Contacts of the helix formed by residues 151 - 158 (chain C) in PDB entry 5T5W
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 ARG 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B TYR* 3.3 44.9 - - + +
133B PRO* 4.6 6.1 - - + +
44C PRO* 5.4 4.2 - - - +
45C ARG* 3.3 20.4 + - - +
47C TRP 5.1 0.8 + - - -
48C ASP* 2.9 30.6 + - - +
49C LEU* 5.5 0.2 - - - +
144C ASN* 5.0 1.8 + - - -
147C ARG* 3.2 41.1 + - - +
150C ALA* 1.3 79.2 - - - +
152C ASP* 1.3 87.7 + - - +
154C ASN* 3.4 3.1 + - - +
155C CYS* 2.9 31.2 + - + +
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Residues in contact with ASP 152 (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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45C ARG* 2.4 48.6 + - - -
49C LEU* 4.1 9.6 - - + +
61C LEU* 3.7 20.4 - - + -
64C GLU* 3.4 7.7 - - - +
144C ASN* 4.9 2.4 - - - +
147C ARG* 3.0 15.4 + - - +
148C LEU* 3.6 12.9 - - - +
151C ARG* 1.3 90.4 + - - +
153C LEU* 1.3 67.4 + - - +
155C CYS* 3.2 4.1 + - - +
156C VAL* 3.0 26.9 + - - +
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Residues in contact with LEU 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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6C ILE* 5.7 1.3 - - + -
9C PHE* 3.9 37.2 - - + +
12C LEU* 4.4 6.1 - - + -
61C LEU* 3.7 23.4 - - + +
96C ILE* 3.8 44.6 - - + -
100C LEU* 5.0 7.2 - - + -
148C LEU* 2.6 25.9 + - + +
149C LEU* 3.7 21.5 - - + +
152C ASP* 1.3 73.1 - - - +
154C ASN* 1.3 63.4 + - - +
156C VAL* 3.3 2.6 + - + -
157C ALA* 2.9 26.0 + - + +
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Residues in contact with ASN 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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133B PRO* 3.8 30.9 + - + +
9C PHE 4.7 4.3 - - - -
10C LYS* 2.8 41.1 + - - +
149C LEU 4.0 5.2 + - - +
150C ALA 3.3 23.3 + - - +
151C ARG 3.4 4.1 + - - +
152C ASP 3.2 0.8 - - - -
153C LEU* 1.3 79.0 - - - +
155C CYS* 1.3 58.3 + - - +
157C ALA* 3.7 5.4 - - - +
158C SER* 2.8 43.6 + - - -
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Residues in contact with CYS 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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49C LEU* 4.5 13.5 - - + -
50C ARG* 4.2 9.4 - - - +
57C ARG* 4.1 22.0 + - - -
151C ARG* 2.9 19.5 + - + +
152C ASP* 3.7 6.3 - - - +
154C ASN* 1.3 76.8 + - - +
156C VAL* 1.3 63.5 + - - +
158C SER* 3.1 10.0 + - - -
159C GLY 3.5 8.0 + - - +
162C CYS* 2.1 56.5 - - - +
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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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6C ILE* 3.6 27.6 - - + +
49C LEU* 3.7 20.2 - - + -
57C ARG* 3.9 23.6 - - + +
58C PRO* 3.8 22.0 - - + -
61C LEU* 3.7 18.4 - - + -
100C LEU* 4.1 11.9 - - + -
152C ASP 3.0 16.7 + - - +
153C LEU* 3.9 1.6 - - + +
155C CYS* 1.3 75.4 - - - +
157C ALA* 1.3 62.0 + - - +
159C GLY* 3.1 14.4 + - - -
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Residues in contact with ALA 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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6C ILE* 3.2 34.9 - - + +
7C ALA* 3.7 19.2 - - - +
9C PHE* 4.0 4.9 - - + -
10C LYS* 3.6 31.6 - - + +
153C LEU* 2.9 18.6 + - + +
154C ASN 3.8 0.4 - - - +
156C VAL* 1.3 77.5 - - - +
158C SER* 1.3 59.6 - - - +
159C GLY* 3.2 2.2 + - - -
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Residues in contact with SER 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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10C LYS* 3.3 29.4 - - - +
154C ASN* 2.8 28.4 + - - -
155C CYS* 3.1 6.8 + - - -
157C ALA* 1.3 75.8 - - - +
159C GLY* 1.3 63.6 + - - +
160C ASP 3.2 1.0 + - - -
161C LEU* 2.9 32.9 + - - +
162C CYS* 4.0 17.5 - - - -
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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