Contacts of the helix formed by residues 149 - 160 (chain A) in PDB entry 5TKM
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 ASP 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LYS* 4.3 8.2 + - - +
147A ILE 3.3 1.3 + - - +
148A MET* 1.3 73.7 - - - +
150A TYR* 1.3 65.8 + - - +
151A GLU* 3.2 28.4 + - - +
152A GLU* 2.9 47.7 + - - +
153A PHE* 3.1 13.9 + - - -
174A PHE* 3.9 3.6 - - - -
178A TYR* 3.8 28.6 + - + +
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP* 1.3 75.5 - - - +
151A GLU* 1.3 79.6 + - + +
153A PHE* 3.2 4.0 + - - +
154A ALA* 3.0 33.6 + - + +
168A PHE* 3.7 30.2 + + - +
170A PRO* 3.7 29.9 - - + +
174A PHE* 3.6 28.0 - + + -
175A ASP* 6.1 0.2 - - - +
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Residues in contact with GLU 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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149A ASP* 3.3 23.0 - - - +
150A TYR* 1.3 99.3 + - + +
152A GLU* 1.3 59.1 + - + +
154A ALA* 3.4 5.5 + - - +
155A TYR* 2.9 27.9 + - - +
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Residues in contact with GLU 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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91A PHE* 3.9 23.8 - - + -
117A THR* 5.8 0.2 - - - +
119A SER* 2.7 26.2 + - - -
146A LYS* 2.7 31.3 + - - +
148A MET* 3.2 13.6 - - + -
149A ASP* 2.9 36.6 + - - +
151A GLU* 1.3 75.7 - - + +
153A PHE* 1.3 59.5 + - - +
155A TYR* 3.2 7.8 + - + +
156A CYS* 2.8 33.6 + - - -
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Residues in contact with PHE 153 (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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17A PHE* 3.9 22.1 - + - -
21A PHE* 3.2 37.5 - - + -
23A ASN* 4.3 8.7 - - + -
121A ALA* 4.0 16.4 - - + -
148A MET* 3.5 39.7 - - + +
149A ASP 3.1 24.9 + - - -
150A TYR* 3.6 7.0 - - - +
152A GLU* 1.3 75.6 - - - +
154A ALA* 1.3 56.3 + - - +
156A CYS* 3.3 4.0 + - - +
157A TRP* 2.9 28.4 + - - +
168A PHE* 3.7 19.1 - + + -
171A TRP* 3.7 15.9 - + - -
174A PHE* 3.4 28.5 - + - -
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Residues in contact with ALA 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A TYR* 3.0 36.9 + - + +
151A GLU* 3.7 6.3 - - - +
153A PHE* 1.3 75.4 - - - +
155A TYR* 1.3 63.2 + - - +
157A TRP* 3.2 8.9 + - - +
158A GLU* 3.0 23.9 + - - +
168A PHE* 4.3 10.0 - - + -
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Residues in contact with TYR 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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38A GLU* 2.4 43.5 + - - -
40A LYS* 5.3 2.9 + - - -
49A LEU* 5.5 2.1 - - - +
91A PHE* 4.1 26.2 - + - -
151A GLU 2.9 18.9 + - - +
152A GLU* 3.6 8.5 - - + +
154A ALA* 1.3 75.3 - - - +
156A CYS* 1.3 63.3 + - - +
158A GLU* 3.4 3.0 + - - -
159A ASN* 3.0 55.0 + - - +
160A PHE* 4.3 6.3 - + - -
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Residues in contact with CYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.9 18.4 - - + -
21A PHE* 5.5 0.9 - - - -
36A CYS* 4.7 4.9 - - - -
91A PHE* 3.4 48.5 - - - -
148A MET* 3.9 7.2 - - + -
152A GLU 2.8 19.1 + - - +
153A PHE* 3.6 5.4 - - - +
155A TYR* 1.3 75.4 - - - +
157A TRP* 1.3 61.7 + - - +
160A PHE* 2.7 46.3 + - + +
161A VAL* 3.5 5.4 + - - +
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Residues in contact with TRP 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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14A ARG* 3.5 32.5 - - + -
17A PHE* 3.7 30.0 - + + -
18A TYR* 3.6 35.0 - + - -
153A PHE 2.9 14.5 + - - +
154A ALA 3.5 8.3 - - - +
156A CYS* 1.3 76.7 - - - +
158A GLU* 1.3 66.0 + - - +
161A VAL* 3.4 32.3 - - + +
163A ASN* 3.0 40.1 + - + +
166A GLN* 2.9 27.5 + - + -
167A GLN* 3.4 21.8 - - - -
168A PHE* 3.6 28.0 - + + -
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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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11A ARG* 2.2 32.0 + - - -
154A ALA 3.0 15.9 + - - +
155A TYR* 3.6 7.2 - - + +
157A TRP* 1.3 84.2 - - - +
159A ASN* 1.3 65.1 - - - +
163A ASN* 3.6 13.6 + - - +
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Residues in contact with ASN 159 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLU 4.4 1.2 - - - +
11A ARG* 3.2 29.3 + - - +
38A GLU* 4.8 2.4 - - - +
52A THR* 6.5 0.2 - - + -
155A TYR* 3.0 59.3 + - + +
158A GLU* 1.3 92.7 - - - +
160A PHE* 1.3 81.5 + - + +
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Residues in contact with PHE 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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10A GLU 4.5 5.2 - - - -
11A ARG* 3.2 9.9 - - - +
12A MET* 2.8 32.5 + - + +
36A CYS* 3.6 36.8 - - + -
37A TYR 3.4 28.0 - - - -
38A GLU* 3.7 20.6 - - + -
52A THR* 4.2 8.7 - - + -
53A GLY 3.8 17.9 - - - -
54A VAL* 3.9 7.6 - - + +
91A PHE* 3.8 26.0 - + - -
155A TYR* 4.3 6.3 - + - -
156A CYS* 2.7 33.3 + - + +
159A ASN* 1.3 87.1 - - + +
161A VAL* 1.3 59.0 + - + +
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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