Contacts of the helix formed by residues 60 - 68 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58L THR* 3.6 20.4 + - - +
59L SER* 1.3 83.5 + - - +
61L GLN* 1.3 61.0 + - - +
62L ALA* 3.8 13.9 - - + +
63L ALA* 3.3 35.8 + - - +
64L LEU* 4.3 1.0 + - - +
80L ILE* 3.9 3.0 - - - +
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Residues in contact with GLN 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L TYR* 3.1 21.3 + - - +
59L SER 4.1 1.0 + - - -
60L ASN* 1.3 69.4 - - - +
62L ALA* 1.3 60.6 + - - +
63L ALA 3.2 2.7 - - - -
64L LEU* 3.0 24.8 + - + +
65L ILE* 3.1 31.9 + - + +
69L LEU* 5.3 1.3 - - + -
72L THR* 2.7 31.4 + - - +
78L PHE* 3.6 38.9 - - + +
80L ILE* 4.3 8.2 - - + +
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Residues in contact with ALA 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L ASN* 3.5 12.9 - - + +
61L GLN* 1.3 78.7 - - - +
63L ALA* 1.3 56.6 + - - +
65L ILE* 3.8 13.8 - - + +
66L SER* 3.0 29.1 + - - -
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Residues in contact with ALA 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L TYR* 3.8 15.0 - - + +
58L THR* 3.5 23.3 - - + -
60L ASN* 3.3 28.9 - - - +
61L GLN 3.2 0.8 - - - -
62L ALA* 1.3 78.2 - - - +
64L LEU* 1.3 60.8 + - - +
66L SER* 3.5 5.3 + - - -
67L LEU* 3.3 29.7 + - - +
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Residues in contact with LEU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43L ALA* 4.5 4.5 - - + +
46L PHE* 3.4 36.9 - - + +
47L GLN* 3.7 18.8 - - + +
50L TYR* 4.7 0.9 - - + -
58L THR* 3.2 34.3 - - + +
60L ASN 4.4 1.3 - - - +
61L GLN* 3.0 9.8 + - - +
63L ALA* 1.3 73.8 - - - +
65L ILE* 1.3 63.0 + - - +
67L LEU* 3.5 11.9 + - - +
68L GLY 3.5 1.4 + - - -
69L LEU* 3.3 43.1 + - + +
78L PHE* 4.6 10.5 - - + -
80L ILE* 3.8 22.2 - - + -
90L MET* 4.6 0.9 - - - -
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Residues in contact with ILE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L GLN* 3.1 45.6 + - + +
62L ALA* 3.9 11.0 - - - +
64L LEU* 1.3 74.4 - - - +
66L SER* 1.3 64.7 + - - +
68L GLY* 3.3 11.1 + - - -
69L LEU* 3.5 21.8 - - + +
70L LYS 3.9 19.7 - - - +
71L SER* 4.7 13.5 - - - +
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Residues in contact with SER 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62L ALA 3.0 18.9 + - - -
63L ALA* 3.7 8.3 - - - -
64L LEU 3.4 0.2 - - - -
65L ILE* 1.3 77.8 - - - +
67L LEU* 1.3 65.0 + - - +
68L GLY 3.5 0.3 + - - -
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Residues in contact with LEU 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ALA* 4.4 7.8 - - - +
29I LYS* 5.5 4.7 + - - +
30I ARG* 4.2 13.0 - - - +
46L PHE* 3.9 21.3 - - + +
49L MET* 3.6 23.2 - - + +
50L TYR* 3.4 51.8 - - + +
53L ASP* 4.6 8.1 - - - +
54L ASN* 5.7 0.7 - - - +
63L ALA 3.3 16.0 + - - +
64L LEU* 3.8 9.9 - - - +
65L ILE 3.3 0.4 - - - -
66L SER* 1.3 84.9 - - - +
68L GLY* 1.3 55.8 + - - +
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Residues in contact with GLY 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ASN* 2.8 24.8 + - - -
26I ALA* 4.9 1.3 - - - -
46L PHE* 3.3 13.9 - - - -
65L ILE 3.3 8.2 + - - -
66L SER 3.3 0.6 - - - -
67L LEU* 1.3 79.8 - - - +
69L LEU* 1.3 69.9 + - - +
70L LYS* 3.6 3.5 + - - +
106M 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