Contacts of the helix formed by residues 118 - 127 (chain C) in PDB entry 5SY1
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 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C LYS 5.6 0.7 - - - +
117C LEU* 1.3 78.6 - - + +
119C ASP* 1.3 60.0 + - - +
120C GLU* 4.1 6.5 + - - +
121C GLU* 3.1 23.0 + - - +
122C VAL* 3.0 23.5 + - - +
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Residues in contact with ASP 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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107C ARG* 3.3 41.1 + - - -
115C GLU* 6.1 0.9 - - - +
117C LEU 3.9 1.0 + - - -
118C THR* 1.3 70.7 - - - +
120C GLU* 1.3 55.1 + - - +
121C GLU 3.3 0.2 - - - -
122C VAL* 3.2 11.0 + - - +
123C ASP* 2.7 46.8 + - - +
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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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118C THR* 3.2 6.6 + - - +
119C ASP* 1.3 78.4 - - - +
121C GLU* 1.3 57.0 + - - +
123C ASP* 3.1 13.0 + - + +
124C GLU* 2.9 43.7 + - + +
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Residues in contact with GLU 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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602A ASN* 3.1 34.4 + - - +
605A ARG* 5.0 2.3 + - - -
609A HIS* 4.1 28.9 + - + +
117C LEU* 4.4 17.0 - - + -
118C THR* 3.1 21.1 + - - +
120C GLU* 1.3 75.8 - - - +
122C VAL* 1.3 65.6 + - - +
124C GLU* 3.3 11.2 + - - +
125C MET* 3.3 23.8 + - - +
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Residues in contact with VAL 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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103C ALA* 5.1 4.3 - - + +
106C LEU* 3.7 25.8 - - + -
107C ARG* 4.3 20.9 - - + +
110C MET* 3.9 28.5 - - + -
115C GLU* 6.3 0.4 - - + -
117C LEU* 4.4 6.1 - - + +
118C THR 3.0 16.0 + - - +
119C ASP* 3.2 25.1 + - - +
121C GLU* 1.3 75.7 - - - +
123C ASP* 1.3 63.6 + - - +
125C MET* 3.2 26.6 + - + +
126C ILE* 3.7 9.4 - - - +
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Residues in contact with ASP 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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103C ALA* 5.1 6.6 - - - +
107C ARG* 4.9 6.2 + - - -
119C ASP* 2.7 39.4 + - - +
120C GLU* 3.1 14.7 + - + +
122C VAL* 1.3 75.6 - - - +
124C GLU* 1.3 63.3 + - + +
125C MET 3.4 0.5 + - - -
126C ILE* 3.5 11.1 + - - +
127C ARG* 3.3 30.3 + - - +
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Residues in contact with GLU 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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599A LYS* 5.4 14.0 - - - +
602A ASN* 4.1 26.8 + - - +
603A ALA* 5.8 0.7 - - - -
606A ALA* 4.1 9.1 - - - +
120C GLU* 2.9 31.1 + - + +
121C GLU* 3.6 16.6 - - - +
122C VAL 3.2 0.4 - - - -
123C ASP* 1.3 76.5 - - - +
125C MET* 1.3 65.4 + - - +
127C ARG* 3.8 22.9 + - - +
128C GLU* 4.1 2.8 + - - +
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Residues in contact with MET 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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606A ALA* 3.8 19.5 - - + +
609A HIS* 3.7 27.4 - - + +
610A TRP* 3.1 49.8 - - + +
613A LEU* 5.6 4.9 - - + -
106C LEU* 4.1 17.0 - - - -
110C MET* 5.0 7.4 - - - +
117C LEU* 3.7 23.6 - - + -
121C GLU 3.3 14.5 + - - +
122C VAL* 3.2 20.6 + - + +
124C GLU* 1.3 77.7 - - - +
126C ILE* 1.3 65.6 + - + +
128C GLU* 3.2 20.1 + - - +
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Residues in contact with ILE 126 (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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610A TRP* 3.8 21.5 - - + -
101C ILE* 5.6 3.4 - - + +
102C SER 5.5 1.8 - - - +
103C ALA* 4.8 21.8 - - + +
106C LEU* 4.1 22.4 - - + -
122C VAL 3.7 13.2 - - - +
123C ASP* 3.5 7.5 + - - +
124C GLU 3.4 0.4 - - - -
125C MET* 1.3 77.3 - - + +
127C ARG* 1.3 66.1 + - - +
129C ALA* 3.0 18.0 + - + +
130C ASP* 3.0 29.7 + - - +
135C GLY 5.1 7.6 - - - +
136C GLN* 5.9 0.2 - - - -
137C VAL* 4.5 23.3 - - + -
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Residues in contact with ARG 127 (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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123C ASP* 3.3 28.0 + - - +
124C GLU* 4.0 21.8 - - - +
125C MET 3.2 0.4 - - - -
126C ILE* 1.3 86.7 + - - +
128C GLU* 1.3 60.1 + - - +
130C ASP* 2.8 40.9 + - - +
135C GLY* 4.7 9.9 + - - -
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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