Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 4OWW
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 1.3 76.3 - - - +
68A GLU* 1.3 61.5 + - - +
69A ARG* 3.8 8.2 + - - +
70A GLU* 3.2 31.1 + - - +
71A ALA* 2.9 23.4 + - - +
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Residues in contact with GLU 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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66A VAL 3.8 0.8 + - - -
67A SER* 1.3 70.8 - - - +
69A ARG* 1.3 61.9 + - - +
71A ALA* 3.8 9.4 - - - -
72A ASN* 2.8 46.2 + - - +
106A LYS* 4.8 24.5 - - - +
109A ARG* 5.8 2.3 + - - -
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Residues in contact with ARG 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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67A SER* 3.1 9.7 - - - +
68A GLU* 1.3 84.2 - - - +
70A GLU* 1.3 62.8 + - + +
72A ASN* 3.3 4.9 + - - +
73A ASP* 2.9 50.9 + - - +
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Residues in contact with GLU 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 VAL* 3.6 21.4 - - + +
67A SER* 3.2 32.7 + - - +
69A ARG* 1.3 84.8 - - + +
71A ALA* 1.3 61.1 + - - +
73A ASP* 3.5 8.3 + - - +
74A ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 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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62A MET 4.0 5.6 - - - -
63A THR* 3.9 25.6 - - + +
66A VAL* 3.7 18.1 - - + +
67A SER 2.9 16.1 + - - +
68A GLU* 3.9 11.0 - - + +
69A ARG 3.2 0.2 - - - -
70A GLU* 1.3 78.0 - - - +
72A ASN* 1.3 65.8 + - - +
74A ALA* 3.4 4.5 + - - +
75A LEU* 3.2 26.0 + - - +
106A LYS* 5.7 5.4 - - - +
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Residues in contact with ASN 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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68A GLU* 2.8 38.5 + - - +
69A ARG* 3.8 6.1 - - - +
71A ALA* 1.3 76.2 - - - +
73A ASP* 1.3 61.7 + - - +
75A LEU* 3.5 7.6 + - - +
76A ASN* 2.8 45.6 + - - +
106A LYS* 5.0 5.9 - - - +
110A ASP* 3.2 30.7 + - - +
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Residues in contact with ASP 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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69A ARG* 2.9 37.2 + - - +
70A GLU* 3.7 9.1 - - - +
71A ALA 3.3 0.2 - - - -
72A ASN* 1.3 79.6 - - - +
74A ALA* 1.3 56.3 + - - +
76A ASN* 3.4 5.3 + - - +
77A ALA* 2.9 32.4 + - - +
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Residues in contact with ALA 74 (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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62A MET* 3.5 36.7 - - + +
70A GLU 3.1 15.2 + - - +
71A ALA 3.7 0.4 - - - +
72A ASN 3.3 0.2 - - - -
73A ASP* 1.3 75.6 - - - +
75A LEU* 1.3 59.2 + - - +
77A ALA* 3.2 6.5 + - - +
78A TYR* 2.9 31.0 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.5 11.2 - - + +
62A MET* 3.6 20.2 - - + +
63A THR* 3.9 23.8 - - + -
71A ALA 3.2 11.9 + - - +
72A ASN* 3.6 11.4 - - - +
73A ASP 3.3 0.2 - - - -
74A ALA* 1.3 76.5 - - - +
76A ASN* 1.3 58.5 + - - +
78A TYR* 3.1 2.6 + - - +
79A VAL* 2.9 35.6 + - - +
89A ILE* 3.7 28.7 - - + +
93A LEU* 4.6 16.6 - - + -
110A ASP* 4.0 25.6 - - + +
114A VAL* 4.5 12.6 - - + -
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Residues in contact with ASN 76 (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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72A ASN* 2.8 37.4 + - - +
73A ASP* 3.9 5.1 - - - +
75A LEU* 1.3 77.2 - - - +
77A ALA* 1.3 61.0 + - - +
79A VAL* 3.9 8.0 + - - +
80A CYS* 3.6 25.6 + - - -
113A LEU* 5.2 4.9 - - - +
114A VAL* 3.8 24.5 + - - +
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Residues in contact with ALA 77 (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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73A ASP 2.9 19.8 + - - +
74A ALA* 3.6 6.3 - - - +
76A ASN* 1.3 76.1 - - - +
78A TYR* 1.3 63.8 + - - +
80A CYS* 3.5 12.5 + - - +
81A LYS* 3.0 28.8 + - - +
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Residues in contact with TYR 78 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.0 14.8 - - + +
62A MET* 3.5 23.8 - - + -
74A ALA 2.9 17.6 + - - +
75A LEU 3.6 1.1 - - - +
77A ALA* 1.3 73.6 - - - +
79A VAL* 1.3 64.7 + - - +
80A CYS 3.1 2.2 - - - -
81A LYS* 3.0 34.7 + - + +
85A GLN* 3.4 42.3 - - + +
88A GLU* 2.6 28.5 + - + -
89A ILE* 3.5 28.0 - - + -
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Residues in contact with VAL 79 (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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75A LEU 2.9 22.7 + - - +
76A ASN* 4.1 7.2 - - - +
77A ALA 3.4 0.2 - - - -
78A TYR* 1.3 75.3 - - - +
80A CYS* 1.3 60.0 + - - +
81A LYS 3.4 0.5 + - - -
82A GLY* 3.4 17.2 + - - +
85A GLN 4.7 0.4 - - - -
86A HIS* 3.5 40.4 - - + +
89A ILE* 3.7 32.1 - - + -
90A CYS* 6.1 0.2 - - - -
114A VAL* 3.9 20.0 - - + +
116A ARG* 3.7 21.3 + - - +
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Residues in contact with CYS 80 (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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76A ASN 3.6 15.4 + - - -
77A ALA* 3.5 13.2 + - - +
78A TYR 3.1 0.8 - - - -
79A VAL* 1.3 75.6 - - - +
81A LYS* 1.3 69.9 + - - +
82A GLY* 3.0 5.9 + - - -
116A ARG* 3.7 25.8 - - - +
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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