Contacts of the helix formed by residues 156 - 165 (chain C) in PDB entry 5L08
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 LYS 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C VAL* 4.4 17.9 - - + +
151C ILE* 3.5 29.5 - - - +
152C LEU* 4.5 1.5 - - - +
153C GLY* 2.9 18.7 + - - +
155C GLY* 1.3 87.1 + - - +
157C LEU* 1.3 60.2 + - - +
158C ASP 3.1 2.9 - - - -
159C ILE* 2.8 37.3 + - + +
160C LEU* 3.2 12.5 + - - +
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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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101C TYR* 4.1 15.5 - - + -
104C MET* 4.6 11.0 - - + -
105C LEU* 4.0 26.9 - - + -
108C ILE* 5.0 2.9 - - + -
152C LEU* 4.4 10.3 - - + -
153C GLY 2.7 15.1 + - - +
154C GLU 4.4 7.6 - - - +
156C LYS* 1.3 77.2 - - - +
158C ASP* 1.3 60.5 + - - +
159C ILE 3.1 3.2 + - - -
160C LEU* 3.8 5.1 + - + +
161C LYS* 3.7 19.6 + - - +
175C ILE* 3.9 29.3 - - + +
178C TYR* 3.7 42.4 - - + -
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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 GLU 5.4 3.5 - - - +
155C GLY* 4.8 6.4 - - - +
156C LYS* 3.1 1.8 - - - +
157C LEU* 1.3 80.6 - - - +
159C ILE* 1.3 68.7 + - + +
161C LYS* 2.9 49.3 + - - +
162C ARG* 5.0 1.9 + - - +
175C ILE* 4.3 10.2 - - - +
176C ASN* 4.3 2.6 - - - +
178C TYR* 5.6 6.5 - - - +
179C GLU* 5.6 1.4 - - - +
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Residues in contact with ILE 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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127C GLU* 5.9 0.4 - - - +
151C ILE 5.1 5.4 - - - +
155C GLY 4.5 3.4 - - - +
156C LYS* 2.8 41.6 + - + +
158C ASP* 1.3 86.6 - - + +
160C LEU* 1.3 67.9 + - - +
161C LYS 3.1 1.3 - - - -
162C ARG* 3.0 59.8 + - - +
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Residues in contact with LEU 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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105C LEU* 5.2 3.8 - - + -
108C ILE* 5.9 2.2 - - + -
120C PHE* 6.4 1.3 - - + -
124C LEU* 5.3 4.7 - - + -
127C GLU* 5.8 4.9 - - + -
143C PHE* 3.8 20.0 - - + -
146C MET* 3.7 41.3 - - + -
151C ILE 5.3 4.6 + - - +
152C LEU* 3.8 23.6 - - + -
156C LYS 3.2 9.9 + - - +
157C LEU* 4.2 6.7 - - + +
159C ILE* 1.3 79.6 - - - +
161C LYS* 1.3 58.5 + - - +
162C ARG* 2.9 6.5 + - - +
163C VAL* 3.1 37.9 + - + +
164C CYS* 3.4 18.0 + - - -
175C ILE* 6.4 0.9 - - + -
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Residues in contact with LYS 161 (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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157C LEU 3.7 4.0 + - - +
158C ASP* 2.9 52.2 + - - +
159C ILE 3.0 1.0 + - - -
160C LEU* 1.3 78.0 - - - +
162C ARG* 1.3 65.1 + - + +
163C VAL 3.1 0.7 - - - -
164C CYS* 3.6 12.3 - - - -
165C ALA* 3.2 23.0 + - - +
172C LEU* 3.7 23.0 - - + +
175C ILE* 3.7 30.9 - - + +
176C ASN* 2.8 29.6 + - - +
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Residues in contact with ARG 162 (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 GLU* 2.8 36.1 + - - +
158C ASP 5.3 1.6 - - - +
159C ILE* 3.0 43.9 + - - +
160C LEU 2.9 1.6 + - - +
161C LYS* 1.3 82.5 - - + +
163C VAL* 1.3 67.8 + - + +
165C ALA* 4.7 2.7 - - - +
166C GLN* 2.9 23.5 + - - +
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Residues in contact with VAL 163 (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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120C PHE* 4.8 4.3 - - + -
123C LEU* 3.3 46.8 - - + +
124C LEU* 6.4 1.3 - - + -
126C GLU* 6.4 0.7 - - + -
127C GLU* 3.2 34.3 - - + +
160C LEU* 3.1 28.0 + - + +
162C ARG* 1.3 86.7 - - + +
164C CYS* 1.3 65.8 + - - +
165C ALA 3.4 1.6 - - - -
166C GLN* 3.3 28.3 + - - +
167C ILE* 3.7 1.9 + - - +
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Residues in contact with CYS 164 (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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108C ILE* 5.5 8.1 - - - -
120C PHE* 3.9 21.1 - - - -
143C PHE* 6.0 1.6 - - - -
160C LEU* 3.5 36.8 - - - -
161C LYS* 3.6 14.6 - - - +
163C VAL* 1.3 76.3 - - - +
165C ALA* 1.3 59.8 + - - +
167C ILE* 3.0 5.9 + - - +
168C ASN 2.9 28.8 + - - +
171C LEU* 3.9 20.3 - - + +
172C LEU* 4.1 6.5 - - + -
175C ILE* 4.7 8.5 - - + -
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Residues in contact with ALA 165 (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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161C LYS 3.2 8.2 + - - +
162C ARG* 5.1 3.6 - - - +
164C CYS* 1.3 77.6 - - - +
166C GLN* 1.3 62.7 + - + +
167C ILE 3.1 1.7 + - - -
168C ASN 3.5 10.3 + - - -
169C LYS* 3.4 28.9 + - + +
172C LEU* 3.7 29.1 - - + +
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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