Contacts of the helix formed by residues 136 - 142 (chain F) in PDB entry 3EGC
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 HIS 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109F ILE* 3.3 10.0 - - + +
112F GLU* 2.9 33.6 + - - -
129F LEU* 4.8 0.9 - - + -
131F PRO* 3.6 13.7 - - + +
132F SER 2.9 28.8 + - - -
134F GLY 3.0 24.1 + - - -
135F GLU* 1.3 74.3 - - - +
137F ASP* 1.3 65.4 + - - +
138F TYR* 3.1 6.3 - + - -
139F LEU* 3.1 31.9 + - + +
155F GLU 5.9 0.8 + - - -
156F LEU* 4.1 23.6 + - + +
158F ILE* 3.2 20.4 - - + +
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Residues in contact with ASP 137 (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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135F GLU* 3.5 26.2 - - + +
136F HIS* 1.3 74.5 - - - +
138F TYR* 1.3 57.2 + - - +
139F LEU 3.0 5.2 - - - -
140F ARG* 2.8 36.0 + - + +
141F THR* 3.2 14.5 + - + +
158F ILE* 4.3 7.9 - - - -
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Residues in contact with TYR 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F ILE* 4.8 4.3 - - + -
112F GLU* 2.7 32.6 + - - +
113F ARG* 3.5 47.6 - - + -
116F VAL* 3.4 27.5 - - + +
135F GLU* 3.7 23.8 + - - -
136F HIS* 4.0 3.1 - - - -
137F ASP* 1.3 77.6 - - - +
139F LEU* 1.3 85.2 + - + +
141F THR* 3.7 3.1 - - - -
142F GLU* 2.8 67.3 + - + +
143F LEU* 5.7 0.4 - - + -
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Residues in contact with LEU 139 (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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116F VAL* 4.0 12.3 - - + -
127F LEU* 5.3 1.3 - - + -
129F LEU* 4.1 17.5 - - + -
136F HIS* 3.1 34.8 + - + +
137F ASP 3.0 0.8 - - - -
138F TYR* 1.3 110.7 - - + +
140F ARG* 1.3 60.1 + - - +
143F LEU* 3.5 45.6 - - + +
149F ILE* 4.3 18.6 - - + +
156F LEU* 4.1 21.5 - - + -
158F ILE* 4.6 8.7 - - + -
161F CYS* 5.8 1.6 - - - -
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Residues in contact with ARG 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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137F ASP* 2.8 20.9 + - - +
139F LEU* 1.3 83.5 - - - +
141F THR* 1.3 75.3 + - + +
143F LEU 4.0 9.1 - - - +
158F ILE* 3.8 35.9 - - + +
159F PRO* 4.9 11.3 - - - +
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Residues in contact with THR 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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137F ASP* 3.2 10.7 + - + +
138F TYR* 3.8 3.1 + - - -
140F ARG* 1.3 102.1 - - + +
142F GLU* 1.3 81.6 + - - +
143F LEU 3.4 5.3 + - - +
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Residues in contact with GLU 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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113F ARG* 4.6 8.3 - - - +
120F PHE* 4.9 4.7 - - - -
138F TYR* 2.8 46.7 + - + +
141F THR* 1.3 102.9 + - - +
143F LEU* 1.3 74.0 + - + +
144F PRO* 4.6 0.5 - - - +
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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