Contacts of the helix formed by residues 138 - 148 (chain F) in PDB entry 5ZX2
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 138 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817C GLU* 3.9 30.8 + - + +
821C LEU* 6.0 0.9 - - - +
1161C ASN* 4.5 6.9 + - - +
1162C LEU* 5.9 0.4 - - + +
470D LYS* 5.5 8.5 + - - +
136F LEU 3.5 3.0 + - - +
137F PRO* 1.3 69.9 - - - +
139F THR* 1.3 66.7 + - - +
140F GLU* 3.6 13.5 + - - +
141F ILE* 3.7 24.6 + - + +
142F LYS* 3.1 23.9 + - - +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137F PRO* 3.6 11.7 + - - +
138F ASP* 1.3 72.4 + - - +
140F GLU* 1.3 69.1 + - - +
142F LYS* 3.0 9.9 + - + +
143F GLU* 2.9 53.8 + - + +
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ASP* 3.5 8.3 + - - +
139F THR* 1.3 79.9 - - - +
141F ILE* 1.3 65.5 - - + +
143F GLU* 3.4 5.6 + - - +
144F ALA* 2.9 25.9 + - - +
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817C GLU* 4.4 14.8 - - + +
820C LEU* 4.3 21.5 - - + -
821C LEU* 3.6 42.0 - - + -
1162C LEU* 4.0 25.4 - - + -
138F ASP* 3.6 29.7 + - + +
139F THR 3.3 0.4 - - - -
140F GLU* 1.3 78.0 - - + +
142F LYS* 1.3 57.9 + - - +
144F ALA* 3.3 6.0 + - + +
145F LEU* 2.9 30.3 + - + +
195F LEU* 5.5 7.0 - - + -
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160C ALA 4.2 10.1 + - - -
1161C ASN* 3.2 33.9 + - - +
1162C LEU* 5.0 7.6 - - - +
1163C GLY* 5.0 2.5 - - - +
137F PRO* 3.8 26.3 - - - +
138F ASP 3.1 16.2 + - - +
139F THR* 3.0 10.6 + - + +
141F ILE* 1.3 78.5 - - - +
143F GLU* 1.3 62.0 + - + +
145F LEU* 3.2 7.4 + - - +
146F GLN* 2.9 36.5 + - + +
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Residues in contact with GLU 143 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F THR* 2.9 35.8 + - + +
140F GLU* 4.0 5.1 - - - +
142F LYS* 1.3 82.0 - - + +
144F ALA* 1.3 62.7 + - - +
146F GLN* 3.2 16.4 + - - +
147F ALA* 3.3 12.8 + - - +
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F GLU 2.9 18.3 + - - +
141F ILE* 3.6 8.1 - - + +
142F LYS 3.3 0.2 - - - -
143F GLU* 1.3 76.6 - - - +
145F LEU* 1.3 61.9 + - - +
147F ALA* 3.2 10.4 + - - +
148F LEU* 3.7 3.8 + - - +
191F LEU* 3.9 16.3 - - + +
194F LEU* 3.6 41.2 - - + +
195F LEU* 5.0 12.6 - - + -
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820C LEU* 4.0 30.7 - - + -
1162C LEU* 3.5 47.1 - - + +
141F ILE* 2.9 19.5 + - + +
142F LYS 3.6 4.5 - - - +
144F ALA* 1.3 76.3 - - - +
146F GLN* 1.3 61.1 + - - +
148F LEU* 3.3 20.9 + - + +
153F ARG* 3.0 39.1 + - + +
156F VAL* 5.7 2.0 - - + -
157F TYR* 6.0 7.4 - - + +
191F LEU* 3.9 25.4 - - + -
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Residues in contact with GLN 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162C LEU 4.9 0.7 - - - +
1163C GLY* 4.3 21.8 + - - +
142F LYS* 2.9 20.4 + - + +
143F GLU* 3.4 13.0 - - - +
144F ALA 3.2 0.4 - - - -
145F LEU* 1.3 79.0 - - - +
147F ALA* 1.3 60.9 + - - +
148F LEU 3.3 8.7 - - - +
153F ARG* 3.8 31.8 + - - +
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Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F GLU 3.3 6.9 + - - +
144F ALA 3.2 2.7 + - - +
146F GLN* 1.3 75.4 - - - +
148F LEU* 1.3 64.9 + - - +
149F PRO* 3.7 2.6 - - - +
190F GLN* 4.4 5.1 - - - +
194F LEU* 3.6 29.4 - - + -
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Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144F ALA 3.7 3.9 + - - +
145F LEU* 3.3 17.2 + - + +
146F GLN 3.2 2.4 - - - +
147F ALA* 1.3 81.4 - - - +
149F PRO* 1.3 76.8 - - + +
152F PHE* 3.6 35.4 - - + +
153F ARG* 3.2 26.0 + - + +
156F VAL* 4.6 3.4 - - + -
187F GLY* 3.8 16.8 - - - +
190F GLN* 3.4 36.6 - - + +
191F LEU* 3.9 28.7 - - + +
194F LEU* 5.5 2.9 - - + -
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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