Contacts of the helix formed by residues 73 - 90 (chain G) 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 73 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E LYS* 5.1 7.6 + - + -
24G SER* 4.6 5.9 + - - -
25G ASN* 5.5 6.7 - - - +
28G ALA* 3.5 33.6 + - + +
71G VAL* 3.3 5.0 - - + +
72G VAL* 1.3 100.5 + - + +
74G PRO* 1.3 65.7 - - + +
75G ALA* 4.5 2.7 - - + +
76G ALA* 3.0 20.5 + - + +
77G LYS* 2.9 29.8 + - - +
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Residues in contact with PRO 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASN* 5.6 4.5 - - - +
72G VAL 3.8 7.6 - - - +
73G HIS* 1.3 83.7 - - + +
75G ALA* 1.3 65.3 + - + +
77G LYS* 3.2 27.6 + - + +
78G THR* 3.3 16.3 - - - +
519G THR* 4.7 19.7 - - + -
521G LYS* 5.7 3.1 - - + -
55H MET* 4.9 10.0 - - + +
57H ILE* 4.4 21.8 - - + -
63H LEU* 3.6 15.5 - - + +
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASN* 3.4 41.5 - - + +
29G CYS* 4.2 3.1 - - - -
73G HIS* 3.3 1.3 - - + -
74G PRO* 1.3 81.7 - - + +
76G ALA* 1.3 59.3 + - - +
78G THR* 2.3 33.0 + - - -
79G LEU 3.6 2.3 + - - -
513G ILE* 3.6 22.0 - - + +
55H MET* 5.6 3.0 - - - +
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASN 5.5 0.2 + - - -
28G ALA* 4.6 7.9 - - + +
29G CYS* 3.7 21.6 - - - -
32G ILE* 4.0 17.3 - - + +
71G VAL* 3.7 12.1 - - + -
73G HIS* 3.0 26.2 + - + +
75G ALA* 1.3 76.3 - - - +
77G LYS* 1.3 64.5 + - - +
78G THR 3.2 0.2 - - - -
79G LEU* 3.4 4.4 + - - +
80G VAL* 3.2 24.3 + - - +
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Residues in contact with LYS 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G VAL* 2.9 44.0 + - + +
72G VAL* 3.3 6.9 + - - +
73G HIS 2.9 29.9 + - - +
74G PRO* 3.3 18.6 - - + +
75G ALA 3.2 0.2 - - - -
76G ALA* 1.3 77.4 - - - +
78G THR* 1.3 58.3 + - - +
80G VAL* 3.2 10.3 + - - +
81G ASP* 2.9 37.2 + - - +
63H LEU* 3.7 31.6 - - + -
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Residues in contact with THR 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G PRO 3.3 15.5 - - - +
75G ALA* 2.3 29.7 + - - +
77G LYS* 1.3 77.9 - - - +
79G LEU* 1.3 60.5 + - - +
81G ASP* 3.2 8.3 + - - +
82G ILE* 3.1 31.8 + - - +
509G ALA* 5.2 1.6 - - - -
512G LEU* 4.9 13.7 - - + -
513G ILE* 3.3 19.9 - - + +
55H MET* 3.7 28.3 - - + -
63H LEU* 4.6 6.1 - - + -
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Residues in contact with LEU 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G CYS* 4.4 19.7 - - + +
32G ILE* 4.3 16.8 - - + -
75G ALA 3.6 2.0 + - - +
76G ALA* 3.4 9.8 + - - +
77G LYS 3.3 0.4 - - - -
78G THR* 1.3 79.9 + - - +
80G VAL* 1.3 64.5 + - - +
82G ILE* 3.8 0.5 + - - +
83G ALA* 3.2 22.7 + - - +
97G VAL* 3.9 24.0 - - + +
98G THR* 4.0 32.7 + - + +
101G ALA* 3.9 17.3 - - + -
102G ALA* 4.9 4.5 - - + +
105G LEU* 6.2 1.1 - - + -
509G ALA* 4.0 17.7 - - + -
513G ILE* 4.3 13.2 - - + -
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Residues in contact with VAL 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G ILE* 5.0 9.4 - - + -
66G LEU* 4.8 25.1 - - + +
69G LEU* 5.5 2.0 - - + -
71G VAL* 4.0 23.3 - - + -
76G ALA 3.2 16.6 + - - +
77G LYS* 3.2 10.0 + - - +
79G LEU* 1.3 76.4 - - - +
81G ASP* 1.3 58.9 + - - +
83G ALA* 3.0 7.0 + - - +
84G LYS* 2.6 68.5 + - + +
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Residues in contact with ASP 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G LYS* 2.9 28.8 + - - +
78G THR* 3.2 8.2 + - - +
80G VAL* 1.3 84.6 - - - +
82G ILE* 1.3 56.0 + - + +
84G LYS* 3.8 7.8 - - - +
