Contacts of the helix formed by residues 106 - 113 (chain C) in PDB entry 5H1C
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 SER 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C THR* 3.4 1.3 + - - -
105C GLY* 1.3 80.9 - - - +
107C LYS* 1.3 62.9 + - - +
108C GLU* 4.8 1.8 - - - -
109C LEU* 3.2 34.1 + - - +
110C ASP* 3.0 29.4 + - - +
327C PHE* 5.0 1.1 - - - +
334C VAL* 3.3 11.5 - - - +
335C GLY* 3.5 28.0 - - - -
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Residues in contact with LYS 107 (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 SER* 1.3 72.4 - - - +
108C GLU* 1.3 65.3 + - + +
110C ASP* 2.8 27.4 + - - +
111C LYS* 2.9 27.5 + - - +
336C ASP* 4.9 11.7 + - - +
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Residues in contact with GLU 108 (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 SER* 3.6 1.4 + - - +
107C LYS* 1.3 78.6 - - + +
109C LEU* 1.3 58.1 + - + +
111C LYS* 3.2 17.3 + - + +
112C LEU* 2.9 33.3 + - - +
325C ALA* 4.2 10.4 - - + +
326C MET* 2.7 40.0 + - - +
327C PHE* 5.0 1.3 - - + -
335C GLY 5.8 1.1 - - - +
336C ASP* 4.3 23.1 + - - +
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Residues in contact with LEU 109 (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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104C THR* 3.1 31.2 - - + +
106C SER* 3.2 20.0 + - - +
107C LYS 3.2 0.4 - - - -
108C GLU* 1.3 74.6 - - + +
110C ASP* 1.3 59.5 + - - +
112C LEU* 3.7 24.0 - - + -
113C LEU* 2.9 42.2 + - + +
136C ILE* 5.0 10.8 - - + -
300C LEU* 6.4 0.2 - - + -
312C CYS* 3.9 20.6 - - + -
325C ALA* 5.5 1.3 - - + +
326C MET 5.6 0.4 - - - +
327C PHE* 4.0 27.1 - - + -
334C VAL* 3.7 17.5 - - + -
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Residues in contact with ASP 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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103C THR* 3.7 22.8 - - - +
104C THR* 3.2 28.2 + - - +
106C SER 3.0 23.4 + - - +
107C LYS* 2.8 16.4 + - - +
109C LEU* 1.3 78.0 - - - +
111C LYS* 1.3 58.1 + - + +
114C GLN* 3.1 4.3 + - - +
115C GLY* 2.4 39.5 + - - +
116C GLY 4.2 4.8 + - - +
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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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107C LYS* 2.9 24.2 + - - +
108C GLU* 3.5 16.6 - - + +
109C LEU 3.1 0.2 - - - -
110C ASP* 1.3 77.7 - - + +
112C LEU* 1.3 68.1 + - + +
114C GLN* 3.2 19.4 + - - +
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Residues in contact with LEU 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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108C GLU 2.9 16.7 + - - +
109C LEU* 3.7 29.6 - - + +
111C LYS* 1.3 80.4 - - - +
113C LEU* 1.3 66.2 + - + +
114C GLN* 3.3 2.3 + - - -
312C CYS* 3.7 22.7 - - + +
314C ILE* 3.7 15.3 - - + +
320C LEU* 3.3 17.3 - - - +
323C ALA* 3.7 17.0 - - + +
324C GLU* 3.5 35.7 - - - +
325C ALA* 3.5 23.1 - - + +
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Residues in contact with LEU 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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101C GLN* 4.6 1.2 - - - +
104C THR* 3.7 28.9 - - + -
109C LEU* 2.9 24.1 + - + +
112C LEU* 1.3 81.8 - - + +
114C GLN* 1.3 72.1 + - - +
116C GLY* 3.5 23.2 - - - +
117C ILE* 4.1 21.1 - - + -
298C THR* 6.5 0.7 - - - -
300C LEU* 4.0 37.9 - - + -
312C CYS* 5.5 0.7 - - - -
314C ILE* 4.9 5.4 - - + -
320C LEU* 3.7 14.7 - - + +
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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