Contacts of the helix formed by residues 59 - 73 (chain A) in PDB entry 6W6Y
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 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN* 2.9 36.9 + - - +
55A LYS* 4.8 1.4 - - - +
57A THR 3.1 1.2 - - - -
58A ASN* 1.3 78.6 - - - +
60A ALA* 1.3 62.8 + - - +
61A MET 3.2 2.7 - - - -
62A GLN* 3.2 16.3 + - - +
63A VAL* 3.2 35.2 + - + +
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Residues in contact with ALA 60 (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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57A THR* 3.0 19.0 + - - +
58A ASN 3.2 2.8 + - - +
59A ASN* 1.3 75.9 - - - +
61A MET* 1.3 62.8 + - - +
63A VAL* 3.4 6.8 + - - +
64A GLU* 3.1 24.9 + - - +
86A HIS* 3.6 26.4 - - + +
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Residues in contact with MET 61 (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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35A VAL* 5.5 2.0 - - + -
37A ASN* 4.5 6.3 - - - -
45A HIS* 3.8 18.6 - - + -
50A ALA 4.8 0.4 - - - +
53A LEU* 4.0 22.2 - - + -
54A ASN* 3.4 23.3 - - - +
57A THR* 3.0 24.2 + - + +
60A ALA* 1.3 77.5 - - - +
62A GLN* 1.3 56.9 + - - +
64A GLU* 3.4 3.4 + - - +
65A SER* 2.9 34.2 + - - +
84A SER 5.7 0.4 - - - +
85A GLY* 5.5 2.0 - - - +
86A HIS* 3.6 21.2 + - + -
88A LEU* 4.9 4.3 - - + -
92A CYS* 3.9 27.1 - - + -
94A HIS* 3.8 22.7 - - + +
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Residues in contact with GLN 62 (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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43A LEU 2.8 25.4 + - - -
44A LYS* 3.8 6.4 - - - +
45A HIS* 2.8 37.5 + - - +
54A ASN* 2.8 16.8 + - - +
59A ASN* 3.2 29.5 + - - +
61A MET* 1.3 70.4 - - - +
63A VAL* 1.3 61.2 + - + +
65A SER* 3.3 1.6 + - - -
66A ASP* 2.8 65.9 + - - +
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Residues in contact with VAL 63 (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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59A ASN* 3.2 30.0 + - - +
60A ALA* 3.8 9.4 - - - +
62A GLN* 1.3 74.7 - - - +
64A GLU* 1.3 63.7 + - - +
66A ASP* 3.4 8.7 + - - +
67A ASP* 3.2 21.5 + - + +
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Residues in contact with GLU 64 (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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60A ALA 3.1 16.1 + - - +
61A MET* 3.8 4.0 - - - +
63A VAL* 1.3 79.0 - - - +
65A SER* 1.3 62.4 + - - +
67A ASP* 3.2 8.8 + - - +
68A TYR* 3.0 21.2 + - - +
83A LEU* 3.5 26.9 - - + +
84A SER* 2.9 38.3 + - - +
86A HIS* 2.7 32.4 + - + +
94A HIS* 5.2 1.7 + - - -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 25.5 - - - +
45A HIS* 2.8 31.5 + - - -
61A MET 2.9 19.7 + - - -
62A GLN 3.6 3.8 - - - -
64A GLU* 1.3 75.1 + - - +
66A ASP* 1.3 60.5 + - - +
68A TYR* 3.1 2.6 + - - +
69A ILE* 2.9 35.1 + - - +
83A LEU* 4.0 17.3 - - - +
94A HIS* 4.1 4.7 + - - -
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Residues in contact with ASP 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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42A TYR 5.2 1.7 - - - +
43A LEU 4.7 0.9 - - - +
44A LYS* 4.4 15.2 + - - +
62A GLN* 2.8 48.4 + - - +
63A VAL* 3.7 9.2 - - - +
64A GLU 3.3 0.2 - - - -
65A SER* 1.3 75.5 - - - +
67A ASP* 1.3 57.2 + - - +
69A ILE* 3.4 6.3 + - - +
70A ALA* 2.9 30.5 + - - +
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Residues in contact with ASP 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 VAL* 3.2 13.3 + - + +
64A GLU* 3.6 13.1 - - + +
65A SER 3.2 0.2 - - - -
66A ASP* 1.3 76.4 - - - +
68A TYR* 1.3 65.0 + - - +
70A ALA* 3.4 12.0 + - - +
71A THR* 3.4 25.9 + - - +
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Residues in contact with TYR 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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43A LEU* 3.8 17.9 - - + -
64A GLU 3.0 13.4 + - - +
65A SER 3.1 7.4 + - - +
67A ASP* 1.3 79.6 + - - +
69A ILE* 1.3 66.5 + - + +
71A THR* 3.3 1.8 + - - -
72A ASN* 2.8 71.8 + - + +
73A GLY 3.9 17.9 + - - -
75A LEU* 3.8 20.1 - - + +
81A CYS* 3.4 33.0 - - - -
83A LEU* 4.2 21.5 - - + -
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Residues in contact with ILE 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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41A VAL 3.8 21.1 - - - +
42A TYR* 3.6 43.7 - - + +
43A LEU* 4.0 10.3 - - + -
44A LYS* 5.5 5.4 - - - +
65A SER 2.9 21.0 + - - +
66A ASP* 3.8 6.1 - - - +
68A TYR* 1.3 85.5 - - + +
70A ALA* 1.3 69.9 + - - +
73A GLY* 2.8 44.6 + - - +
74A PRO* 4.0 2.2 - - + -
75A LEU* 4.8 0.4 - - + +
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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 ASP 2.9 18.2 + - - +
67A ASP* 3.6 9.9 - - - +
68A TYR 3.3 0.2 - - - -
69A ILE* 1.3 80.5 - - - +
71A THR* 1.3 64.1 + - + +
73A GLY 4.9 0.3 + - - -
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Residues in contact with THR 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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67A ASP* 3.4 23.1 + - - +
68A TYR* 3.3 3.7 + - - -
70A ALA* 1.3 86.9 - - + +
72A ASN* 1.4 84.6 + - - +
73A GLY 3.8 0.2 - - - -
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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
----------------------------------------------------------
68A TYR* 2.8 59.5 + - + +
71A THR* 1.4 100.4 + - - +
73A GLY* 1.3 63.2 - - - +
74A PRO 4.8 1.7 - - - +
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Residues in contact with GLY 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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68A TYR* 3.9 10.6 + - - -
69A ILE* 2.8 34.2 + - - +
70A ALA 4.7 0.4 + - - -
71A THR 3.8 0.6 - - - -
72A ASN* 1.3 82.7 - - - +
74A PRO* 1.3 77.3 - - - +
75A LEU 3.9 0.2 + - - -
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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