Contacts of the helix formed by residues 140 - 152 (chain C) in PDB entry 4PKO
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 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C PRO 5.7 0.3 - - - +
139C SER* 1.3 86.6 + - - +
141C SER* 1.3 58.8 + - - +
142C LYS* 3.0 18.3 - - + +
143C ALA* 2.9 50.8 + - - +
144C ILE* 3.2 9.0 + - - +
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Residues in contact with SER 141 (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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139C SER 3.6 1.6 + - - -
140C ASP* 1.3 69.5 - - - +
142C LYS* 1.3 60.1 + - - +
143C ALA 3.3 0.2 - - - -
144C ILE* 3.8 14.7 - - - +
145C ALA* 2.9 29.6 + - - +
163C ALA* 3.5 14.5 + - - +
167C ASP* 2.8 36.9 + - - +
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Residues in contact with LYS 142 (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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140C ASP* 3.0 13.8 + - + +
141C SER* 1.3 79.2 - - - +
143C ALA* 1.3 57.1 + - - +
145C ALA* 3.3 7.3 + - - +
146C GLN* 2.9 58.2 + - + +
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Residues in contact with ALA 143 (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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138C CYS* 3.8 18.8 - - + -
139C SER 4.8 1.1 - - - +
140C ASP* 2.9 28.7 + - - +
142C LYS* 1.3 76.6 - - - +
144C ILE* 1.3 64.4 + - - +
146C GLN* 3.1 21.9 + - - +
147C VAL* 2.9 25.6 + - + +
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Residues in contact with ILE 144 (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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138C CYS* 4.3 16.6 - - - +
139C SER 3.8 17.3 - - - +
140C ASP 3.2 10.5 + - - +
141C SER* 3.7 18.2 - - - +
143C ALA* 1.3 75.7 - - - +
145C ALA* 1.3 64.0 + - - +
146C GLN 3.1 0.3 + - - -
147C VAL* 3.4 6.1 + - + +
148C GLY* 3.1 22.0 + - - -
159C GLY 4.7 0.3 - - - +
162C ILE* 4.7 5.1 - - + +
163C ALA* 3.6 24.5 - - + +
166C MET* 4.0 37.5 - - + -
167C ASP* 5.6 0.4 - - - +
171C LYS* 3.8 20.0 - - - +
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Residues in contact with ALA 145 (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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141C SER 2.9 18.6 + - - +
142C LYS* 3.5 7.9 - - - +
144C ILE* 1.3 76.6 - - - +
146C GLN* 1.3 54.4 + - + +
149C THR* 2.5 38.0 + - - +
159C GLY* 3.2 26.2 - - - +
160C LYS* 4.2 6.7 - - + +
163C ALA* 3.6 6.3 - - + +
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Residues in contact with GLN 146 (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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142C LYS* 2.9 50.9 + - + +
143C ALA* 3.1 20.0 + - - +
145C ALA* 1.3 77.7 - - + +
147C VAL* 1.3 61.9 + - + +
149C THR* 3.3 4.1 + - - -
150C ILE* 3.0 37.9 + - + +
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Residues in contact with VAL 147 (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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138C CYS* 4.3 14.8 - - - -
143C ALA* 2.9 20.6 + - + +
144C ILE* 4.1 6.1 - - + +
146C GLN* 1.3 71.9 - - + +
148C GLY* 1.3 70.0 + - - +
150C ILE* 3.9 8.1 - - - +
151C SER* 3.1 25.0 + - - -
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Residues in contact with GLY 148 (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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144C ILE 3.1 12.4 + - - -
145C ALA 4.2 0.9 - - - -
147C VAL* 1.3 86.9 - - - +
149C THR* 1.3 60.8 + - - +
151C SER* 3.5 4.3 + - - -
152C ALA* 3.0 25.2 + - - +
158C VAL* 4.2 3.7 - - - +
159C GLY* 4.0 11.2 - - - -
162C ILE* 4.9 16.1 - - - +
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Residues in contact with THR 149 (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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145C ALA* 2.5 25.1 + - - +
146C GLN* 3.3 6.7 + - - -
148C GLY* 1.3 77.5 - - - +
150C ILE* 1.3 65.5 + - + +
152C ALA 3.3 5.0 + - - -
153C ASN 3.3 0.5 + - - -
154C SER* 2.8 32.1 + - - -
155C ASP 3.2 36.2 + - - +
156C GLU* 3.7 18.9 + - + +
159C GLY* 3.0 14.1 + - - +
160C LYS 4.3 0.2 + - - -
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Residues in contact with ILE 150 (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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146C GLN* 3.0 25.5 + - + +
147C VAL* 3.9 7.4 - - - +
148C GLY 3.2 0.4 - - - -
149C THR* 1.3 81.7 - - + +
151C SER* 1.3 62.0 + - - +
152C ALA 3.0 4.5 - - - -
153C ASN* 2.9 19.9 + - - -
154C SER* 4.4 8.5 - - - +
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Residues in contact with SER 151 (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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87C ASP* 2.2 36.1 + - - +
147C VAL* 3.1 18.3 + - - -
148C GLY* 4.0 4.7 - - - -
150C ILE* 1.3 80.2 - - - +
152C ALA* 1.3 57.2 + - - +
153C ASN* 3.1 3.8 + - - +
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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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148C GLY 3.0 17.4 + - - +
149C THR 3.5 6.5 - - - +
150C ILE 3.0 0.8 - - - -
151C SER* 1.3 77.7 - - - +
153C ASN* 1.3 69.8 + - - +
154C SER 3.5 0.4 + - - -
155C ASP* 3.8 13.8 - - + +
158C VAL* 3.5 36.8 - - + -
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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