Contacts of the helix formed by residues 73 - 81 (chain D) 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 ASP 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D SER* 4.6 0.7 - - - -
72D ASN* 1.3 85.1 + - + +
74D GLY* 1.3 52.3 + - - +
75D ALA* 3.1 4.8 - - - +
76D THR* 2.5 64.5 + - + +
99D ASP* 5.6 0.7 - - - +
106D THR* 3.4 22.9 + - - -
107D THR* 3.9 12.1 + - - -
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Residues in contact with GLY 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 3.9 24.5 - - - +
51D SER* 3.9 7.8 + - - -
73D ASP* 1.3 68.9 - - - +
75D ALA* 1.3 59.7 + - - +
76D THR 3.3 0.2 - - - -
77D ILE* 3.3 26.2 + - - +
78D LEU* 2.9 32.5 + - - +
107D THR* 3.8 9.3 + - - +
110D VAL* 5.3 0.4 - - - -
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ASP* 2.8 5.7 + - - +
74D GLY* 1.3 77.0 - - - +
76D THR* 1.3 58.6 + - + +
78D LEU* 3.1 7.7 + - - +
79D LYS* 2.9 33.1 + - - +
95D SER* 3.7 30.7 - - - -
99D ASP* 4.2 11.7 - - - +
106D THR* 3.8 34.3 + - - +
107D THR* 4.9 0.4 + - - -
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D THR* 3.7 9.5 - - - +
72D ASN 2.9 14.7 + - - -
73D ASP* 2.5 44.0 + - + +
75D ALA* 1.3 70.7 - - + +
77D ILE* 1.3 57.5 + - - -
79D LYS* 3.4 10.0 + - + +
80D GLN* 2.9 30.3 + - - +
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529A ASP* 5.5 0.2 - - - +
531A ILE* 3.8 15.7 - - + -
48D ILE* 4.7 11.9 - - + -
51D SER* 4.7 2.2 - - - +
59D LYS* 3.6 35.0 - - + +
61D ILE* 3.7 19.1 - - + -
71D THR* 3.6 33.9 - - + +
72D ASN 4.2 2.5 - - - +
74D GLY* 3.3 27.1 + - - +
75D ALA 3.2 0.6 - - - -
76D THR* 1.3 77.2 + - - +
78D LEU* 1.3 58.4 + - + +
80D GLN* 4.3 5.4 - - - +
81D MET 2.8 37.8 + - - +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D VAL* 4.2 24.9 - - + -
45D ALA* 6.2 0.7 - - - -
48D ILE* 5.1 11.0 - - + -
74D GLY 2.9 18.7 + - - +
75D ALA* 3.1 7.2 + - - +
77D ILE* 1.3 78.3 - - + +
79D LYS* 1.3 57.4 + - - +
81D MET 4.2 5.2 - - - +
82D GLN* 2.9 25.3 - - + +
88D ALA 5.6 0.2 - - - +
91D LEU* 3.7 30.5 - - + +
92D VAL* 3.3 32.7 - - + +
95D SER* 3.4 26.7 - - - +
110D VAL* 4.1 17.0 - - + -
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ALA 2.9 16.6 + - - +
76D THR* 3.7 10.5 - - + +
77D ILE 3.3 0.2 - - - -
78D LEU* 1.3 78.3 - - - +
80D GLN* 1.3 64.0 + - - +
82D GLN* 3.5 10.1 + - - +
92D VAL* 3.2 26.9 + - + +
95D SER* 3.8 11.3 - - - -
96D LYS* 3.4 46.4 - - - +
99D ASP* 3.4 22.0 + - - +
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Residues in contact with GLN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ILE* 3.8 16.5 - - + +
63D ASP* 3.4 23.3 + - - +
69D THR* 3.4 27.1 + - - +
71D THR* 3.7 24.6 + - - +
76D THR 2.9 17.3 + - - +
77D ILE* 3.8 2.9 - - - +
79D LYS* 1.3 79.8 - - - +
81D MET* 1.3 65.1 + - + +
82D GLN* 3.2 8.7 + - - +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A ILE* 3.8 30.0 - - + +
532A LYS* 3.6 14.4 - - - +
533A LEU* 3.0 39.3 - - + +
44D VAL* 5.6 1.9 - - - +
61D ILE* 3.7 19.5 - - + -
62D GLN 3.3 20.6 - - - +
63D ASP* 3.7 6.3 - - + +
64D GLY 3.4 18.4 - - - +
77D ILE* 2.8 26.8 + - - +
78D LEU* 4.1 3.6 - - - +
80D GLN* 1.3 77.3 - - + +
82D GLN* 1.3 75.9 + - - +
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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