Contacts of the helix formed by residues 139 - 147 (chain C) in PDB entry 3ELP
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 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136C ASP* 2.7 26.1 + - - +
137C CYS 4.1 1.9 - - - -
138C SER* 1.3 86.2 - - - +
140C ILE* 1.3 54.6 + - - +
141C LYS* 3.1 4.3 - - + -
142C LEU* 2.6 54.4 + - + +
143C LEU 3.5 1.9 + - - -
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Residues in contact with ILE 140 (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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137C CYS 4.4 11.4 - - - +
138C SER 3.6 5.1 + - - +
139C LYS* 1.3 70.8 - - - +
141C LYS* 1.3 64.1 + - + +
143C LEU* 3.0 18.9 + - + +
144C GLU* 3.3 11.8 + - + +
168C ASP* 4.1 28.7 - - + +
171C GLY* 4.1 14.6 - - - -
172C CYS* 4.9 7.6 - - - +
175C ILE* 3.4 37.9 - - + -
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Residues in contact with LYS 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 LYS* 2.9 2.8 + - + +
140C ILE* 1.3 77.9 - - + +
142C LEU* 1.3 60.8 + - - +
144C GLU* 3.2 23.7 - - - +
145C ALA* 3.4 7.8 + - - +
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Residues in contact with LEU 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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135C VAL* 3.5 22.3 - - + +
136C ASP* 4.4 19.7 - - + +
139C LYS* 2.6 39.3 + - + +
141C LYS* 1.3 71.9 - - - +
143C LEU* 1.3 63.3 + - - +
145C ALA* 3.7 9.4 + - + +
146C ALA* 3.4 12.6 + - + +
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Residues in contact with LEU 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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108C ILE* 3.7 33.4 - - + -
135C VAL* 4.1 6.7 - - + +
137C CYS* 3.8 20.4 - - - -
139C LYS 3.5 2.7 + - - +
140C ILE* 3.0 14.4 + - + +
142C LEU* 1.3 75.4 - - - +
144C GLU* 1.3 58.8 + - - +
146C ALA* 2.7 26.4 + - + +
147C ILE* 3.0 24.1 + - + +
154C VAL* 4.5 13.0 - - + -
172C CYS* 3.6 40.8 - - + -
175C ILE* 4.8 8.3 - - + -
176C VAL* 4.2 12.8 - - + -
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Residues in contact with GLU 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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140C ILE* 3.3 8.9 + - + +
141C LYS* 3.2 15.0 - - - +
143C LEU* 1.3 80.4 - - - +
145C ALA* 1.3 63.1 + - - +
147C ILE* 3.2 28.4 + - - +
175C ILE* 3.5 38.9 - - + +
178C LYS* 5.1 12.3 + - - +
179C HIS* 5.6 4.0 + - - -
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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 LYS 3.4 7.9 + - - +
142C LEU* 3.8 15.9 - - + +
143C LEU 3.2 0.4 - - - -
144C GLU* 1.3 79.1 - - - +
146C ALA* 1.3 60.7 + - - +
147C ILE 3.9 5.0 - - - +
148C THR* 5.4 0.3 + - - -
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Residues in contact with ALA 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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106C GLN* 3.8 11.6 + - - -
108C ILE* 4.1 13.9 - - + +
133C SER* 5.2 1.8 - - - +
135C VAL* 3.6 32.5 - - + -
142C LEU* 3.4 6.8 + - + +
143C LEU* 2.7 18.9 + - + +
145C ALA* 1.3 72.9 - - - +
147C ILE* 1.3 65.5 + - - +
148C THR* 3.3 11.3 + - - -
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Residues in contact with ILE 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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108C ILE* 5.5 0.4 - - + -
143C LEU* 3.0 21.3 + - + +
144C GLU* 3.2 30.2 + - - +
145C ALA 3.9 6.1 - - - +
146C ALA* 1.3 78.0 - - - +
148C THR* 1.3 71.1 + - - +
149C PRO* 4.9 0.2 - - - +
151C THR* 4.0 10.3 - - + -
154C VAL* 4.8 1.1 - - + -
175C ILE* 4.9 5.2 - - + +
176C VAL* 4.4 30.5 - - + +
179C HIS* 5.4 14.6 - - + +
182C ILE* 4.5 16.2 - - + -
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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