Contacts of the helix formed by residues 64 - 73 (chain A) in PDB entry 2O38
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ALA* 4.4 0.4 - - - -
63A ILE* 1.3 76.7 - - - +
65A GLN* 1.3 59.5 + - - +
66A PRO* 3.5 18.1 - - + +
67A LYS* 3.0 21.0 + - + +
68A VAL* 2.9 27.4 + - - +
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Residues in contact with GLN 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.1 55.2 + - - +
55A ALA* 3.8 9.5 + - - +
58A ALA* 4.2 10.5 - - + +
63A ILE 3.7 1.8 + - - -
64A ASN* 1.3 70.7 - - - +
66A PRO* 1.4 69.9 - - + +
68A VAL* 3.4 1.6 + - - +
69A SER* 3.2 27.3 + - - +
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Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASN* 3.5 16.6 - - + +
65A GLN* 1.4 93.0 - - + +
67A LYS* 1.3 61.5 + - - +
69A SER* 3.4 6.7 + - - -
70A ALA* 3.3 19.6 + - - +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.9 22.2 - - + -
64A ASN* 3.0 26.2 + - + +
66A PRO* 1.3 78.6 - - - +
68A VAL* 1.3 62.6 + - - +
70A ALA* 3.3 4.8 + - - +
71A LEU 3.2 16.5 + - - -
78A GLY* 2.5 38.0 + - - -
79A PHE* 3.3 44.3 - - + +
83A ARG* 5.1 9.2 - - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.9 39.0 - - + +
57A ALA* 4.2 10.3 - - + -
58A ALA* 3.3 39.0 - - + +
61A LEU* 4.4 4.7 - - + -
63A ILE* 3.4 21.8 - - + -
64A ASN 2.9 11.9 + - - +
65A GLN* 3.9 5.2 - - - +
66A PRO 3.4 0.4 - - - -
67A LYS* 1.3 69.2 - - - +
69A SER* 1.3 66.9 + - - +
71A LEU* 3.2 7.1 + - + +
72A ARG* 2.9 28.2 + - + +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.0 27.6 + - - +
65A GLN* 3.2 18.8 + - - +
66A PRO* 3.8 9.6 - - - +
67A LYS 3.4 0.2 - - - -
68A VAL* 1.3 75.2 - - - +
70A ALA* 1.3 64.1 + - - +
72A ARG* 3.3 2.1 + - - +
73A ASN* 3.0 34.2 + - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A PRO 3.3 9.0 + - - +
67A LYS* 3.5 11.2 - - - +
68A VAL 3.2 0.6 - - - -
69A SER* 1.3 79.5 - - - +
71A LEU* 1.3 63.1 + - - +
73A ASN* 3.0 3.9 + - - -
74A TYR 2.9 4.3 + - - -
75A LYS* 2.8 58.5 + - + +
79A PHE* 3.9 6.1 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.1 21.3 - - + -
43A LEU* 3.9 34.1 - - + -
44A ASN* 3.1 23.6 + - - +
47A ILE* 3.8 28.7 - - + -
61A LEU* 4.2 14.4 - - + -
63A ILE* 5.1 2.5 - - + -
67A LYS 3.2 5.0 + - - +
68A VAL* 3.5 11.2 - - + +
70A ALA* 1.3 77.8 - - - +
72A ARG* 1.3 60.9 + - - +
74A TYR* 3.0 18.7 + - - -
76A LEU* 4.2 5.8 - - + -
79A PHE* 3.8 20.3 - - + -
84A LEU* 4.2 9.4 - - + -
87A LEU* 5.1 4.3 - - + -
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Residues in contact with ARG 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASN* 2.9 41.1 + - - +
47A ILE* 3.6 31.6 - - - +
48A ASP* 2.9 30.5 + - - +
52A LEU 5.0 4.4 + - - -
54A GLN* 3.5 35.3 - - + +
57A ALA* 6.0 0.4 - - - -
68A VAL* 2.9 28.8 + - + +
69A SER 3.7 2.5 - - - +
71A LEU* 1.3 76.3 - - - +
73A ASN* 1.3 61.9 + - - +
74A TYR* 3.4 14.6 + - - -
201A ACY 4.0 4.6 + - - +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 5.3 2.1 + - - -
69A SER* 3.0 27.1 + - - +
70A ALA 3.0 3.3 + - - +
72A ARG* 1.3 82.4 + - - +
74A TYR* 1.3 71.3 + - - +
75A LYS* 3.1 27.8 + - + +
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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