Contacts of the helix formed by residues 137 - 143 (chain E) 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 ASP 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLN* 4.2 7.6 - - - +
135E GLU* 3.6 25.4 - - + +
136E HIS* 1.3 73.5 - - - +
138E TYR* 1.3 57.0 + - - +
139E LEU 2.9 5.4 - - - -
140E ARG* 2.9 35.8 + - + +
141E THR* 3.2 14.1 + - + +
158E ILE* 4.2 9.6 - - + -
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Residues in contact with TYR 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLN* 3.0 33.6 - - + +
109E ILE* 4.7 4.3 - - + -
112E GLU* 2.6 38.4 + - - +
113E ARG* 3.7 44.5 - - + -
116E VAL* 3.6 21.3 - - + +
135E GLU 3.7 22.2 - - - -
136E HIS* 3.9 8.5 - + - -
137E ASP* 1.3 77.3 - - - +
139E LEU* 1.3 82.0 + - + +
141E THR* 3.7 0.7 - - - -
142E GLU* 2.8 58.7 + - + +
143E LEU* 5.8 0.7 - - + -
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Residues in contact with LEU 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E VAL* 4.0 12.8 - - + -
127E LEU* 5.3 0.4 - - + -
129E LEU* 4.0 24.2 - - + -
136E HIS* 3.1 30.9 + - + +
137E ASP 2.9 0.8 - - - -
138E TYR* 1.3 114.5 - - + +
140E ARG* 1.3 60.8 + - - +
141E THR 3.5 0.2 + - - -
143E LEU* 3.3 49.0 + - + +
149E ILE* 4.0 17.5 - - + +
156E LEU* 4.1 16.2 - - + -
158E ILE* 4.7 9.0 - - + -
161E CYS* 5.5 1.3 - - - -
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Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.8 8.9 - - - +
224A ALA* 5.3 0.2 - - - +
238A LYS* 5.6 12.3 - - - +
136E HIS 4.1 0.2 + - - -
137E ASP* 2.9 22.7 + - + +
139E LEU* 1.3 81.9 - - - +
141E THR* 1.3 70.8 + - + +
143E LEU 4.1 5.0 - - - +
158E ILE* 3.8 34.4 - - + +
159E PRO* 5.0 10.8 - - - +
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A VAL* 5.0 3.6 - - - +
194A ALA* 2.4 32.6 - - - +
203A LEU* 5.0 1.7 - - - +
219A GLN* 4.1 4.1 + - - +
222A ILE* 4.1 21.2 - - - +
223A ALA* 5.0 0.7 - - - -
224A ALA* 3.4 29.5 - - + +
137E ASP* 3.2 16.3 + - + +
138E TYR* 3.9 2.9 + - - -
140E ARG* 1.3 96.2 - - + +
142E GLU* 1.3 84.5 + - - +
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA 3.4 9.0 - - - -
200A ARG* 3.2 30.6 - - + +
203A LEU* 3.4 30.1 - - + +
207A ARG* 2.6 29.2 + - - +
219A GLN* 4.1 2.1 - - - +
222A ILE* 4.4 1.2 - - - +
113E ARG* 4.5 2.6 - - - +
138E TYR* 2.8 36.5 + - + +
141E THR* 1.3 106.6 + - - +
143E LEU* 1.3 67.6 + - + +
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.6 13.0 - - - +
195A GLY* 3.7 4.5 - - - -
116E VAL* 3.7 17.0 - - + -
117E GLY* 6.0 0.7 - - - -
120E PHE* 3.6 44.6 - - + -
138E TYR* 5.6 0.2 - - + -
139E LEU* 3.3 46.7 + - + +
140E ARG* 4.1 6.8 - - - +
141E THR 3.5 0.8 - - - -
142E GLU* 1.3 91.9 - - + +
144E PRO* 1.3 76.3 - - + +
145E LYS* 3.5 1.9 + - - -
147E PHE* 4.2 11.0 - - + -
149E ILE* 3.8 17.7 - - + -
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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