85G SER* 2.6 38.0 + - - -
63H LEU* 4.8 7.3 - - - +
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Residues in contact with ILE 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G THR* 3.1 17.6 + - - +
79G LEU 4.2 2.7 - - - +
81G ASP* 1.3 81.0 - - + +
83G ALA* 1.3 58.4 + - - +
85G SER* 3.2 11.3 + - - +
86G GLN* 2.8 26.0 + - - +
97G VAL* 3.8 7.2 - - + -
505G ALA* 3.4 41.7 - - + +
508G GLU* 4.7 15.9 - - + -
509G ALA* 3.8 22.2 - - + +
512G LEU* 5.8 7.6 - - + -
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Residues in contact with ALA 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G LEU* 5.1 3.6 - - + -
79G LEU 3.2 18.6 + - - +
80G VAL* 3.0 6.8 + - - +
82G ILE* 1.3 74.1 - - - +
84G LYS* 1.3 55.0 + - + +
86G GLN* 3.2 9.9 + - - +
87G ASP* 2.7 32.9 + - - +
94G THR* 3.6 38.7 + - + +
97G VAL* 4.6 8.9 - - + +
98G THR* 3.7 9.0 - - - +
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Residues in contact with LYS 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ALA* 3.9 5.4 - - - +
66G LEU* 3.3 44.0 + - - -
67G LYS* 3.4 45.9 - - - +
80G VAL* 2.6 38.0 + - + +
81G ASP* 4.0 9.2 - - - +
83G ALA* 1.3 70.8 - - - +
85G SER* 1.3 56.4 + - - +
87G ASP* 3.4 9.7 - - + +
88G ALA* 2.6 35.7 + - - +
94G THR* 5.2 1.3 - - + -
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Residues in contact with SER 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ASP 2.6 23.6 + - - -
82G ILE* 3.3 14.8 - - - +
84G LYS* 1.3 78.0 - - - +
86G GLN* 1.3 60.5 + - - +
88G ALA* 3.4 13.4 + - - +
89G GLU* 3.4 24.4 + - - +
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Residues in contact with GLN 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ILE 2.8 13.3 + - - +
83G ALA 3.4 8.1 - - - +
85G SER* 1.3 75.7 - - - +
87G ASP* 1.3 62.0 + - - +
89G GLU* 3.7 9.8 + - - +
90G VAL* 3.6 16.7 + - - +
92G ASP 3.4 14.1 + - - +
93G GLY* 3.4 30.9 - - - +
97G VAL* 3.8 13.0 - - + -
498G VAL* 3.5 36.2 + - - +
501G ASN* 3.3 32.8 - - - +
502G ALA* 4.3 6.1 - - - -
505G ALA* 3.9 8.5 - - + +
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Residues in contact with ASP 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ALA* 3.5 18.7 - - - +
67G LYS* 3.5 27.2 + - - +
83G ALA 2.7 16.1 + - - +
84G LYS* 3.1 14.9 + - + +
86G GLN* 1.3 74.3 - - - +
88G ALA* 1.3 60.7 + - - +
91G GLY* 3.0 40.1 + - - +
92G ASP 4.5 0.4 - - - +
94G THR* 3.1 25.2 + - - +
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Residues in contact with ALA 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G LYS 2.6 19.2 + - - +
85G SER* 3.4 8.9 + - - +
86G GLN 3.3 0.6 - - - -
87G ASP* 1.3 76.6 - - - +
89G GLU* 1.3 63.7 + - + +
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Residues in contact with GLU 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G SER* 3.4 19.7 + - - +
86G GLN* 4.2 11.0 + - - +
87G ASP 3.3 0.6 - - - -
88G ALA* 1.3 83.6 - - + +
90G VAL* 1.3 67.9 + - + +
190G LEU* 4.8 5.5 - - - +
501G ASN* 4.1 27.1 + - - +
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Residues in contact with VAL 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G GLN* 3.6 6.6 + - - +
87G ASP 4.0 0.2 - - - -
89G GLU* 1.3 87.6 - - + +
91G GLY* 1.3 59.7 + - - +
92G ASP* 4.0 23.1 - - + +
190G LEU* 3.6 36.1 - - + +
394G MET* 4.1 9.5 - - - +
398G ARG* 3.9 29.2 - - + +
498G VAL* 3.8 26.9 - - + -
501G ASN* 5.6 2.9 - - - +
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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