Contacts of the helix formed by residues 71 - 88 (chain N) 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 HIS 71 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26N ALA* 3.7 22.9 - - + +
30N LEU* 3.6 26.0 - - + +
69N ILE* 3.0 45.3 + - + +
70N GLN* 1.3 91.5 + - - +
72N PRO* 1.3 71.7 - - + +
73N THR* 3.6 17.0 - - - +
74N ALA* 3.2 21.6 + - + +
75N SER* 3.6 9.2 + - - -
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Residues in contact with PRO 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K MET* 4.7 12.8 - - + -
51K LEU* 4.2 28.5 - - + -
57K ILE* 3.6 17.6 - - + +
22N VAL* 6.4 2.5 - - + -
23N ASN* 4.6 12.6 - - - +
26N ALA* 5.3 3.6 - - + -
70N GLN* 4.4 3.8 - - + +
71N HIS* 1.3 87.1 - - + +
73N THR* 1.3 70.6 + - + +
75N SER* 3.4 8.4 + - - +
76N LEU* 3.4 20.1 + - + +
521N ILE* 4.6 11.9 - - + -
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Residues in contact with THR 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23N ASN* 3.3 36.8 - - + +
26N ALA* 3.5 25.0 - - + +
27N ALA* 3.8 17.1 + - + +
30N LEU* 3.6 15.3 - - - +
71N HIS* 3.6 1.4 - - - +
72N PRO* 1.3 80.1 - - + +
74N ALA* 1.3 61.8 + - - +
76N LEU* 3.0 17.2 + - + +
77N ILE* 2.9 36.3 + - - +
515N ILE* 6.4 2.5 - - + -
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Residues in contact with ALA 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N LEU* 4.3 7.9 - - + -
64N LEU* 4.4 6.2 - - + +
68N GLN* 4.7 16.9 - - + +
69N ILE 4.1 13.2 - - - +
71N HIS* 3.2 25.4 + - + +
73N THR* 1.3 81.3 + - - +
75N SER* 1.3 61.7 + - - +
77N ILE* 3.5 14.8 - - + +
78N ALA* 3.2 22.9 + - - +
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Residues in contact with SER 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K LEU* 5.9 0.3 - - - +
56K GLY* 4.7 11.6 + - - -
57K ILE* 3.6 30.8 - - - +
71N HIS 3.6 8.6 + - - -
72N PRO* 3.4 11.1 + - - +
73N THR 3.2 0.4 - - - -
74N ALA* 1.3 78.3 - - - +
76N LEU* 1.3 63.5 + - - +
78N ALA* 3.6 6.8 + - - +
79N LYS* 3.5 17.7 + - - +
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Residues in contact with LEU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K MET* 4.7 13.5 - - + -
57K ILE* 3.7 26.2 - - + -
59K MET* 3.8 17.7 - - + -
23N ASN* 6.2 1.8 - - + +
72N PRO* 3.4 18.4 - - + +
73N THR* 3.0 21.2 + - + +
75N SER* 1.3 76.4 - - - +
77N ILE* 1.3 60.8 + - + +
79N LYS* 3.1 33.2 + - - +
80N VAL* 3.5 5.5 + - - +
511N ILE* 3.6 23.9 - - + +
514N ASN* 6.3 2.9 - - + -
515N ILE* 5.0 17.5 - - + -
518N VAL* 6.2 1.8 - - + -
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Residues in contact with ILE 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N ALA* 5.1 13.5 - - + +
30N LEU* 4.3 23.3 - - + -
64N LEU* 3.5 22.1 - - + +
73N THR* 2.9 24.4 + - - +
74N ALA* 3.5 16.8 - - + +
76N LEU* 1.3 75.0 - - + +
78N ALA* 1.3 66.9 + - - +
79N LYS 3.2 0.2 - - - -
80N VAL* 3.6 9.5 - - + +
81N ALA* 3.1 27.5 + - - +
96N VAL* 5.6 16.2 - - + -
99N ILE* 4.2 23.6 - - + -
511N ILE* 4.3 6.5 - - + -
515N ILE* 6.6 0.2 - - + -
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Residues in contact with ALA 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N LEU* 3.7 17.7 - - + +
65N HIS* 3.1 22.0 - - - +
74N ALA 3.2 19.3 + - - +
75N SER* 3.8 8.1 - - - +
76N LEU 3.2 1.0 - - - -
77N ILE* 1.3 79.3 - - - +
79N LYS* 1.3 51.5 + - - +
82N THR* 2.3 33.4 + - - -
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Residues in contact with LYS 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K ILE* 5.3 10.8 - - + -
59K MET* 6.1 2.9 - - - -
75N SER 3.5 8.7 + - - +
76N LEU* 3.1 25.1 + - - +
78N ALA* 1.3 80.2 - - - +
80N VAL* 1.3 79.0 + - - +
82N THR* 3.3 18.7 - - - -
83N ALA* 3.5 8.0 + - - +
510N VAL* 6.2 0.8 - - - +
511N ILE* 5.8 2.4 - - - +
514N ASN* 4.9 12.4 - - - +
