Contacts of the helix formed by residues 113 - 124 (chain E) in PDB entry 2QC8
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 LEU 113 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 6.1 0.8 - - - +
110E GLU 4.1 13.7 - - - +
111E THR* 3.2 11.7 + - - +
112E ASN* 1.3 77.1 - - - +
114E ARG* 1.3 63.7 + - - +
115E HIS 3.3 1.3 - - - -
116E THR* 4.0 4.4 + - - +
117E CYS* 3.4 21.7 + - - +
347E ASP* 3.7 27.8 + - + +
349E PHE* 3.7 10.7 - - + +
350E SER* 3.9 26.0 - - - +
353E GLU* 4.2 4.0 - - - +
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Residues in contact with ARG 114 (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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82E ALA* 3.7 31.5 + - - +
98E LEU* 5.5 2.5 - - - -
99E CYS 5.6 1.3 - - - -
100E GLU* 3.2 33.9 + - + +
112E ASN* 3.0 7.5 + - - +
113E LEU* 1.3 77.7 - - - +
115E HIS* 1.3 59.8 + - - +
117E CYS* 4.3 0.2 - - - -
118E LYS* 2.8 49.8 + - - +
212E ILE* 3.8 22.3 - - + +
216E ASP* 2.7 40.2 + - - -
349E PHE* 3.5 41.8 - - + -
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Residues in contact with HIS 115 (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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100E GLU* 3.2 24.6 + - - +
102E PHE* 3.9 18.9 - + - -
108E PRO* 3.8 24.7 - - + +
112E ASN* 2.8 21.3 + - - +
113E LEU 3.3 0.8 - - - -
114E ARG* 1.3 78.8 - - - +
116E THR* 1.3 65.8 + - - +
118E LYS* 3.5 3.9 + - - +
119E ARG* 3.5 54.1 + - + +
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Residues in contact with THR 116 (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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112E ASN 5.2 0.8 + - - -
113E LEU* 4.0 5.2 + - - -
115E HIS* 1.3 79.3 - - - +
117E CYS* 1.3 66.7 + - - +
119E ARG* 3.2 11.8 + - + +
120E ILE* 3.0 22.0 + - + +
353E GLU* 3.2 30.7 - - - +
357E ARG* 3.6 15.3 - - - +
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Residues in contact with CYS 117 (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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113E LEU 3.4 17.7 + - - +
114E ARG 3.3 4.6 + - - +
116E THR* 1.3 78.1 - - - +
118E LYS* 1.3 63.2 + - - +
120E ILE* 3.3 3.7 + - - +
121E MET* 3.0 40.4 + - - +
212E ILE* 3.7 16.8 - - + -
349E PHE* 3.2 31.2 - - + +
352E THR* 3.3 17.9 - - - -
353E GLU* 3.2 20.3 + - - +
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Residues in contact with LYS 118 (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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100E GLU* 5.2 1.6 - - - +
114E ARG* 2.8 37.5 + - - +
115E HIS* 3.8 6.1 - - - +
117E CYS* 1.3 76.4 - - - +
119E ARG* 1.3 65.2 + - + +
121E MET* 3.3 2.3 + - + +
122E ASP* 2.6 58.2 + - - +
212E ILE* 3.8 35.9 - - + +
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Residues in contact with ARG 119 (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 HIS* 3.5 41.6 + - + +
116E THR* 3.2 11.5 + - + +
118E LYS* 1.3 80.8 - - + +
120E ILE* 1.3 64.6 + - + +
122E ASP* 3.3 9.9 + - - +
123E MET* 3.2 29.3 + - - +
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Residues in contact with ILE 120 (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 THR* 3.0 19.6 + - + +
117E CYS* 3.7 9.4 - - - +
119E ARG* 1.3 76.2 - - + +
121E MET* 1.3 60.7 + - + +
123E MET* 3.3 22.6 + - - +
124E VAL* 3.4 13.9 + - - +
353E GLU* 4.3 15.3 - - + +
356E ILE* 3.4 34.3 - - + -
357E ARG* 3.7 39.3 - - + +
361E LEU* 3.7 23.1 - - + +
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Residues in contact with MET 121 (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 CYS* 3.0 30.4 + - - +
118E LYS* 3.8 4.9 - - - +
120E ILE* 1.3 74.2 - - + +
122E ASP* 1.3 68.4 + - - +
124E VAL* 3.4 13.8 + - - +
125E SER* 3.4 14.2 + - - -
129E PRO* 4.6 6.3 - - - +
131E PHE* 3.6 13.0 - - + -
211E GLY* 3.8 22.0 - - - +
212E ILE* 3.8 25.4 - - + +
352E THR* 3.3 52.3 - - - +
353E GLU* 4.1 1.6 - - - +
356E ILE* 3.8 19.1 - - + -
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Residues in contact with ASP 122 (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 LYS* 2.6 47.8 + - - +
119E ARG* 3.3 11.8 + - - +
121E MET* 1.3 78.4 - - - +
123E MET* 1.3 63.4 + - + +
124E VAL 3.4 0.7 + - - -
125E SER* 3.5 18.1 + - - -
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Residues in contact with MET 123 (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 ARG* 3.2 15.3 + - - +
120E ILE* 3.6 22.0 - - - +
121E MET 3.2 0.4 - - - -
122E ASP* 1.3 79.6 - - + +
124E VAL* 1.3 62.7 + - + +
125E SER 3.5 0.6 + - - -
126E ASN* 5.4 0.3 + - - +
127E GLN* 5.3 1.0 + - - -
361E LEU* 5.3 11.3 - - + +
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Residues in contact with VAL 124 (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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120E ILE 3.4 10.3 + - - +
121E MET* 3.4 10.1 + - - +
122E ASP 3.3 0.4 - - - -
123E MET* 1.3 78.0 - - + +
125E SER* 1.3 58.0 + - - +
126E ASN* 3.2 3.1 - - - -
127E GLN* 3.0 39.2 + - - +
129E PRO* 3.5 18.2 - - + +
356E ILE* 3.5 29.8 - - + -
360E LEU* 3.8 25.1 - - + -
361E LEU* 3.6 31.9 - - + -
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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