Contacts of the helix formed by residues 113 - 124 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33D ILE* 6.2 0.6 - - - +
110D GLU 4.0 16.4 - - - +
111D THR* 3.3 11.7 + - - +
112D ASN* 1.3 75.1 - - - +
114D ARG* 1.3 63.3 + - - +
115D HIS 3.3 1.1 - - - -
116D THR* 4.1 4.0 + - - +
117D CYS* 3.3 22.2 + - - +
347D ASP* 3.2 33.6 + - + +
349D PHE* 3.6 13.3 - - + +
350D SER* 4.0 20.0 - - - +
353D GLU* 4.1 5.0 - - - +
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Residues in contact with ARG 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 3.5 32.7 + - - +
98D LEU* 5.4 2.7 - - - -
99D CYS 5.8 1.1 - - - -
100D GLU* 2.8 43.2 + - + +
112D ASN* 3.2 7.6 + - - +
113D LEU* 1.3 79.0 - - - +
115D HIS* 1.3 67.6 + - - +
118D LYS* 2.8 43.3 + - - +
212D ILE* 3.7 24.3 - - + +
216D ASP* 2.9 37.5 + - - -
349D PHE* 3.5 42.3 - - + -
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Residues in contact with HIS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 3.1 28.0 + - - +
102D PHE* 3.8 18.5 - + - -
108D PRO* 3.8 25.8 - - + +
112D ASN* 3.0 18.6 + - - +
113D LEU 3.3 0.8 - - - -
114D ARG* 1.3 80.2 - - - +
116D THR* 1.3 66.0 + - - +
118D LYS* 3.6 4.1 + - - +
119D ARG* 3.6 48.8 + - + +
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Residues in contact with THR 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ASN 5.0 1.4 + - - -
113D LEU* 4.1 4.9 + - - -
115D HIS* 1.3 77.9 - - - +
117D CYS* 1.3 66.5 + - - +
119D ARG* 3.0 22.6 + - + +
120D ILE* 3.1 14.6 + - + +
353D GLU* 3.3 28.3 - - - +
357D ARG* 3.5 17.0 - - - +
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Residues in contact with CYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LEU 3.3 18.7 + - - +
114D ARG 3.2 4.0 + - - +
116D THR* 1.3 78.6 - - - +
118D LYS* 1.3 63.0 + - - +
120D ILE* 3.2 3.5 + - - +
121D MET* 2.9 42.7 + - - +
212D ILE* 3.6 16.6 - - + -
349D PHE* 3.5 27.6 - - + +
352D THR* 3.6 16.8 - - - -
353D GLU* 3.1 20.0 + - - +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 5.2 1.3 - - - +
114D ARG* 2.8 40.4 + - - +
115D HIS* 3.8 5.6 - - - +
117D CYS* 1.3 74.2 - - - +
119D ARG* 1.3 59.9 + - + +
121D MET* 3.2 2.3 + - - +
122D ASP* 2.7 62.2 + - - +
212D ILE* 3.5 37.5 - - + +
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Residues in contact with ARG 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D HIS* 3.6 37.7 + - + +
116D THR* 3.0 13.9 + - + +
118D LYS* 1.3 81.0 - - + +
120D ILE* 1.3 59.6 - - + +
122D ASP* 3.3 9.3 + - - +
123D MET* 3.0 36.5 + - + +
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D THR* 3.1 16.7 + - + +
117D CYS 3.6 7.0 - - - +
119D ARG* 1.3 75.2 - - + +
121D MET* 1.3 64.4 + - - +
123D MET* 3.3 21.8 + - - +
124D VAL* 3.4 14.7 + - - +
353D GLU* 4.3 16.6 - - + +
356D ILE* 3.5 33.7 - - + -
357D ARG* 3.7 36.6 - - + +
361D LEU* 3.8 22.4 - - + -
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Residues in contact with MET 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D CYS* 2.9 31.3 + - - +
118D LYS* 3.7 4.9 - - - +
120D ILE* 1.3 77.5 - - + +
122D ASP* 1.3 64.5 + - - +
124D VAL* 3.2 16.2 + - - +
125D SER* 3.3 14.4 + - - -
129D PRO* 4.5 4.6 - - + +
131D PHE* 4.1 6.3 - - + -
211D GLY* 3.9 20.2 - - - +
212D ILE* 3.7 29.4 - - + +
352D THR* 3.5 39.3 - - - +
353D GLU* 4.0 2.5 - - - +
356D ILE* 3.6 35.7 - - + -
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Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D LYS* 2.7 53.2 + - - +
119D ARG* 3.3 8.1 + - - +
121D MET* 1.3 76.3 - - - +
123D MET* 1.3 62.6 + - + +
124D VAL 3.6 0.2 + - - -
125D SER* 3.8 15.6 + - - -
212D ILE* 6.0 1.2 - - - +
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ARG* 3.0 20.4 + - - +
120D ILE* 3.7 19.5 - - - +
121D MET 3.1 0.4 - - - -
122D ASP* 1.3 79.5 - - + +
124D VAL* 1.3 62.5 + - + +
125D SER 3.4 1.6 + - - -
126D ASN 5.4 0.2 + - - -
127D GLN* 5.4 0.2 + - - -
361D LEU* 5.3 11.4 - - + -
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE 3.4 15.3 - - - +
121D MET* 3.2 8.3 + - - +
123D MET* 1.3 79.7 - - - +
125D SER* 1.3 57.5 + - - +
126D ASN* 3.3 2.9 - - - -
127D GLN* 2.9 40.2 + - - +
129D PRO* 3.6 11.7 - - + +
356D ILE* 3.7 33.0 - - + -
360D LEU* 3.9 25.4 - - + +
361D LEU* 3.9 27.8 - - + -
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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