Contacts of the helix formed by residues 152 - 160 (chain C) in PDB entry 1U2M
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 ILE 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C ALA* 4.2 4.7 - - + -
26C ILE 2.9 15.7 + - - +
27C VAL* 4.0 8.1 - - + -
124C VAL* 4.6 6.3 - - + +
127C VAL* 4.0 19.1 - - + -
128C ALA 4.9 1.1 - - - +
131C GLN* 4.0 20.4 - - - +
133C ILE* 4.1 17.5 - - + -
136C VAL* 3.9 30.7 - - + -
150C LYS* 4.1 13.5 - - + -
151C ASP* 1.3 72.7 - - - +
153C THR* 1.3 64.0 + - - +
154C ALA 3.3 2.9 - - - -
155C ASP* 3.1 14.2 + - + +
156C VAL* 2.9 39.5 + - + +
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Residues in contact with THR 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.7 11.4 - - - +
28C ASN* 2.7 38.2 + - + +
31C SER* 4.5 10.1 - - - +
32C LEU* 3.5 26.0 - - + +
35C GLN* 4.9 4.5 - - - +
151C ASP* 2.7 24.9 + - - -
152C ILE* 1.3 75.8 - - - +
154C ALA* 1.3 58.9 + - - +
156C VAL* 3.2 4.2 + - - +
157C LEU* 3.0 25.8 + - + +
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Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ASP 4.7 3.6 + - - +
152C ILE 3.3 0.8 - - - -
153C THR* 1.3 76.4 - - - +
155C ASP* 1.3 70.0 + - - +
156C VAL 3.2 0.5 + - - -
157C LEU* 3.4 16.3 + - - +
158C LYS* 3.4 27.3 + - - +
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Residues in contact with ASP 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C VAL* 3.6 18.1 - - + +
131C GLN* 3.2 25.4 + - - +
150C LYS* 5.8 0.3 - - - +
151C ASP 5.4 0.9 + - - +
152C ILE* 3.1 17.4 + - - +
154C ALA* 1.3 81.2 - - - +
156C VAL* 1.3 61.2 + - - +
158C LYS* 3.7 12.7 + - - +
159C GLN* 3.6 23.4 + - - +
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Residues in contact with VAL 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.1 5.8 - - + -
32C LEU* 3.6 23.6 - - + -
120C ILE 4.2 1.8 - - - +
123C ALA* 3.6 19.2 - - + +
124C VAL* 3.8 19.3 - - + +
127C VAL* 3.8 18.2 - - + -
152C ILE* 2.9 42.2 + - + +
153C THR 3.5 7.4 - - - +
155C ASP* 1.3 75.9 - - - +
157C LEU* 1.3 66.0 + - - +
159C GLN* 2.9 13.3 + - - +
160C VAL* 3.2 13.1 + - + +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.9 19.7 - - + +
35C GLN* 2.9 39.9 - - + +
36C VAL* 3.9 24.9 - - + -
39C LYS* 6.6 0.2 - - + -
153C THR* 3.0 12.9 + - + +
154C ALA* 3.7 12.1 - - - +
156C VAL* 1.3 74.6 - - - +
158C LYS* 1.3 67.2 + - + +
160C VAL* 3.0 23.5 + - + +
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ALA* 3.4 21.2 + - - +
155C ASP* 3.8 16.2 - - - +
156C VAL 3.3 0.2 - - - -
157C LEU* 1.3 80.4 - - + +
159C GLN* 1.3 69.3 + - - +
160C VAL 3.4 3.6 - - - +
161C LYS* 5.2 3.6 + - - -
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Residues in contact with GLN 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ALA* 3.9 17.4 - - + +
126C SER* 4.2 15.9 + - - +
127C VAL* 3.7 19.1 - - + -
155C ASP 3.6 13.6 + - - +
156C VAL 2.9 10.1 + - - +
158C LYS* 1.3 85.0 + - - +
160C VAL* 1.3 67.3 + - - +
161C LYS* 3.2 36.2 + - - +
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 5.5 1.3 - - + -
36C VAL* 4.3 37.0 - - + -
39C LYS* 5.9 0.9 + - - -
119C ARG* 4.4 18.6 - - + +
120C ILE* 4.5 11.0 - - + +
123C ALA* 3.8 15.7 - - + -
156C VAL* 3.2 18.8 + - + +
157C LEU* 3.0 19.2 + - + +
158C LYS 4.4 3.6 - - - +
159C GLN* 1.3 78.1 - - - +
161C LYS* 1.3 74.0 + - - +
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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