Contacts of the helix formed by residues 54 - 67 (chain A) in PDB entry 6B0B
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 HIS 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASN* 3.4 6.3 - - - +
52A GLU* 5.1 1.6 - - - -
53A CYS* 1.3 76.1 - - - +
55A ALA* 1.3 55.4 + - - +
56A GLU* 3.0 17.0 - - - +
57A ILE* 2.8 31.4 + - + +
58A CYS 3.1 8.5 + - - -
85A CYS* 3.8 11.7 - - + -
87A SER* 5.4 0.9 - - - -
88A CYS* 3.1 13.1 - - - -
112A TYR* 5.6 6.3 - + - -
200A ZN 2.0 36.0 - - - -
52E GLU* 3.0 33.5 + - - -
54E HIS* 3.2 34.7 + + - -
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Residues in contact with ALA 55 (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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28A ALA* 6.1 0.2 - - + -
29A LEU 4.8 2.2 - - - -
30A LEU* 3.7 20.3 - - + +
47A PHE* 3.3 29.9 - - + +
48A GLU 3.8 8.7 - - - +
49A ASN* 2.8 19.2 + - - +
53A CYS 3.5 1.2 + - - -
54A HIS* 1.3 70.3 - - - +
56A GLU* 1.3 59.9 + - - +
57A ILE 3.4 0.2 - - - -
58A CYS* 3.7 11.3 - - - +
59A PHE* 2.9 31.7 + - - +
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Residues in contact with GLU 56 (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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30A LEU* 4.0 19.0 - - + +
49A ASN* 4.5 1.8 - - - +
54A HIS* 2.8 21.6 + - - +
55A ALA* 1.3 79.5 + - - +
57A ILE* 1.3 56.7 + - - +
59A PHE* 3.2 4.3 - - - -
60A ILE* 2.9 35.5 + - - +
80A LEU* 3.5 25.7 - - + +
82A TRP 4.5 2.4 - - - +
84A PRO* 3.6 28.0 - - + +
85A CYS 5.5 0.4 + - - -
88A CYS* 4.1 20.0 - - + +
92A LEU* 4.2 22.0 - - + -
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Residues in contact with ILE 57 (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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53A CYS* 3.7 19.1 - - - -
54A HIS 2.8 18.8 + - - +
56A GLU* 1.3 69.9 - - - +
58A CYS* 1.3 58.8 + - - +
60A ILE* 3.3 9.6 + - + +
61A ASN* 2.9 40.5 + - - +
88A CYS* 4.0 22.4 - - + -
91A GLU* 4.9 17.0 - - + +
112E TYR* 5.9 0.2 - - - +
114E HIS* 3.7 35.2 - - + +
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Residues in contact with CYS 58 (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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47A PHE* 3.6 30.6 - - + -
48A GLU 5.1 0.2 - - - -
50A LYS* 4.0 20.4 - - - -
53A CYS* 3.5 34.8 - - - -
54A HIS 3.1 6.5 + - - +
55A ALA* 3.8 8.7 - - - +
57A ILE* 1.3 77.2 - - - +
59A PHE* 1.3 55.6 + - - +
61A ASN* 3.3 5.8 + - - +
62A GLU* 2.9 27.2 + - - +
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Residues in contact with PHE 59 (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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30A LEU* 3.7 23.3 - - + -
32A TYR* 3.8 30.5 - + + -
47A PHE* 3.7 17.9 - - + -
55A ALA 2.9 16.0 + - - +
56A GLU* 3.2 24.7 - - - -
58A CYS* 1.3 72.8 - - - +
60A ILE* 1.3 69.7 + - + +
62A GLU* 3.3 0.9 + - - +
63A ILE* 2.9 49.4 + - + +
76A VAL* 5.0 9.9 - - + -
78A CYS* 5.5 4.9 - - - -
92A LEU* 3.6 26.9 - - + -
95A PHE* 5.7 4.9 - + - -
104A LEU* 5.1 17.3 - - + -
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Residues in contact with ILE 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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56A GLU 2.9 22.5 + - - +
57A ILE* 3.6 9.2 - - + +
59A PHE* 1.3 83.7 - - + +
61A ASN* 1.3 65.1 + - - +
63A ILE* 3.3 7.2 + - - +
64A LYS* 2.9 33.2 + - - +
88A CYS 5.2 0.2 - - - +
91A GLU* 3.9 24.7 - - + +
92A LEU* 3.6 44.9 - - + +
95A PHE* 3.9 37.9 - - + -
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Residues in contact with ASN 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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57A ILE* 2.9 28.4 + - - +
58A CYS* 3.8 6.1 - - - +
60A ILE* 1.3 83.3 - - - +
62A GLU* 1.3 57.0 + - - +
64A LYS* 3.4 19.8 + - - +
65A SER* 2.9 35.0 + - - +
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Residues in contact with GLU 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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32A TYR* 3.8 23.3 + - + +
47A PHE* 3.5 28.6 - - + -
58A CYS 2.9 17.8 + - - +
59A PHE* 3.5 5.4 - - - +
60A ILE 3.2 0.2 - - - -
61A ASN* 1.3 74.1 - - - +
63A ILE* 1.3 64.1 + - + +
65A SER* 5.1 3.7 - - - -
66A MET* 2.9 46.1 + - + +
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Residues in contact with ILE 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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32A TYR* 4.9 15.7 - - + -
34A LEU* 4.3 21.3 - - + -
59A PHE* 2.9 46.0 + - + +
60A ILE* 3.7 4.7 - - - +
62A GLU* 1.3 76.5 - - + +
64A LYS* 1.3 63.2 + - - +
66A MET* 3.2 30.1 - - - +
67A GLY 4.1 0.9 + - - -
68A LEU* 3.8 33.4 - - + +
95A PHE* 3.9 24.2 - - + -
102A LEU* 6.0 5.6 - - + -
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Residues in contact with LYS 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 ILE* 2.9 21.2 + - - +
61A ASN* 3.4 21.7 + - - +
62A GLU 3.1 0.2 - - - -
63A ILE* 1.3 80.1 - - - +
65A SER* 1.3 60.4 + - - +
66A MET 3.3 2.7 + - - -
67A GLY* 3.9 7.1 + - - -
68A LEU* 5.2 3.2 + - - +
95A PHE* 4.5 27.5 - - + -
1G U 3.7 33.3 + - - -
2G U 4.3 6.4 + - - -
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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
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61A ASN* 2.9 20.9 + - - +
62A GLU* 3.7 5.2 - - - -
64A LYS* 1.3 74.4 - - - +
66A MET* 1.3 59.8 + - - +
67A GLY 3.5 0.7 - - - -
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Residues in contact with MET 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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34A LEU* 4.5 15.5 - - + -
43A THR* 5.4 11.9 - - + -
62A GLU* 2.9 27.1 + - + +
63A ILE* 3.2 37.9 - - + +
65A SER* 1.3 80.0 - - - +
67A GLY* 1.3 79.9 + - - +
68A LEU* 5.1 4.5 - - + -
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Residues in contact with GLY 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 4.1 0.2 + - - -
64A LYS 3.9 7.4 + - - -
65A SER 3.5 2.4 - - - -
66A MET* 1.3 97.7 - - - +
68A LEU* 1.3 65.3 + - - +
69A ASP* 4.2 5.9 - - - +
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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