Contacts of the helix formed by residues 56 - 64 (chain J) in PDB entry 1I43
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 56 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55J ASN* 1.3 81.6 - - - +
57J ASP* 1.3 67.9 + - - +
58J GLY 3.3 7.1 + - - -
59J SER* 3.4 4.2 + - - -
60J VAL* 3.1 25.7 + - - +
430K ASP* 3.0 38.6 + - - +
432K ASP* 6.5 0.2 - - - -
433K ASP* 3.1 17.5 + - - -
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Residues in contact with ASP 57 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J SER* 1.3 70.8 + - - +
58J GLY* 1.3 57.5 + - - +
60J VAL* 2.8 8.7 + - - +
61J ALA* 2.7 35.1 + - - +
126J LEU* 3.7 11.1 - - + +
243J LEU* 3.3 36.8 - - + +
246J LYS* 3.0 38.3 + - - -
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Residues in contact with GLY 58 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J SER* 3.3 8.3 + - - -
57J ASP* 1.3 80.7 - - - +
59J SER* 1.3 62.2 + - - +
60J VAL 3.1 0.3 + - - -
61J ALA* 3.1 12.2 + - - +
62J ILE* 3.3 17.8 + - - +
311J HIS* 3.4 46.3 - - - +
430K ASP* 4.8 1.1 - - - -
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Residues in contact with SER 59 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J LEU* 3.8 21.7 - - - +
56J SER* 3.4 6.6 + - - -
57J ASP 3.3 0.4 - - - -
58J GLY* 1.3 74.2 - - - +
60J VAL* 1.3 56.9 + - - +
62J ILE* 3.4 1.1 + - - +
63J HIS* 3.1 32.9 + - - +
429K GLU* 3.7 17.8 - - - +
430K ASP* 3.1 24.9 + - - +
433K ASP* 2.7 31.7 + - - +
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Residues in contact with VAL 60 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J TYR* 5.6 5.6 - - + +
51J ALA 6.2 0.2 - - - +
54J LEU* 4.0 28.5 - - + +
56J SER 3.1 16.5 + - - +
57J ASP* 2.8 13.3 + - - +
59J SER* 1.3 73.7 - - - +
61J ALA* 1.3 54.9 + - - +
62J ILE 2.7 12.0 + - - -
64J ALA* 2.7 52.0 + - + +
125J ALA* 3.7 20.2 - - + +
126J LEU* 3.9 18.2 - - + +
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Residues in contact with ALA 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57J ASP 2.7 14.5 + - - +
58J GLY* 3.1 12.7 + - - +
60J VAL* 1.3 74.1 - - - +
62J ILE* 1.3 58.0 + - + +
122J LYS* 3.0 27.2 + - - +
126J LEU* 4.1 24.0 - - + -
243J LEU* 5.4 1.8 - - + -
307J MET* 3.3 30.5 - - + +
310J LEU* 4.4 11.7 - - + -
311J HIS* 5.1 2.5 - - - +
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Residues in contact with ILE 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58J GLY 3.3 13.0 + - - +
59J SER 3.7 6.7 - - - +
60J VAL 2.7 2.0 + - - -
61J ALA* 1.3 81.9 - - - +
63J HIS* 1.3 83.6 + - + +
66J GLU* 3.2 0.9 - - - +
122J LYS* 2.8 17.3 + - - +
308J LYS* 2.9 48.9 + - + +
311J HIS* 3.9 3.8 - - + -
392K CYS* 4.2 8.7 - - + +
393K GLU* 4.2 14.6 - - + -
428K VAL* 3.2 35.0 - - + -
429K GLU* 3.8 19.3 - - + +
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Residues in contact with HIS 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J TYR* 3.4 5.7 - - - -
54J LEU* 4.0 16.2 - - + +
59J SER 3.1 15.7 + - - +
62J ILE* 1.3 95.7 - - + +
64J ALA* 1.3 67.3 + - - +
65J GLY 3.1 0.3 + - - -
66J GLU* 3.0 18.2 + - - -
67J ARG* 3.1 49.2 + - + +
308J LYS* 6.0 0.2 - - - -
382K ILE* 3.7 17.8 + - + +
384K TYR* 4.2 10.1 - + - -
393K GLU* 4.0 17.4 - - + +
394K SER 4.7 0.2 + - - -
429K GLU* 2.8 37.9 + - + +
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J TYR* 3.7 13.6 - - + -
60J VAL* 2.7 47.7 + - + +
62J ILE 3.6 0.8 - - - -
63J HIS* 1.3 70.6 - - - +
65J GLY* 1.3 59.4 + - - +
118J VAL 4.4 0.3 - - - +
122J LYS* 2.9 46.7 - - + +
125J ALA* 3.7 17.9 - - + -
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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