Contacts of the helix formed by residues 113 - 123 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F GLU 4.4 13.0 - - - +
111F THR* 3.3 12.6 + - - +
112F ASN* 1.3 74.6 - - - +
114F ARG* 1.3 63.7 + - - +
115F HIS 3.2 2.6 + - - -
116F THR* 3.8 5.2 + - - +
117F CYS* 3.3 21.8 + - - +
347F ASP* 3.6 35.3 + - + +
349F PHE* 3.9 11.5 - - + +
350F SER* 4.2 17.5 - - - +
353F GLU* 3.8 6.1 - - - +
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ALA* 3.7 31.8 + - - +
98F LEU* 5.0 3.3 - - - +
99F CYS 5.6 1.3 - - - -
100F GLU* 3.1 33.8 + - + +
112F ASN* 3.3 8.9 + - - +
113F LEU* 1.3 78.1 - - - +
115F HIS* 1.3 64.4 + - - +
117F CYS* 4.1 0.7 - - - -
118F LYS* 3.0 39.5 + - - +
212F ILE* 3.7 23.4 - - + +
216F ASP* 2.7 40.4 + - - -
349F PHE* 3.5 43.2 - - + -
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Residues in contact with HIS 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLU* 3.2 28.7 + - - +
102F PHE* 3.9 18.0 - + - -
108F PRO* 3.9 28.5 - - + +
112F ASN* 3.1 16.9 + - - +
113F LEU 3.2 1.2 - - - -
114F ARG* 1.3 78.0 - - - +
116F THR* 1.3 64.3 + - - +
118F LYS* 3.5 9.8 + - - +
119F ARG* 3.5 47.6 + - + +
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Residues in contact with THR 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ASN 5.3 0.6 + - - -
113F LEU* 3.8 6.1 + - - -
115F HIS* 1.3 78.3 - - - +
117F CYS* 1.3 64.3 + - - +
119F ARG* 3.3 14.2 + - - +
120F ILE* 3.2 21.1 + - + +
353F GLU* 3.1 28.3 - - - +
357F ARG* 3.4 18.2 - - - +
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Residues in contact with CYS 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU 3.3 16.7 + - - +
114F ARG 3.7 4.9 - - - +
115F HIS 3.3 0.6 - - - -
116F THR* 1.3 80.8 - - - +
118F LYS* 1.3 56.3 + - - +
120F ILE* 3.3 2.8 + - - +
121F MET* 3.0 47.4 + - - +
212F ILE* 3.8 14.8 - - + -
349F PHE* 3.3 28.3 - - + +
352F THR* 3.7 15.5 - - - -
353F GLU* 3.2 21.2 + - - +
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Residues in contact with LYS 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F GLU* 5.4 1.6 - - - +
114F ARG* 3.0 33.3 + - - +
115F HIS* 3.7 6.5 - - - +
116F THR 3.3 0.2 - - - -
117F CYS* 1.3 76.4 - - - +
119F ARG* 1.3 57.4 + - + +
121F MET* 3.4 3.4 + - - +
122F ASP* 2.9 58.5 + - - +
212F ILE* 3.6 32.6 - - + +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F HIS* 3.6 41.1 + - + +
116F THR* 3.3 14.2 + - + +
118F LYS* 1.3 78.0 - - + +
120F ILE* 1.3 61.8 + - + +
122F ASP* 3.7 9.2 + - - +
123F MET* 3.4 39.0 + - + +
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F THR* 3.2 15.1 + - + +
117F CYS 3.6 7.2 - - - +
118F LYS 3.2 0.2 - - - -
119F ARG* 1.3 73.5 - - + +
121F MET* 1.3 67.3 + - - +
122F ASP 3.1 0.9 - - - -
123F MET* 2.9 34.1 + - + +
124F VAL* 3.6 7.3 + - - +
353F GLU* 4.1 19.1 - - + +
356F ILE* 3.4 34.1 - - + -
357F ARG* 3.5 39.5 - - + +
361F LEU* 4.1 20.6 - - + +
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Residues in contact with MET 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F CYS* 3.0 32.1 + - - +
118F LYS* 3.7 6.5 - - - +
120F ILE* 1.3 74.9 - - + +
122F ASP* 1.3 63.3 + - - +
124F VAL* 3.2 17.4 + - - +
125F SER* 3.3 12.3 + - - -
129F PRO* 4.6 5.5 - - - +
131F PHE* 4.1 8.1 - - + -
211F GLY* 3.8 22.7 - - - -
212F ILE* 3.7 26.7 - - + +
352F THR* 3.5 49.8 - - - +
353F GLU* 4.0 1.8 - - - +
356F ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F LYS* 2.9 49.3 + - - +
119F ARG* 3.8 9.2 - - - +
120F ILE 3.1 0.2 - - - -
121F MET* 1.3 73.6 - - - +
123F MET* 1.3 60.6 + - + +
124F VAL 3.1 5.2 - - - -
125F SER* 3.1 22.7 + - - +
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Residues in contact with MET 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ARG* 3.4 31.3 + - + +
120F ILE* 2.9 30.4 + - + +
122F ASP* 1.3 76.4 - - - +
124F VAL* 1.3 67.9 + - + +
125F SER 3.9 0.2 - - - -
127F GLN* 5.0 0.9 + - - -
361F LEU* 4.3 20.4 - - + +
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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