Contacts of the helix formed by residues 80 - 86 (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 ASN 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B LYS* 6.3 0.4 - - - +
75B GLN* 3.6 19.7 + - + +
79B GLY* 1.3 77.5 - - - +
81B ARG* 1.3 68.2 + - - +
82B ALA* 3.0 11.8 + - - +
83B MET* 2.7 54.9 + - - +
84B LEU* 2.9 16.9 + - - +
213C TYR* 5.3 1.1 - - - -
218C TYR* 4.0 12.6 - - - +
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Residues in contact with ARG 81 (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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80B ASN* 1.3 77.3 - - - +
82B ALA* 1.3 63.3 + - - +
84B LEU* 3.4 1.6 + - - +
85B LEU* 3.0 28.4 + - - +
213C TYR* 3.2 35.5 + - + +
214C LEU* 3.2 38.6 + - + -
215C THR 4.7 0.6 - - - -
216C ARG 2.9 30.3 + - - +
217C LYS* 4.3 1.8 - - - +
218C TYR* 3.3 57.8 + - + +
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Residues in contact with ALA 82 (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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80B ASN* 3.0 9.4 + - - +
81B ARG* 1.3 78.4 - - - +
83B MET* 1.3 64.5 + - + +
85B LEU* 3.2 5.9 + - - +
86B GLY* 2.9 21.3 + - - -
214C LEU* 4.0 14.0 - - + +
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Residues in contact with MET 83 (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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75B GLN* 4.5 9.2 - - - +
77B ARG 5.8 0.4 - - - +
78B MET 4.6 4.7 - - - +
79B GLY* 3.7 15.3 - - - -
80B ASN* 2.7 51.5 + - - +
82B ALA* 1.3 71.9 - - + +
84B LEU* 1.3 62.9 + - - +
86B GLY* 3.2 9.9 + - - -
87B LYS* 3.4 28.9 + - - +
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Residues in contact with LEU 84 (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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76B PRO* 5.4 0.4 - - + -
78B MET* 4.0 28.0 - - + -
79B GLY 4.4 8.2 - - - +
80B ASN 2.9 16.6 + - - +
81B ARG 3.7 3.8 - - - +
83B MET* 1.3 76.8 - - - +
85B LEU* 1.3 64.0 + - + +
87B LYS* 3.0 17.1 + - - -
88B ILE* 3.6 1.1 + - + +
195B THR* 3.6 30.3 - - + +
197B PRO* 3.7 30.3 - - + -
222B MET* 3.3 34.5 - - + +
213C TYR* 3.4 27.4 - - + +
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Residues in contact with LEU 85 (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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81B ARG 3.0 9.8 + - - +
82B ALA* 3.2 5.4 + - - +
84B LEU* 1.3 76.1 - - - +
86B GLY* 1.3 61.3 + - - +
87B LYS 3.1 1.4 + - - -
88B ILE* 3.2 30.6 - - + +
89B PHE* 5.5 1.0 - - - -
197B PRO* 4.3 16.4 - - + -
210C PRO* 4.2 23.1 - - + +
211C VAL* 5.7 0.2 - - - -
213C TYR* 3.2 35.2 - - + -
214C LEU* 3.3 43.7 - - + -
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Residues in contact with GLY 86 (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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82B ALA 2.9 14.2 + - - -
83B MET* 3.2 5.1 + - - -
84B LEU 3.1 0.4 - - - -
85B LEU* 1.3 77.2 - - - +
87B LYS* 1.3 60.8 + - - +
88B ILE* 3.4 1.3 + - - -
89B PHE* 5.0 6.6 - - - -
53C ASN* 4.8 9.4 - - - +
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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