Contacts of the helix formed by residues 55 - 70 (chain G) in PDB entry 1NZX
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 55 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G SER* 5.8 3.8 - - - +
35G LYS* 5.2 3.8 + - - -
53G GLU* 4.2 13.7 - - - +
54G GLY* 1.3 72.9 - - - -
56G LYS* 1.3 84.7 + - - +
57G GLU* 3.3 4.3 - - + +
58G ASP* 2.7 22.8 + - - +
59G VAL* 2.9 18.1 + - - +
227G THR* 3.4 35.6 - - - +
228G ALA* 4.5 6.3 - - - +
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Residues in contact with LYS 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ASP* 1.3 86.2 + - - +
57G GLU* 1.3 62.8 + - + +
59G VAL* 3.2 2.6 + - - +
60G ASP* 2.9 51.8 + - - +
227G THR 5.3 0.4 - - - +
231G ALA* 3.9 35.6 + - + +
234G SER* 5.5 9.7 + - - -
235G HIS* 6.1 2.4 - - - +
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Residues in contact with GLU 57 (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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32G VAL* 4.0 26.0 - - + -
55G ASP* 3.3 3.6 - - + +
56G LYS* 1.3 80.7 - - + +
58G ASP* 1.3 62.6 + - - +
60G ASP* 3.5 17.6 + - - +
61G LYS* 3.3 25.6 + - - +
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Residues in contact with ASP 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ILE* 3.4 25.6 - - + +
24G ILE* 3.7 7.4 - - + +
30G ASP 4.1 1.4 - - - +
31G ALA* 3.3 6.8 - - - +
32G VAL* 2.9 37.8 + - - +
33G SER* 5.2 1.0 + - - -
53G GLU 4.2 1.9 - - - +
54G GLY* 3.4 4.5 - - - -
55G ASP* 2.7 36.3 + - - +
57G GLU* 1.3 75.2 + - - +
59G VAL* 1.3 65.8 + - - +
61G LYS* 3.2 14.2 + - + +
62G ALA* 3.1 19.1 + - - +
221G VAL* 4.2 7.5 - - + +
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Residues in contact with VAL 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ASP 2.9 14.4 + - - +
56G LYS 3.2 7.8 + - - +
58G ASP* 1.3 76.0 - - - +
60G ASP* 1.3 58.9 + - - +
62G ALA* 3.2 8.1 + - - +
63G VAL* 2.9 45.9 + - + +
190G VAL* 4.8 2.0 - - + -
221G VAL* 4.3 12.1 - - + -
228G ALA* 3.6 32.5 - - + +
231G ALA* 3.9 19.5 - - + +
232G ILE* 3.6 32.1 - - + +
235G HIS* 4.4 4.3 - - + -
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Residues in contact with ASP 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G LYS* 2.9 39.2 + - - +
57G GLU* 3.5 24.1 - - - +
58G ASP 3.2 0.2 - - - -
59G VAL* 1.3 76.4 - - - +
61G LYS* 1.3 62.0 + - + +
63G VAL* 3.9 1.4 - - - +
64G LYS* 3.1 40.8 + - - +
231G ALA* 5.8 0.3 - - - +
235G HIS* 3.5 30.0 + - - +
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Residues in contact with LYS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.6 20.9 - - + +
29G HIS* 3.4 36.6 + - - +
30G ASP 4.8 4.4 + - - -
32G VAL* 3.9 23.9 - - + +
57G GLU 3.3 15.0 + - - +
58G ASP* 3.2 11.7 + - - +
60G ASP* 1.3 79.0 - - + +
62G ALA* 1.3 61.4 + - - +
64G LYS* 3.4 9.5 + - - +
65G ALA* 3.0 23.4 + - - +
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Residues in contact with ALA 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.5 20.4 - - + +
58G ASP 3.1 9.8 + - - +
59G VAL 3.5 7.6 - - - +
61G LYS* 1.3 77.0 - - - +
63G VAL* 1.3 60.0 + - - +
65G ALA* 3.1 3.8 + - - +
66G ALA* 2.9 29.5 + - - +
190G VAL* 3.9 23.3 - - + -
219G ASN* 3.7 14.2 + - + -
221G VAL* 3.9 11.9 - - + -
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Residues in contact with VAL 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G VAL* 2.9 28.5 + - + +
