Contacts of the helix formed by residues 115 - 122 (chain C) in PDB entry 1SIW
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 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ASP* 2.9 36.2 + - - +
110C LYS 4.1 0.2 + - - -
111C ARG* 2.7 35.9 + - - +
114C PHE* 1.3 70.3 - - - +
116C PRO* 1.3 62.9 - - - +
117C ARG* 4.5 1.4 + - - +
118C VAL* 2.9 12.1 + - - +
119C ARG* 2.8 31.7 + - - -
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Residues in contact with PRO 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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131B THR* 4.0 14.1 - - + -
133B GLU* 5.9 5.4 - - + +
114C PHE 3.1 11.2 - - - +
115C SER* 1.3 84.2 - - - +
117C ARG* 1.3 62.4 + - + +
119C ARG* 3.9 4.4 - - + +
120C ALA* 2.9 34.3 + - - +
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Residues in contact with ARG 117 (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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97B ILE* 3.3 23.1 - - - +
98B ASP* 3.1 36.1 + - - -
102B GLU* 3.1 37.8 + - - +
130B ILE* 3.8 17.6 - - + +
131B THR* 3.6 22.2 - - + +
43C LEU* 3.1 33.9 + - + +
44C ASP* 5.2 5.8 + - + -
115C SER* 3.3 1.8 + - - +
116C PRO* 1.3 81.1 - - + +
118C VAL* 1.3 54.0 + - + +
120C ALA* 4.6 0.2 - - - -
121C THR* 2.7 37.9 + - - +
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Residues in contact with VAL 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C SER* 4.5 11.9 - - - +
43C LEU* 5.0 2.2 - - + -
44C ASP* 4.0 8.1 - - + +
111C ARG* 3.6 39.3 - - + +
112C ARG* 3.5 46.8 + - - +
115C SER* 2.9 25.3 + - - +
117C ARG* 1.3 75.6 - - - +
119C ARG* 1.3 61.7 + - - +
121C THR* 3.4 5.1 + - - -
122C THR* 3.0 28.6 + - - -
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Residues in contact with ARG 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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112C ARG 3.4 20.8 + - - +
113C LEU* 2.8 52.9 + - - +
114C PHE* 5.1 3.6 - - - -
115C SER 2.8 15.5 + - - +
116C PRO* 3.9 5.4 - - + +
118C VAL* 1.3 77.6 - - - +
120C ALA* 1.3 62.6 + - - +
122C THR* 3.2 27.9 + - - +
127C ILE* 4.1 13.6 - - - +
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Residues in contact with ALA 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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130B ILE 3.6 6.3 - - - +
131B THR* 3.6 36.6 - - - +
116C PRO 2.9 18.8 + - - +
117C ARG 4.3 1.6 - - - +
119C ARG* 1.3 77.2 - - - +
121C THR* 1.3 59.5 - - - +
122C THR 4.9 1.8 - - - +
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Residues in contact with THR 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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130B ILE* 3.4 26.9 - - + +
236B TRP* 3.5 35.4 - - + -
40C SER* 5.8 1.4 - - - -
43C LEU* 3.5 18.7 - - + +
117C ARG 2.7 21.9 + - - +
118C VAL* 3.5 5.4 + - - -
119C ARG 3.1 0.4 - - - -
120C ALA* 1.3 79.0 - - - +
122C THR* 1.3 62.9 + - - +
123C THR* 4.1 4.2 + - - +
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Residues in contact with THR 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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112C ARG* 2.6 39.3 + - + +
118C VAL 3.0 8.9 + - - +
119C ARG* 3.2 26.7 + - - +
120C ALA 4.9 1.6 - - - +
121C THR* 1.3 82.6 - - - +
123C THR* 1.3 73.2 + - - +
126C ASP* 3.3 8.7 - - - +
127C ILE* 3.9 25.9 - - + +
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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