Contacts of the helix formed by residues 108 - 114 (chain B) 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 TYR 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.8 19.4 - + - -
105A ALA* 3.9 23.2 - - + +
106A ASN* 3.7 35.2 - - + +
1103A ASP* 2.6 36.3 + - + -
1105A LEU* 3.8 11.3 + - - +
1108A LEU* 3.8 1.2 - - - +
1169A VAL* 4.1 18.4 - - + -
105B ASP* 3.6 20.0 - - - -
106B PHE* 3.0 40.9 + - + -
107B ASP* 1.3 74.2 - - - +
109B GLN* 1.3 57.5 + - - +
110B ASN 3.0 0.2 - - - -
111B LEU* 2.8 35.2 + - + +
112B HIS* 3.3 6.8 - - - -
124B ALA* 4.0 12.1 - - + -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA* 2.6 38.5 + - + +
107A ARG 5.2 1.2 + - - -
109A LYS* 6.1 3.0 - - - +
107B ASP* 3.2 2.1 - - + -
108B TYR* 1.3 77.4 - - - +
110B ASN* 1.3 57.4 + - - +
111B LEU 3.1 0.4 - - - -
112B HIS* 3.0 31.7 + - - +
113B THR* 2.8 45.7 + - + +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1234A ASP* 6.1 0.9 - - - +
107B ASP* 3.0 22.5 + - + +
108B TYR 3.0 1.0 + - - -
109B GLN* 1.3 78.7 - - - +
111B LEU* 1.3 56.5 + - - +
113B THR* 4.0 6.5 + - - -
114B ALA* 3.1 36.6 + - - +
115B PRO* 5.8 2.0 - - - +
122B PRO* 3.8 6.5 - - - +
123B ILE 3.1 30.1 + - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN* 3.8 18.8 - - - +
155A GLY* 6.0 1.0 - - - -
157A PHE* 4.9 5.4 - - - -
775A LEU* 3.6 25.0 - - + +
780A LEU* 3.9 18.9 - - + +
1168A ILE* 3.7 42.6 - - + +
108B TYR* 2.8 26.0 + - + +
110B ASN* 1.3 77.5 - - - +
112B HIS* 1.3 63.8 + - + +
114B ALA* 4.6 2.5 + - - +
122B PRO* 3.9 15.6 - - - +
123B ILE* 3.7 31.2 - - - +
124B ALA* 4.3 7.2 - - + -
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Residues in contact with HIS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA 3.9 0.2 + - - -
106A ASN* 2.8 35.3 + - - -
107A ARG 3.5 26.2 + - - -
108A LEU* 4.2 8.2 - - + +
112A MET* 4.3 17.6 - - + +
157A PHE* 4.2 24.0 - - - +
775A LEU* 3.5 25.8 - - + +
108B TYR 3.3 16.8 - - - -
109B GLN* 3.0 34.2 + - - +
111B LEU* 1.3 81.5 - - + +
113B THR* 1.3 62.5 + - + +
114B ALA 3.5 2.5 + - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE 5.8 0.9 - - - -
109B GLN* 2.8 42.2 + - + +
110B ASN* 4.0 6.1 + - - -
112B HIS* 1.3 75.0 - - + +
114B ALA* 1.3 66.9 + - - +
115B PRO* 3.1 6.9 - - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLY* 3.7 9.6 - - - -
156A GLY* 2.9 23.4 + - - -
157A PHE 4.4 3.3 + - - +
110B ASN* 3.1 27.5 + - - +
111B LEU 4.8 2.5 - - - +
112B HIS 3.5 2.9 - - - +
113B THR* 1.3 76.0 + - - +
115B PRO* 1.3 68.8 - - + +
118B SER* 4.3 5.2 - - - +
122B PRO* 3.5 29.6 - - + -
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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