Contacts of the helix formed by residues 61 - 67 (chain F) in PDB entry 6NR8
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 61 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F ASP* 3.2 1.0 - - - +
60F GLY* 1.3 79.0 - - - +
62F VAL* 1.3 61.5 + - + +
63F LEU 3.3 0.4 - - - -
64F LEU* 3.1 6.7 + - - +
65F HIS* 2.7 63.5 + - - -
78F ALA* 3.4 12.6 - - - +
81F ALA* 4.1 3.0 - - + +
82F THR* 3.4 31.3 + - - +
85F ASP* 3.4 24.5 + - - +
92F THR* 3.3 20.1 + - + -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F THR* 4.6 22.7 - - + -
58F LYS 5.0 1.3 - - - +
59F ASP* 3.7 30.6 - - + +
61F ASN* 1.3 77.2 - - + +
63F LEU* 1.3 64.9 + - - +
65F HIS* 3.2 11.3 + - + +
66F GLU* 3.1 24.2 + - + +
85F ASP* 5.4 4.0 - - - +
389F ASP* 5.2 12.6 - - + +
393F ASP* 5.8 0.2 - - - +
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Residues in contact with LEU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 3.8 31.6 - - + -
37F ASN* 3.9 17.7 - - + +
45F LYS* 4.2 11.4 - - + -
47F LEU* 3.8 7.2 - - + -
57F THR* 3.2 38.8 - - - +
58F LYS* 4.4 0.7 - - - -
59F ASP 3.3 31.2 + - - +
60F GLY* 4.9 1.3 - - - +
61F ASN 3.3 0.4 - - - -
62F VAL* 1.3 77.9 - - - +
64F LEU* 1.3 61.6 + - - +
66F GLU* 4.7 2.9 - - + +
67F MET* 3.3 36.4 + - + +
523H GLN* 3.7 17.7 - - - +
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Residues in contact with LEU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F LEU* 4.2 27.4 - - + -
34F LEU* 4.7 6.5 - - + -
60F GLY 3.3 20.0 - - - +
61F ASN* 3.1 12.7 + - - +
63F LEU* 1.3 79.2 - - - +
65F HIS* 1.3 62.6 + - - +
66F GLU 3.4 0.3 + - - -
67F MET* 3.6 22.8 - - + +
69F ILE* 3.9 17.1 - - + +
74F ALA* 4.2 17.7 - - + +
77F ILE* 4.0 17.9 - - + +
78F ALA* 3.8 37.0 - - + +
81F ALA* 5.0 2.9 - - + -
96F VAL* 5.1 5.8 - - + -
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Residues in contact with HIS 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ASN* 2.7 52.9 + - - +
62F VAL* 3.2 11.3 + - + +
64F LEU* 1.3 76.9 - - - +
66F GLU* 1.3 62.9 + - - +
67F MET 4.3 2.3 - - - +
68F GLN* 5.1 1.7 - - - +
78F ALA* 3.1 29.2 + - + +
82F THR* 3.2 11.6 + - + -
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 4.1 16.4 - - + -
50F GLY* 3.3 37.9 - - - +
51F ALA* 3.4 9.0 - - - +
55F LYS* 3.3 30.9 - - + -
57F THR* 5.2 12.7 - - + +
62F VAL* 3.1 15.9 + - + +
63F LEU* 3.7 4.0 + - - +
64F LEU 3.3 0.2 - - - -
65F HIS* 1.3 78.8 - - - +
67F MET* 1.3 65.8 + - - +
68F GLN* 3.1 16.3 - - - +
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Residues in contact with MET 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.8 12.1 - - + -
33F VAL* 6.0 3.6 - - + -
34F LEU* 5.0 9.4 - - + -
47F LEU* 3.7 30.5 - - + -
50F GLY* 4.6 1.1 - - - -
63F LEU* 3.3 29.6 + - + +
64F LEU* 3.6 24.8 + - + +
65F HIS 4.3 2.6 - - - +
66F GLU* 1.3 80.4 - - - +
68F GLN* 1.3 60.0 + - - +
69F ILE* 2.9 31.5 + - + +
19H ALA* 4.6 15.3 - - + -
20H LYS 4.2 14.1 - - - +
21H HIS* 5.6 3.6 - - - -
523H GLN* 4.8 14.1 - - - +
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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