Contacts of the helix formed by residues 109 - 115 (chain C) in PDB entry 3IKH
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 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 3.3 42.4 - - + +
29A GLY 4.3 4.5 + - - +
30A VAL* 6.1 1.0 - - - +
8C ASN* 6.2 0.7 - - - +
91C ASP* 3.2 10.1 - - - -
107C THR* 4.2 0.9 - - + +
108C THR* 1.3 80.6 - - - +
110C ALA* 1.3 58.5 + - - +
111C ALA 3.2 0.3 + - - -
112C ALA* 3.2 8.2 + - + -
113C ASP* 2.7 60.1 + - - +
138C ASN* 4.4 9.0 - - + +
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Residues in contact with ALA 110 (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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88C GLN* 3.4 28.8 + - - +
89C HIS* 5.0 7.0 - - + +
91C ASP* 3.1 2.9 + - - +
108C THR* 4.6 4.4 - - - -
109C THR* 1.3 78.1 + - - +
111C ALA* 1.3 60.2 + - - +
113C ASP* 3.7 8.6 + - - +
114C THR* 2.8 27.0 + - - -
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Residues in contact with ALA 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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59C ALA* 3.5 28.7 - - + +
60C THR 4.9 4.3 - - - -
86C PHE* 5.2 2.5 - - + -
88C GLN* 4.5 8.3 - - + -
89C HIS 3.5 22.2 + - - +
90C SER* 4.4 2.7 - - - -
91C ASP* 3.0 23.6 + - - +
110C ALA* 1.3 74.9 - - - +
112C ALA* 1.3 68.2 + - - +
114C THR* 3.1 16.8 + - - -
115C PHE 3.4 6.9 + - - -
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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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7C GLY 5.1 2.5 - - - +
8C ASN* 4.7 13.7 - - + -
59C ALA* 4.4 10.9 - - - +
91C ASP* 3.0 17.6 + - - +
109C THR* 3.2 12.7 + - + +
111C ALA* 1.3 73.9 - - - +
113C ASP* 1.3 63.1 + - - +
115C PHE* 3.1 13.5 + - - +
120C MSE 4.6 1.2 - - - +
138C ASN* 5.6 2.9 - - + +
139C PHE* 4.1 23.3 - - + -
143C LYS* 3.0 21.1 + - - -
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Residues in contact with ASP 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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109C THR* 2.7 52.0 + - - +
110C ALA* 3.9 8.9 + - - +
112C ALA* 1.3 73.8 - - - +
114C THR* 1.3 61.4 + - - +
115C PHE 3.6 3.3 + - - -
116C SER* 4.6 2.3 + - - -
138C ASN 5.4 2.9 - - - +
139C PHE* 5.8 3.1 - - - -
143C LYS* 4.3 9.2 + - - +
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Residues in contact with THR 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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86C PHE* 3.8 25.7 - - + -
87C ASN 5.7 1.6 - - - +
88C GLN* 3.6 21.5 + - + +
110C ALA 2.8 18.6 + - - -
111C ALA* 3.1 9.6 + - - -
113C ASP* 1.3 76.5 - - - +
115C PHE* 1.3 60.2 + - - +
116C SER* 3.0 10.4 + - - -
119C GLU* 3.3 8.8 - - - +
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Residues in contact with PHE 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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57C ILE* 3.6 18.6 - - + -
58C ALA 3.9 6.3 - - - -
59C ALA* 3.8 30.5 - - + -
82C PRO* 3.4 33.0 - - + -
86C PHE* 3.5 19.7 - + + -
111C ALA 3.4 1.2 + - - -
112C ALA 3.1 10.6 + - - +
113C ASP 4.4 0.2 - - - -
114C THR* 1.3 75.0 - - - +
116C SER* 1.3 64.5 + - - +
119C GLU* 3.6 36.6 - - + -
120C MSE 3.3 27.8 - - + +
123C HIS* 3.8 18.4 - + - -
143C LYS* 2.9 24.5 + - - -
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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