Contacts of the helix formed by residues 71 - 76 (chain P) in PDB entry 2I2X
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 ASP 71 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68P ASP* 3.2 37.2 + - + +
69P PRO* 4.2 2.8 - - - +
70P ILE* 1.3 96.3 + - - +
72P LEU* 1.3 55.7 + - - +
73P ILE 3.0 5.4 - - - -
74P ASP* 3.1 7.4 + - - +
75P ASP* 2.8 41.0 + - - +
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Residues in contact with LEU 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ILE* 5.0 8.5 - - + -
43P ILE* 4.5 3.4 - - + -
59P LEU* 3.6 27.1 - - + -
62P ALA* 3.8 26.2 - - + -
63P ILE* 4.1 12.3 - - + -
67P LYS 3.9 9.0 - - - +
68P ASP* 3.4 27.7 + - + +
70P ILE 3.4 0.6 - - - -
71P ASP* 1.3 74.9 - - - +
73P ILE* 1.3 60.0 + - - +
75P ASP* 4.2 7.4 - - + -
76P ALA* 2.9 44.3 + - + +
77P LEU* 3.0 15.8 + - - +
112P CYS* 4.8 7.0 - - - -
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Residues in contact with ILE 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P ILE* 3.4 35.0 - - + +
72P LEU* 1.3 78.3 - - - +
74P ASP* 1.3 66.5 + - - +
77P LEU* 3.6 11.4 - - + +
78P MET* 2.9 38.5 + - + +
109P ILE* 4.4 28.9 - - + -
112P CYS* 4.0 25.8 - - + -
120P PRO* 3.7 35.4 - - + -
121P LYS 6.0 2.0 - - - +
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Residues in contact with ASP 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70P ILE 4.6 1.3 + - - -
71P ASP* 3.1 8.2 + - - +
73P ILE* 1.3 85.6 - - - +
75P ASP* 1.3 69.3 + - - +
76P ALA 3.6 0.4 + - - -
78P MET* 3.6 26.8 - - - +
79P VAL* 3.4 17.0 - - - +
121P LYS 5.0 10.5 - - - +
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Residues in contact with ASP 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40P ILE* 3.6 28.7 - - + +
68P ASP* 4.9 5.5 - - - +
71P ASP* 2.8 38.7 + - - +
72P LEU* 4.2 9.4 - - + -
74P ASP* 1.3 83.5 - - - +
76P ALA* 1.3 58.5 + - - +
79P VAL* 3.5 16.6 - - - +
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Residues in contact with ALA 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ILE* 3.8 14.6 - - + +
43P ILE* 3.8 31.2 - - + -
44P ALA* 4.7 4.0 - - - -
47P ILE* 4.3 2.3 - - - +
59P LEU* 4.7 0.2 - - + -
72P LEU* 2.9 34.1 + - + +
75P ASP* 1.3 79.3 - - - +
77P LEU* 1.3 60.9 + - + +
78P MET 3.5 0.9 - - - -
79P VAL* 3.4 1.8 + - - +
80P GLY* 3.0 27.0 + - - -
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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