 33.0 - - + +
139A PHE* 2.7 49.3 + - + -
140A LEU* 3.6 6.5 - - - -
142A LYS* 1.3 86.4 + - - +
144A LEU* 1.3 63.2 + - + +
145A ASN 4.1 2.4 - - - +
147A ALA* 3.5 13.3 - - - +
401A PO4 4.3 4.0 + - - +
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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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63A LYS* 4.4 6.5 - - + -
77A ILE* 4.0 25.6 - - + -
113A ILE* 3.7 45.5 - - + -
117A GLU* 6.0 1.8 - - - +
123A LEU* 5.4 1.6 - - + -
140A LEU* 3.0 41.1 + - + +
141A LEU* 4.0 3.6 - - - +
143A THR* 1.3 77.1 - - + +
145A ASN* 1.3 66.2 + - - +
146A GLY 3.1 0.9 + - - -
147A ALA* 3.0 19.4 + - + +
149A MET* 5.7 3.4 - - + +
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Residues in contact with ASN 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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141A LEU* 3.0 22.3 + - + +
142A LYS* 3.5 16.2 + - - +
143A THR 3.4 2.3 - - - +
144A LEU* 1.3 75.5 - - - +
146A GLY* 1.3 63.7 + - - +
147A ALA 3.2 1.1 + - - -
302A CL 3.5 26.4 - - - +
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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