Contacts of the helix formed by residues 110 - 116 (chain C) in PDB entry 1DBF
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 GLU 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR* 3.2 20.6 - - - +
11C THR* 3.4 22.0 - - - +
23C LYS* 3.1 24.8 + - + -
26C GLN* 3.0 23.5 + - - +
109C LEU* 1.4 75.2 - - + +
111C LYS* 1.3 62.5 + - + +
113C VAL* 3.0 32.4 + - - +
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Residues in contact with LYS 111 (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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11C THR* 3.0 22.0 + - + +
12C VAL 5.4 1.9 + - - +
13C GLU* 2.5 37.5 + - - +
85C LEU* 3.9 16.6 - - + +
86C LYS 6.1 0.4 - - - +
110C GLU* 1.3 75.3 - - - +
112C ALA* 1.3 56.8 - - - +
113C VAL* 3.0 13.2 + - - +
114C VAL* 3.4 20.8 + - - +
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Residues in contact with ALA 112 (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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9C ALA* 3.8 35.2 - - + +
10C THR* 3.9 5.8 - - - +
11C THR* 3.8 3.0 - - - +
85C LEU* 3.6 21.5 - - + -
88C CYS* 4.6 0.2 - - - -
108C TYR* 3.3 13.4 - - - +
109C LEU 2.9 14.7 + - - +
111C LYS* 1.3 75.9 - - - +
113C VAL* 1.3 63.9 + - - +
114C VAL 3.0 2.2 - - - +
115C LEU* 2.9 18.2 + - + +
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Residues in contact with VAL 113 (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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108C TYR 3.6 21.1 - - - +
109C LEU* 3.5 1.0 + - - -
110C GLU 3.0 27.2 + - - +
111C LYS* 3.0 5.3 - - - +
112C ALA* 1.3 78.5 - - - +
114C VAL* 1.3 64.3 + - + +
116C ARG* 3.0 38.4 + - - +
119C LEU* 3.5 25.1 - - + +
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Residues in contact with VAL 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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85C LEU* 4.6 11.9 - - + -
111C LYS 3.4 17.0 + - - +
112C ALA* 3.0 1.7 - - - -
113C VAL* 1.3 83.5 - - + +
115C LEU* 1.3 73.6 + - + +
116C ARG 3.2 0.4 - - - -
119C LEU* 4.7 7.9 - - - +
120C SER* 3.0 39.2 - - - +
123C LYS* 6.5 1.1 - - + -
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Residues in contact with LEU 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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57B PHE* 6.5 0.2 - - + -
203B SO4 5.4 0.2 - - - +
9C ALA* 3.7 30.5 - - + -
85C LEU* 4.5 10.8 - - + -
88C CYS* 4.6 0.4 - - - -
90C ARG* 4.3 20.4 - - - +
108C TYR* 3.8 9.1 - - + -
112C ALA* 2.9 22.8 + - + +
114C VAL* 1.3 87.8 - - + +
116C ARG* 1.3 62.7 + - - +
117C PRO* 3.2 1.9 - - - +
120C SER* 4.6 3.5 - - - -
253C GOL 2.7 63.7 + - - +
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Residues in contact with ARG 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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108C TYR* 2.8 47.7 + - + +
109C LEU* 4.0 13.1 - - - +
113C VAL* 3.0 32.2 + - - +
115C LEU* 1.3 76.0 - - - +
117C PRO* 1.3 60.9 - - + +
118C ASP* 3.4 21.8 - - - +
119C LEU* 2.6 37.3 + - - +
120C SER* 2.7 16.5 + - - -
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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