Contacts of the helix formed by residues 54 - 67 (chain A) in PDB entry 1X6E
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 GLN 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TYR* 3.4 21.0 + - - -
52A PHE* 3.4 19.3 - - - +
53A SER* 1.3 91.7 + - - +
55A ASN* 1.3 66.7 + - - +
56A SER* 3.4 10.1 - - - +
57A GLY* 3.4 12.4 + - - +
58A LEU 3.4 0.5 + - - -
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Residues in contact with ASN 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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43A TYR* 3.4 39.6 - - + +
54A GLN* 1.3 70.4 + - - +
56A SER* 1.3 60.0 + - - +
57A GLY 2.7 16.5 + - - -
58A LEU* 2.8 22.7 + - - +
59A ILE* 3.0 51.2 + - - +
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Residues in contact with SER 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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54A GLN* 3.4 7.7 - - - +
55A ASN* 1.3 84.3 + - - +
57A GLY* 1.3 58.6 + - - +
59A ILE* 4.3 8.0 - - - +
60A ASN* 3.9 16.6 + - - +
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Residues in contact with GLY 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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52A PHE* 4.0 11.8 - - - -
54A GLN* 3.4 10.7 + - - +
55A ASN 2.7 2.2 + - - -
56A SER* 1.3 80.1 - - - +
58A LEU* 1.3 63.1 + - - +
59A ILE 3.3 0.4 - - - -
60A ASN* 3.5 7.2 + - - +
61A HIS* 3.3 19.6 + - - +
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Residues in contact with LEU 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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43A TYR* 3.8 20.2 - - + -
44A LYS 3.5 11.0 - - - +
45A CYS* 3.3 28.3 - - + +
52A PHE* 3.4 41.8 - - + -
54A GLN 3.4 6.8 + - - +
55A ASN* 2.8 21.4 + - - +
57A GLY* 1.3 69.6 - - - +
59A ILE* 1.3 68.8 + - + +
61A HIS* 3.0 5.2 + - - +
62A GLN* 3.0 50.5 + - + +
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Residues in contact with ILE 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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55A ASN* 3.0 48.5 + - - +
56A SER* 4.3 7.6 - - - +
58A LEU* 1.3 78.9 - - + +
60A ASN* 1.3 55.5 + - - +
62A GLN* 2.7 29.0 + - + +
63A ARG* 2.8 30.6 + - + +
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Residues in contact with ASN 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 SER 3.9 11.6 + - - +
57A GLY* 3.5 10.0 + - - +
58A LEU 3.4 0.6 - - - -
59A ILE* 1.3 79.0 - - - +
61A HIS* 1.3 56.7 + - - +
62A GLN 3.3 0.7 - - - -
63A ARG* 3.5 26.5 - - - +
64A ILE* 2.8 24.1 - - - +
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Residues in contact with HIS 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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45A CYS* 3.8 7.4 - - - -
48A CYS* 3.2 11.9 - - - -
50A LYS* 3.3 36.0 + - + +
52A PHE* 3.2 33.0 - + + -
57A GLY 3.3 4.1 + - - +
58A LEU 3.0 8.4 + - - +
59A ILE 3.0 1.0 - - - -
60A ASN* 1.3 78.8 - - - +
62A GLN* 1.3 51.5 + - - +
64A ILE* 3.7 15.1 - - + +
65A HIS* 2.6 42.1 + + - -
401A ZN 2.4 35.9 - - - -
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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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44A LYS 4.2 0.2 + - - -
45A CYS* 3.5 29.4 - - - +
46A LEU* 4.2 25.9 + - - +
47A GLU* 4.7 7.3 + - - +
58A LEU* 3.0 43.6 + - + +
59A ILE* 2.7 14.6 + - + +
61A HIS* 1.3 79.2 - - - +
63A ARG* 1.3 62.9 + - - +
64A ILE 3.2 1.8 - - - -
65A HIS* 3.2 22.3 + - + +
66A THR* 3.3 12.4 - - - +
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Residues in contact with ARG 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 ILE* 2.8 23.1 + - + +
60A ASN* 3.5 33.8 + - - +
62A GLN* 1.3 76.6 - - - +
64A ILE* 1.3 62.0 + - + +
66A THR* 3.4 11.1 - - + +
67A SER* 2.7 47.3 + - - +
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Residues in contact with ILE 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 ASN* 2.8 28.3 - - - +
61A HIS* 3.7 16.6 - - + +
63A ARG* 1.3 81.8 - - + +
65A HIS* 1.3 92.2 + - + +
67A SER* 2.4 24.2 - - - +
68A GLY* 4.2 3.1 - - - -
69A PRO* 5.5 0.5 - - - +
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Residues in contact with HIS 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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45A CYS* 4.2 0.2 - - - -
47A GLU* 3.3 38.1 - - + -
48A CYS* 4.3 8.1 - - + -
61A HIS* 2.6 27.9 + + - -
62A GLN* 3.5 14.4 - - - +
63A ARG 3.1 0.4 - - - -
64A ILE* 1.3 97.8 - - + +
66A THR* 1.3 66.2 + - - +
67A SER 3.0 4.2 + - - -
68A GLY* 4.4 0.5 + - - -
70A SER 4.3 3.3 - - - +
72A GLY* 3.5 32.9 + - - +
401A ZN 2.3 35.4 - - - -
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Residues in contact with THR 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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47A GLU* 5.4 5.0 + - - +
62A GLN 3.3 17.5 - - - +
63A ARG* 3.4 16.8 - - + +
65A HIS* 1.3 76.3 - - - +
67A SER* 1.3 62.9 + - - +
68A GLY 4.1 1.6 + - - -
70A SER 5.4 1.6 - - - +
71A SER* 5.6 2.6 - - - -
72A GLY* 5.1 6.5 + - - +
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Residues in contact with SER 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 ARG* 2.7 27.5 + - - +
64A ILE* 2.4 27.9 - - - +
65A HIS 4.1 0.7 - - - -
66A THR* 1.3 83.0 + - - +
68A GLY* 1.3 56.6 + - - +
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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