Contacts of the helix formed by residues 60 - 68 (chain A) in PDB entry 6XXD
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 60 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A THR* 3.6 21.0 + - - +
59A SER* 1.3 83.2 + - - +
61A GLN* 1.3 60.0 + - - +
62A ALA* 3.8 12.8 - - + +
63A ALA* 3.3 35.8 + - - +
64A LEU 4.3 0.9 + - - -
80A ILE* 3.9 2.2 - - - +
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Residues in contact with GLN 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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39A TYR* 3.1 21.1 + - - +
59A SER 4.1 0.6 + - - -
60A ASN* 1.3 70.2 - - - +
62A ALA* 1.3 61.2 + - - +
63A ALA 3.2 2.5 - - - -
64A LEU* 3.0 25.1 + - + +
65A ILE* 3.1 32.3 + - + +
69A LEU* 5.3 1.3 - - + -
72A THR* 2.7 30.1 + - - +
78A PHE* 3.6 38.4 - - + +
80A ILE* 4.3 7.1 - - + +
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Residues in contact with ALA 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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60A ASN* 3.5 12.9 - - + +
61A GLN* 1.3 78.1 - - - +
63A ALA* 1.3 56.0 + - - +
65A ILE* 3.8 13.3 - - + +
66A SER* 3.0 29.1 + - - -
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Residues in contact with ALA 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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50A TYR* 3.8 15.7 - - + +
58A THR* 3.5 22.4 - - + -
60A ASN* 3.3 28.8 - - - +
61A GLN 3.2 0.6 - - - -
62A ALA* 1.3 77.9 - - - +
64A LEU* 1.3 61.2 + - - +
66A SER* 3.5 5.9 + - - -
67A LEU* 3.3 29.3 + - - +
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Residues in contact with LEU 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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43A ALA 4.5 4.0 - - - +
46A PHE* 3.4 36.9 - - + +
47A GLN* 3.7 19.3 - - + +
50A TYR* 4.7 1.1 - - + -
58A THR* 3.2 33.4 - - + +
60A ASN 4.4 1.3 - - - +
61A GLN* 3.0 10.3 + - - +
63A ALA* 1.3 74.4 - - - +
65A ILE* 1.3 63.4 + - - +
67A LEU* 3.5 12.5 + - - +
68A GLY 3.5 0.9 + - - -
69A LEU* 3.3 43.7 + - + +
78A PHE* 4.6 11.4 - - + -
80A ILE* 3.8 22.4 - - + -
90A MET* 4.6 0.4 - - - -
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Residues in contact with ILE 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 GLN* 3.1 45.3 + - + +
62A ALA* 3.9 10.8 - - + +
63A ALA 3.3 0.2 - - - -
64A LEU* 1.3 74.3 - - - +
66A SER* 1.3 65.9 + - - +
68A GLY* 3.3 11.3 + - - -
69A LEU* 3.5 22.9 - - + +
70A LYS 3.9 18.6 - - - +
71A SER* 4.7 13.9 - - - +
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Residues in contact with SER 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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62A ALA 3.0 17.7 + - - -
63A ALA* 3.7 8.7 - - - -
64A LEU 3.4 0.2 - - - -
65A ILE* 1.3 77.8 - - - +
67A LEU* 1.3 63.8 + - - +
68A GLY* 3.5 0.7 + - - -
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Residues in contact with LEU 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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46A PHE* 3.9 19.8 - - + +
49A MET* 3.6 23.7 - - + +
50A TYR* 3.4 51.6 - - + +
53A ASP* 4.6 7.9 - - - +
54A ASN* 5.7 0.7 - - - +
63A ALA 3.3 16.3 + - - +
64A LEU* 3.8 9.4 - - - +
65A ILE 3.3 0.6 - - - -
66A SER* 1.3 83.2 - - - +
68A GLY* 1.3 57.2 + - - +
26F ALA* 4.4 7.6 - - - +
29F LYS* 5.6 3.8 + - - +
30F ARG* 4.2 12.8 - - - +
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Residues in contact with GLY 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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46A PHE* 3.3 13.7 - - - -
65A ILE 3.3 7.9 + - - -
66A SER 3.3 0.6 - - - -
67A LEU* 1.3 80.3 - - - +
69A LEU* 1.3 68.5 + - - +
70A LYS* 3.6 3.1 + - - +
23F ASN* 2.8 25.6 + - - -
26F ALA* 4.9 1.3 - - - -
106I ASP 4.8 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