Contacts of the helix formed by residues 151 - 158 (chain C) in PDB entry 4G5S
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 151 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ASN* 6.0 0.2 - - - -
149C ASN* 3.1 11.7 + - - -
150C ASP* 1.3 77.2 - - - +
152C ALA* 1.3 63.5 + - - +
153C SER 3.7 0.4 - - - -
154C TYR* 3.8 4.2 - - - +
155C TYR* 3.1 31.4 + - - -
176C ARG* 3.1 37.2 - - - +
178C ARG* 4.0 4.7 - - - -
401C GDP 3.5 19.9 + - - -
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Residues in contact with ALA 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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80C SER* 3.9 22.2 - - - +
84C ILE* 4.8 6.7 - - + -
140C PHE* 5.1 3.1 - - + -
148C LEU* 3.8 27.6 - - + -
149C ASN* 3.3 17.0 + - - +
150C ASP 3.3 2.2 - - - -
151C SER* 1.3 75.6 - - - +
153C SER* 1.3 69.0 + - - +
155C TYR* 3.0 6.9 + - - +
156C LEU* 2.9 29.1 + - + +
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Residues in contact with SER 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C TRP* 4.2 16.6 - - - -
140C PHE* 3.8 29.1 - - - -
150C ASP 4.9 5.7 + - - -
152C ALA* 1.3 80.2 + - - +
154C TYR* 1.3 58.7 + - - +
156C LEU* 3.8 0.4 - - - -
157C ASN* 2.9 47.6 + - - -
176C ARG* 5.9 0.9 + - - -
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Residues in contact with TYR 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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150C ASP 5.3 0.2 + - - -
151C SER* 3.8 8.5 - - - +
152C ALA 3.1 0.6 + - - -
153C SER* 1.3 83.8 + - - +
155C TYR* 1.3 89.8 + + - +
157C ASN* 4.2 2.1 - - - +
158C ASP* 3.3 34.8 + - - +
161C ARG* 3.5 7.8 + - - -
170C THR* 4.7 0.2 + - - -
172C GLN* 3.2 41.5 - - + +
173C ASP* 2.7 24.8 + - - -
176C ARG* 3.4 56.3 - - + +
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Residues in contact with TYR 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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73C VAL* 3.6 29.6 - - + -
76C ASN* 4.2 24.0 - - + -
77C THR* 4.0 26.2 - - + +
80C SER* 5.6 0.9 - - - -
151C SER* 3.1 22.2 - - - +
152C ALA* 3.0 4.5 + - - +
154C TYR* 1.3 101.8 - + - +
156C LEU* 1.3 63.6 + - - +
158C ASP* 3.6 6.0 - - + +
159C LEU* 3.5 18.0 + - - +
161C ARG* 6.0 0.2 - - - -
162C ILE* 3.9 14.0 - - + +
173C ASP* 2.4 32.3 + - + -
176C ARG* 3.0 27.1 - - + -
177C THR* 2.8 21.9 + - + +
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Residues in contact with LEU 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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77C THR* 3.6 34.3 - - + +
80C SER* 5.4 0.7 - - - -
81C ILE* 4.5 16.2 - - + +
84C ILE* 4.0 19.7 - - + -
127C ILE* 4.7 13.7 - - + -
131C TRP* 3.4 65.1 + - + -
152C ALA* 2.9 24.8 + - + +
153C SER 4.0 0.4 - - - +
155C TYR* 1.3 78.1 - - - +
157C ASN* 1.3 57.7 + - - +
159C LEU* 3.2 24.8 - - + +
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Residues in contact with ASN 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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131C TRP* 2.9 29.6 + - - +
153C SER* 2.9 32.2 + - - +
154C TYR* 4.2 1.7 - - - +
156C LEU* 1.3 73.7 - - - +
158C ASP* 1.3 67.0 + - - +
159C LEU* 3.1 9.4 + - - +
160C ASP* 4.9 1.6 + - - +
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Residues in contact with ASP 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 TYR* 3.3 28.8 + - + +
155C TYR* 3.6 6.9 - - + +
156C LEU 3.4 0.2 - - - -
157C ASN* 1.3 83.3 - - - +
159C LEU* 1.3 62.8 + - - +
160C ASP 3.5 2.0 - - - -
161C ARG* 3.0 54.3 + - - +
162C ILE* 3.4 17.8 + - + +
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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