Contacts of the helix formed by residues 113 - 123 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ILE* 6.2 0.8 - - - +
110C GLU 4.2 14.1 - - - +
111C THR* 3.5 10.6 + - - +
112C ASN* 1.3 78.1 - - - +
114C ARG* 1.3 64.4 + - - +
115C HIS 3.4 1.3 - - - -
116C THR* 4.1 4.6 + - - +
117C CYS* 3.3 22.3 + - - +
347C ASP* 3.7 28.0 + - + +
349C PHE* 3.7 12.2 - - + +
350C SER* 4.0 24.7 - - - +
353C GLU* 4.0 5.2 - - - +
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Residues in contact with ARG 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 3.6 30.8 + - - +
98C LEU* 5.3 2.9 - - - -
99C CYS 5.7 1.6 - - - -
100C GLU* 3.0 36.5 + - + +
112C ASN* 3.1 6.3 + - - +
113C LEU* 1.3 79.2 - - - +
115C HIS* 1.3 67.4 + - - +
117C CYS* 4.2 0.2 - - - -
118C LYS* 2.9 43.9 + - - +
212C ILE* 3.7 24.1 - - + +
216C ASP* 2.7 38.7 + - - -
349C PHE* 3.6 42.7 - - + -
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Residues in contact with HIS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU* 3.2 24.5 + - - +
102C PHE* 4.1 18.2 - + - -
108C PRO* 3.9 25.8 - - + +
112C ASN* 2.9 20.7 + - - +
113C LEU 3.4 0.2 - - - -
114C ARG* 1.3 79.2 - - - +
116C THR* 1.3 65.9 + - - +
118C LYS* 3.5 9.3 + - - +
119C ARG* 3.5 47.9 + - + +
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASN 5.2 1.4 + - - -
113C LEU* 4.1 5.3 + - - -
114C ARG 3.5 0.2 - - - -
115C HIS* 1.3 78.8 - - - +
117C CYS* 1.3 67.2 + - - +
119C ARG* 3.1 13.9 + - + +
120C ILE* 3.0 21.6 + - + +
353C GLU* 3.4 14.8 - - - +
357C ARG* 3.4 29.2 - - - +
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Residues in contact with CYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU 3.3 19.2 + - - +
114C ARG 3.2 3.9 + - - +
116C THR* 1.3 78.1 - - - +
118C LYS* 1.3 63.5 + - - +
120C ILE* 3.0 4.5 + - - +
121C MET* 2.9 38.7 + - - +
212C ILE* 3.5 19.5 - - + -
349C PHE* 3.4 26.7 - - + +
352C THR* 3.6 16.8 - - - -
353C GLU* 3.3 22.3 + - - +
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C GLU* 5.4 1.3 - - - +
114C ARG* 2.9 39.4 + - - +
115C HIS* 3.7 6.1 - - - +
117C CYS* 1.3 73.3 - - - +
119C ARG* 1.3 65.4 + - + +
121C MET* 3.4 2.6 + - - +
122C ASP* 3.1 48.2 + - - +
212C ILE* 3.6 35.4 - - + +
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Residues in contact with ARG 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C HIS* 3.5 41.7 + - + +
116C THR* 3.1 13.7 + - + +
118C LYS* 1.3 80.9 - - + +
120C ILE* 1.3 64.8 + - + +
122C ASP* 3.2 17.3 + - - +
123C MET* 3.2 28.6 + - + +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C THR* 3.0 20.1 + - + +
117C CYS 3.6 6.1 - - - +
119C ARG* 1.3 77.4 - - + +
121C MET* 1.3 61.6 + - - +
123C MET* 3.2 35.6 + - + +
124C VAL* 3.8 6.8 + - - +
353C GLU* 4.1 15.3 - - + -
356C ILE* 3.4 34.8 - - + +
357C ARG* 3.5 46.2 - - + +
361C LEU* 3.9 18.6 - - + -
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Residues in contact with MET 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C CYS* 2.9 28.8 + - - +
118C LYS* 3.7 6.1 - - - +
119C ARG 3.3 0.2 - - - -
120C ILE* 1.3 75.8 - - + +
122C ASP* 1.3 66.0 + - - +
124C VAL* 3.0 18.9 + - - +
125C SER* 3.2 13.3 + - - -
129C PRO* 4.4 5.6 - - + +
131C PHE* 3.7 13.5 - - + -
211C GLY* 3.8 26.0 - - - +
212C ILE* 3.8 20.6 - - + +
352C THR* 3.5 45.3 - - - +
353C GLU* 4.7 0.9 - - - -
356C ILE* 3.7 21.8 - - + -
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Residues in contact with ASP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 3.1 47.0 + - - +
119C ARG* 3.2 12.6 + - - +
121C MET* 1.3 80.0 - - - +
123C MET* 1.3 60.5 + - + +
125C SER* 3.3 20.6 + - - -
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ARG* 3.2 21.4 + - + +
120C ILE* 3.2 36.2 + - + +
121C MET 3.1 0.8 - - - -
122C ASP* 1.3 77.5 - - - +
124C VAL* 1.3 65.2 + - + +
125C SER 3.6 0.4 - - - -
127C GLN* 5.3 0.5 + - - -
361C LEU* 4.2 19.8 - - + +
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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