60G ASP 3.9 2.2 - - - +
62G ALA* 1.3 73.9 - - - +
64G LYS* 1.3 59.7 + - + +
66G ALA* 3.2 3.0 + - - +
67G ARG* 2.8 28.6 + - - +
161G VAL* 4.4 5.2 - - + -
190G VAL* 3.9 16.1 - - + +
232G ILE* 5.9 0.2 - - + -
235G HIS* 3.4 47.1 - - + +
237G ASP* 3.8 25.8 - - + +
238G VAL* 3.9 16.4 - - + -
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ASP* 3.1 31.2 + - - +
61G LYS* 3.7 7.4 - - - +
63G VAL* 1.3 78.6 - - + +
65G ALA* 1.3 56.4 + - - +
67G ARG* 3.8 6.3 - - - +
68G ALA* 3.0 29.6 + - - +
235G HIS* 6.2 1.3 - - + +
237G ASP* 5.4 1.3 - - - +
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Residues in contact with ALA 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.7 14.6 - - + -
25G ASN* 3.6 34.9 - - - +
61G LYS 3.0 14.1 + - - +
62G ALA 3.1 8.5 + - - +
64G LYS* 1.3 73.5 - - - +
66G ALA* 1.3 65.3 + - - +
68G ALA* 3.3 7.9 + - - +
69G ALA* 3.0 23.2 + - - +
216G GLY* 4.0 5.2 - - - -
219G ASN* 3.9 6.5 - - - +
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Residues in contact with ALA 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ALA 2.9 12.6 + - - +
63G VAL 3.4 7.4 - - - +
65G ALA* 1.3 76.4 - - - +
67G ARG* 1.3 63.9 + - - +
69G ALA* 3.0 13.9 + - - +
70G PHE* 3.0 13.9 + - - +
161G VAL* 4.1 7.2 - - + -
188G VAL* 3.8 22.1 - - + +
189G VAL 4.7 1.6 - - - +
190G VAL* 4.0 14.6 - - + -
216G GLY 3.3 15.2 + - - +
219G ASN* 3.7 11.4 - - - +
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Residues in contact with ARG 67 (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 VAL 2.8 19.5 + - - +
64G LYS* 3.8 6.5 - - - +
66G ALA* 1.3 73.2 - - - +
68G ALA* 1.3 63.1 + - - +
70G PHE* 3.1 36.5 + - - -
71G GLN* 3.2 43.8 + - + +
161G VAL* 3.5 16.1 - - + +
237G ASP* 3.0 51.1 + - - +
239G ASP* 2.7 35.1 + - - -
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Residues in contact with ALA 68 (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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64G LYS 3.0 18.8 + - - +
65G ALA* 3.5 7.6 - - - +
67G ARG* 1.3 76.8 - - - +
69G ALA* 1.3 62.5 + - - +
71G GLN* 3.1 28.6 + - - +
74G SER* 4.3 4.5 - - - -
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Residues in contact with ALA 69 (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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65G ALA 3.0 10.4 + - - +
66G ALA 3.0 9.7 + - - +
68G ALA* 1.3 76.2 - - - +
70G PHE* 1.3 55.5 + - - +
74G SER* 2.7 25.9 + - - -
76G TRP* 3.6 14.5 - - + +
77G ARG* 4.3 0.2 - - - +
188G VAL* 4.2 7.2 - - + -
214G PRO* 5.8 0.9 - - + -
215G PRO 3.5 24.7 - - - +
216G GLY 3.7 13.7 - - - -
217G VAL* 4.0 7.9 - - + +
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Residues in contact with PHE 70 (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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66G ALA 3.0 10.9 + - - +
67G ARG* 3.6 33.0 - - - +
68G ALA 3.1 0.6 - - - -
69G ALA* 1.3 76.8 - - - +
71G GLN* 1.3 57.9 + - - +
76G TRP* 4.8 0.7 - + - -
77G ARG* 2.7 64.8 + - - -
158G PRO* 3.7 25.8 - - + -
159G VAL 5.0 0.7 - - - -
160G GLY* 3.6 26.9 - - - -
186G GLY 3.6 23.6 - - - -
187G ASN* 4.5 0.9 - - - -
188G VAL* 4.0 24.0 - - + -
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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
------------------------------------------------------------
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