Contacts of the strand formed by residues 136 - 141 (chain E) in PDB entry 3CQ6
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 GLU 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E ARG 3.0 10.0 + - - +
115E THR* 3.2 28.9 - - + +
116E ALA* 2.7 34.3 + - - +
130E ALA* 5.0 0.2 - - - -
134E HIS 4.0 1.0 + - - -
135E THR* 1.3 72.1 - - - +
137E PHE* 1.3 64.9 + - - +
138E ILE* 4.9 8.4 - - + +
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Residues in contact with PHE 137 (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 ALA* 3.4 11.4 - - + -
118E GLY* 3.8 33.0 - - - -
120E GLN* 3.8 25.6 - - - -
126E HIS* 4.5 2.7 - - + -
127E PRO* 3.9 46.0 - - + +
130E ALA* 4.0 19.7 - - + -
135E THR 3.6 2.0 + - - -
136E GLU* 1.3 79.8 - - - +
138E ILE* 1.3 73.6 + - - +
139E ALA* 4.2 11.4 + - + -
166E PHE* 4.2 15.3 - + - -
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Residues in contact with ILE 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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115E THR* 4.1 28.7 - - + +
116E ALA 2.7 15.7 + - - +
117E LEU* 3.4 24.7 - - + +
118E GLY 3.0 26.7 + - - +
136E GLU* 4.9 10.1 - - - +
137E PHE* 1.3 80.7 - - - +
139E ALA* 1.3 67.6 + - - +
140E VAL* 4.5 3.6 - - + -
156E GLU* 5.2 2.0 - - + -
160E LYS* 3.9 49.1 - - + +
162E PRO* 5.2 3.1 - - + -
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Residues in contact with ALA 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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118E GLY 3.6 5.2 - - - -
120E GLN* 3.7 24.2 - - + +
137E PHE* 4.1 12.9 + - + -
138E ILE* 1.3 75.0 - - - +
140E VAL* 1.3 63.0 + - - +
141E SER* 4.2 1.4 + - - -
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Residues in contact with VAL 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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117E LEU* 3.7 28.9 - - + -
118E GLY 3.0 6.4 + - - +
119E PHE* 3.1 25.0 - - + +
120E GLN* 3.0 22.5 + - - -
138E ILE* 4.5 2.7 - - + -
139E ALA* 1.3 75.5 - - - +
141E SER* 1.3 71.8 + - - +
152E VAL* 4.4 31.9 - - + +
153E ALA* 4.5 4.3 - - + -
156E GLU* 3.7 28.7 - - + -
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Residues in contact with SER 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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119E PHE* 5.6 0.2 - - - -
120E GLN* 3.7 8.1 - - - -
139E ALA 4.1 1.9 + - - -
140E VAL* 1.3 80.7 - - - +
142E ARG* 1.3 70.4 + - - +
149E ASP* 4.8 1.0 + - - +
152E VAL* 4.2 14.8 - - - +
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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