Contacts of the helix formed by residues 117 - 125 (chain C) in PDB entry 2DFS
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 THR 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110C THR* 4.1 2.5 - - - -
115C LYS 5.5 1.1 - - - +
116C LEU* 1.3 78.6 - - - +
118C ASP* 1.4 62.9 + - - +
119C GLU* 3.1 31.9 + - + +
120C GLU* 3.3 27.5 + - - +
121C VAL* 3.2 21.5 + - - +
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Residues in contact with ASP 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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106C ARG* 2.7 40.7 + - - +
110C THR* 4.1 16.5 + - - +
117C THR* 1.4 70.8 - - - +
119C GLU* 1.3 52.8 + - - +
121C VAL* 3.0 4.5 + - - +
122C ASP* 2.7 41.6 + - - +
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Residues in contact with GLU 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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117C THR* 3.1 28.9 + - - +
118C ASP* 1.3 76.4 - - - +
120C GLU* 1.4 54.4 + - + +
122C ASP* 3.9 7.4 - - - +
123C GLU* 2.9 29.5 + - - +
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Residues in contact with GLU 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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802A ARG* 2.6 53.9 + - - +
805A GLN* 3.5 31.3 + - - +
115C LYS 4.8 0.5 - - - +
116C LEU* 3.6 13.7 - - + +
117C THR* 3.3 39.7 + - - +
119C GLU* 1.4 75.6 - - + +
121C VAL* 1.3 57.3 + - - +
123C GLU* 3.4 3.5 + - - +
124C MET* 3.0 28.1 + - - +
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Residues in contact with VAL 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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102C ALA 5.7 0.9 - - - +
105C LEU* 5.2 7.9 - - + -
106C ARG* 3.9 38.8 - - + +
109C MET* 3.9 21.5 - - + -
110C THR* 3.8 20.6 - - + -
116C LEU* 4.6 7.2 - - + -
117C THR 3.2 13.0 + - - +
118C ASP 3.0 8.4 + - - +
120C GLU* 1.3 75.2 - - - +
122C ASP* 1.3 57.0 + - - +
124C MET* 3.2 8.7 + - + +
125C ILE* 3.0 38.2 + - + +
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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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106C ARG* 2.6 41.7 + - - -
118C ASP* 2.7 22.9 + - - +
119C GLU* 3.9 7.6 + - - +
121C VAL* 1.3 68.9 - - - +
123C GLU* 1.3 66.1 + - - +
125C ILE* 3.3 25.9 + - - +
126C ARG* 3.7 10.4 - - - +
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Residues in contact with GLU 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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805A GLN* 3.3 34.7 + - - +
809A TYR* 3.3 30.7 - - - +
119C GLU 2.9 19.0 + - - +
120C GLU 3.6 4.9 - - - +
121C VAL 3.4 0.2 - - - -
122C ASP* 1.3 76.3 - - - +
124C MET* 1.3 60.6 + - - +
126C ARG* 2.8 63.3 + - - +
127C GLU* 3.4 6.1 - - - +
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Residues in contact with MET 124 (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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801A VAL* 3.3 48.7 - - + +
804A HIS* 4.1 17.7 - - + -
805A GLN* 3.5 27.4 - - + +
105C LEU* 6.2 0.2 - - + -
120C GLU 3.0 16.5 + - - +
121C VAL* 3.2 10.5 + - + +
123C GLU* 1.3 75.2 - - - +
125C ILE* 1.3 60.4 + - + +
126C ARG 3.2 1.5 + - - -
127C GLU* 3.4 16.7 + - + +
128C ALA* 3.6 10.0 + - - +
141C PHE* 4.1 28.0 - - + -
145C MET* 5.4 3.6 - - - -
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Residues in contact with ILE 125 (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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102C ALA* 6.0 8.7 - - + -
105C LEU* 4.8 15.5 - - + -
106C ARG* 3.8 11.2 - - - +
121C VAL* 3.0 22.3 + - + +
122C ASP* 3.3 36.6 - - - +
124C MET* 1.3 77.3 - - + +
126C ARG* 1.3 62.1 + - - +
127C GLU 3.4 0.4 - - - -
128C ALA* 3.8 24.8 - - + +
130C ILE* 5.5 11.7 - - + +
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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