Contacts of the helix formed by residues 82 - 89 (chain B) in PDB entry 1IAX
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 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLU* 5.1 4.6 + - - -
75B ILE* 3.0 27.3 - - - +
83B PHE* 1.3 68.1 + - - +
84B LYS* 3.3 3.6 - - - +
85B ALA* 3.3 20.7 + - - +
86B ILE* 3.3 15.2 + - - +
316B TYR* 3.7 19.0 + - - -
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Residues in contact with PHE 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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60A LEU* 3.5 29.4 - - + -
63A ILE* 3.9 19.7 - - + -
64A GLU* 4.3 23.6 + - + +
67A ILE* 3.5 24.5 - - + -
282A LEU* 3.9 19.3 - - + -
285A PHE* 4.0 19.5 - + - -
317A PHE* 4.4 7.9 - + - -
75B ILE* 4.1 25.5 - - + +
82B SER* 1.3 74.6 + - - +
84B LYS* 1.3 59.6 + - - +
85B ALA 3.1 0.5 + - - -
86B ILE* 3.1 17.5 + - + +
87B ALA* 2.7 46.7 + - + +
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Residues in contact with LYS 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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57A GLN* 5.3 6.7 + - - +
60A LEU* 3.4 43.7 - - + +
61A ASP* 4.2 11.3 - - - +
64A GLU* 3.3 35.5 + - - +
82B SER* 3.3 1.3 - - - -
83B PHE* 1.3 79.8 - - - +
85B ALA* 1.3 56.3 + - - +
87B ALA* 3.7 0.9 - - - +
88B ASN* 2.9 34.0 + - - +
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Residues in contact with ALA 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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82B SER* 3.3 18.2 + - - +
83B PHE 3.1 0.6 + - - -
84B LYS* 1.3 79.0 - - - +
86B ILE* 1.3 61.1 + - + +
88B ASN* 3.8 1.2 - - - +
89B PHE* 2.9 34.5 + - + +
95B LEU* 6.0 0.2 - - - -
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Residues in contact with ILE 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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285A PHE* 5.1 2.9 - - + -
75B ILE* 4.7 14.8 - - + +
82B SER 3.5 12.6 - - - +
83B PHE* 3.1 31.2 - - + +
85B ALA* 1.3 80.9 - - + +
87B ALA* 1.3 59.0 + - - +
88B ASN 3.5 0.2 + - - -
89B PHE* 3.7 4.6 + - - -
95B LEU* 3.8 21.1 - - + -
312B THR* 2.7 46.7 + - - +
313B GLN* 5.1 9.6 - - + -
316B TYR* 3.6 48.2 - - + -
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Residues in contact with ALA 87 (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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60A LEU* 4.4 4.3 - - + -
281A GLY 4.4 4.5 - - - +
282A LEU* 3.6 17.2 - - + -
283A PRO* 3.3 22.3 - - - +
284A GLY 3.4 9.2 + - - -
285A PHE* 4.5 11.2 - - + -
83B PHE* 2.7 50.3 + - + +
84B LYS* 3.7 5.6 - - - +
86B ILE* 1.3 76.0 - - - +
88B ASN* 1.3 57.7 + - - +
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Residues in contact with ASN 88 (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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55A GLU* 2.9 40.5 + - - +
56A ASN 5.1 2.8 + - - +
57A GLN* 3.0 36.0 + - + +
60A LEU* 5.1 4.9 - - + -
281A GLY 4.5 4.9 + - - +
283A PRO* 3.4 23.9 - - - +
84B LYS 2.9 16.9 + - - +
85B ALA* 4.4 1.3 - - - +
87B ALA* 1.3 74.8 + - + +
89B PHE* 1.3 67.2 + - - +
90B GLN* 3.3 15.8 + - - +
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Residues in contact with PHE 89 (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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284A GLY* 3.2 24.8 - - - -
85B ALA* 2.9 19.9 + - + +
86B ILE* 4.1 8.1 - - - +
87B ALA 3.6 0.6 - - - -
88B ASN* 1.3 75.7 - - - +
90B GLN* 1.3 63.5 + - - +
91B ASP* 3.3 38.4 - - + -
93B HIS* 5.6 0.2 - - + -
94B GLY* 3.1 39.5 - - - -
95B LEU* 3.7 23.1 - - + -
96B PRO* 4.9 6.1 - - + -
312B THR* 3.4 14.1 - - + +
315B GLN* 5.7 0.9 - - - -
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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