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Residues in contact with VAL 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N LEU 4.2 0.7 - - - +
77N ILE* 3.6 15.9 - - + +
79N LYS* 1.3 93.8 - - - +
81N ALA* 1.3 63.5 + - + +
82N THR 3.2 1.8 - - - -
83N ALA* 3.4 7.7 + - - +
84N GLN* 3.2 24.4 + - - +
95N ASN* 4.5 4.9 + - + +
99N ILE* 5.2 5.2 - - + -
507N SER* 4.5 22.3 - - - +
510N VAL* 4.9 8.1 - - + -
511N ILE* 3.7 50.7 - - + -
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Residues in contact with ALA 81 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N GLY 6.2 0.4 - - - -
61N ASN* 5.2 2.6 - - - +
64N LEU* 3.7 19.3 - - + -
65N HIS* 4.1 7.6 + - - +
77N ILE 3.1 20.1 + - - +
80N VAL* 1.3 75.5 - - + +
82N THR* 1.3 60.5 + - - +
84N GLN* 3.9 2.1 - - - +
85N ASP* 3.0 27.4 + - - +
92N THR* 4.4 11.0 - - - +
95N ASN* 3.7 24.7 - - - +
96N VAL* 5.6 3.1 - - + -
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Residues in contact with THR 82 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N HIS* 3.1 16.4 + - + -
78N ALA 2.3 27.0 + - - -
79N LYS* 3.3 12.0 + - - -
80N VAL 3.2 0.4 - - - -
81N ALA* 1.3 77.0 - - - +
83N ALA* 1.3 50.8 + - - +
85N ASP* 2.9 6.9 + - + +
86N ASP* 2.5 58.0 + - - +
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Residues in contact with ALA 83 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N LYS 3.5 7.5 + - - +
80N VAL* 3.4 10.0 + - - +
82N THR* 1.3 75.7 - - - +
84N GLN* 1.3 61.3 + - - +
86N ASP* 3.7 12.3 - - - +
87N ILE* 2.8 45.8 + - + +
503N GLN* 5.3 4.3 - - - +
507N SER* 6.1 2.9 - - - -
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Residues in contact with GLN 84 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80N VAL 3.2 11.3 + - - +
81N ALA 3.9 2.9 - - - +
82N THR 3.2 0.2 - - - -
83N ALA* 1.3 78.4 - - - +
85N ASP* 1.3 56.5 + - - +
88N THR* 3.0 33.9 + - - +
89N GLY 2.9 19.1 + - - -
90N ASP 3.0 26.8 + - - +
91N GLY* 4.2 8.5 - - - +
92N THR* 4.4 3.1 - - + +
95N ASN* 3.4 31.7 + - - +
500N VAL* 4.2 14.4 + - - +
503N GLN* 3.3 31.2 - - - +
504N LEU* 4.3 4.8 + - - -
507N SER* 3.7 18.3 + - - +
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Residues in contact with ASP 85 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61N ASN* 2.6 35.7 + - + +
65N HIS* 5.0 3.6 - - - +
81N ALA 3.0 18.9 + - - +
82N THR* 2.9 7.9 + - + +
84N GLN* 1.3 73.7 - - - +
86N ASP* 1.3 68.7 + - - +
88N THR 4.0 0.5 - - - -
89N GLY* 3.2 19.9 + - - +
92N THR* 4.1 7.8 - - + +
396N ARG* 2.7 35.0 + - - -
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Residues in contact with ASP 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82N THR* 2.5 48.8 + - - +
83N ALA* 3.7 10.4 - - - +
85N ASP* 1.3 78.2 - - - +
87N ILE* 1.3 67.9 + - + +
88N THR 4.8 0.7 - - - -
186N ILE* 5.2 10.2 - - - +
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Residues in contact with ILE 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83N ALA* 2.8 30.0 + - + +
86N ASP* 1.3 78.3 - - + +
88N THR* 1.3 70.2 + - - +
185N PRO* 4.6 10.4 - - - +
186N ILE* 4.6 7.3 - - - +
400N ASN* 4.6 4.3 + - - -
499N CYS* 4.8 7.3 - - - -
503N GLN* 3.4 44.2 - - + +
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Residues in contact with THR 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N GLN* 3.0 22.8 + - - -
85N ASP 4.0 1.3 - - - -
86N ASP 4.8 0.2 - - - -
87N ILE* 1.3 85.3 - - - +
89N GLY* 1.3 60.3 + - - +
90N ASP* 3.5 13.9 - - + +
186N ILE* 3.3 24.3 - - - +
396N ARG* 3.9 2.4 - - - +
400N ASN* 3.3 29.1 - - - +
499N CYS* 3.4 27.3 + - - -
500N VAL* 3.7 24.7 - - + -
503N GLN* 4.2 1.9 - - - +
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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
------------------------------------------------------------
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