Contacts of the helix formed by residues 149 - 160 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B LYS* 4.3 7.4 + - - +
147B ILE 3.3 1.7 + - - +
148B MET* 1.3 72.8 - - - +
150B TYR* 1.3 66.1 + - - +
151B GLU* 3.2 27.9 + - - +
152B GLU* 2.9 48.1 + - - +
153B PHE* 3.1 13.5 + - - -
174B PHE* 3.9 3.6 - - - -
178B TYR* 3.8 28.6 + - + +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASP* 1.3 73.7 - - - +
151B GLU* 1.3 79.1 + - + +
153B PHE* 3.2 4.9 + - - +
154B ALA* 3.0 31.5 + - + +
168B PHE* 3.7 30.7 + + - +
170B PRO* 3.7 29.8 - - + +
174B PHE* 3.6 27.8 - + + -
175B ASP* 6.1 0.2 - - - +
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Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASP* 3.3 22.1 - - - +
150B TYR* 1.3 97.2 + - + +
152B GLU* 1.3 59.1 + - + +
154B ALA* 3.4 6.2 + - - +
155B TYR* 2.9 28.2 + - - +
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B PHE* 3.9 23.2 - - + -
117B THR* 5.8 0.3 - - - +
119B SER* 2.7 26.1 + - - -
146B LYS* 2.7 30.1 + - - +
148B MET* 3.2 13.2 - - + -
149B ASP* 2.9 37.4 + - - +
151B GLU* 1.3 77.3 - - + +
153B PHE* 1.3 59.6 + - - +
155B TYR* 3.6 6.9 - - - +
156B CYS* 2.8 34.1 + - - -
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.9 21.2 - + - -
21B PHE* 3.2 37.7 - - + -
23B ASN* 4.3 8.3 - - + -
121B ALA* 4.0 15.9 - - + -
148B MET* 3.5 39.5 - - + +
149B ASP 3.1 23.7 + - - -
150B TYR* 3.6 6.5 - - - +
152B GLU* 1.3 77.0 - - - +
154B ALA* 1.3 57.1 + - - +
156B CYS* 3.3 4.2 + - - +
157B TRP* 2.9 28.6 + - - +
168B PHE* 3.7 20.1 - + + -
171B TRP* 3.7 16.6 - + - -
174B PHE* 3.4 28.0 - + - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR* 3.0 37.1 + - + +
151B GLU* 3.7 6.3 - - - +
153B PHE* 1.3 76.2 - - - +
155B TYR* 1.3 62.9 + - - +
157B TRP* 3.2 9.6 + - - +
158B GLU* 3.0 23.7 + - - +
168B PHE* 4.3 9.1 - - + -
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU* 2.4 45.0 + - - -
40B LYS* 5.3 2.3 + - - -
49B LEU* 5.5 2.3 - - - +
91B PHE* 4.1 26.2 - + + -
151B GLU 2.9 18.7 + - - +
152B GLU* 3.6 8.3 - - - +
154B ALA* 1.3 75.5 - - - +
156B CYS* 1.3 61.6 + - - +
158B GLU* 3.4 3.2 + - + -
159B ASN* 3.0 54.6 + - - +
160B PHE* 4.3 6.7 - + - -
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Residues in contact with CYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.9 18.4 - - + -
21B PHE* 5.5 0.9 - - - -
36B CYS* 4.7 4.7 - - - -
91B PHE* 3.4 47.6 - - - -
148B MET* 3.9 7.0 - - - -
152B GLU 2.8 20.0 + - - +
153B PHE* 3.6 5.2 - - - +
155B TYR* 1.3 75.3 - - - +
157B TRP* 1.3 62.0 + - - +
160B PHE* 2.7 48.0 + - + -
161B VAL* 3.5 5.3 + - - +
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Residues in contact with TRP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.5 31.2 - - + -
17B PHE* 3.7 30.2 - + + -
18B TYR* 3.6 34.5 - + - -
153B PHE 2.9 14.6 + - - +
154B ALA 3.5 8.5 - - - +
156B CYS* 1.3 77.2 - - - +
158B GLU* 1.3 66.8 + - - +
161B VAL* 3.4 31.7 - - + +
163B ASN* 3.0 40.7 + - + +
166B GLN* 2.9 28.7 + - + -
167B GLN* 3.4 20.3 - - - -
168B PHE* 3.6 28.3 - + + -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ARG* 2.2 31.5 + - - -
154B ALA 3.0 15.3 + - - +
155B TYR* 3.6 7.4 - - + +
156B CYS 3.1 0.2 - - - -
157B TRP* 1.3 84.6 - - - +
159B ASN* 1.3 64.3 - - - +
163B ASN* 3.6 13.1 + - - +
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Residues in contact with ASN 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU 4.4 1.4 - - - +
11B ARG* 3.2 28.7 + - - +
38B GLU* 4.8 2.4 - - - +
52B THR* 6.5 0.4 - - + -
155B TYR* 3.0 59.3 + - + +
158B GLU* 1.3 93.4 - - - +
160B PHE* 1.3 81.1 + - + +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU 4.5 4.0 - - - -
11B ARG* 3.2 9.7 - - - +
12B MET* 2.8 32.5 + - + +
36B CYS* 3.6 34.5 - - + -
37B TYR 3.4 26.5 - - - -
38B GLU* 3.7 21.3 - - + -
52B THR* 4.2 8.5 - - + -
53B GLY 3.8 19.1 - - - -
54B VAL* 3.9 7.6 - - + -
91B PHE* 3.8 24.7 - + - -
155B TYR* 4.3 6.1 - + - -
156B CYS* 2.7 33.8 + - + +
159B ASN* 1.3 90.0 - - + +
161B VAL* 1.3 59.3 + - + +
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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