Contacts of the helix formed by residues 78 - 99 (chain D) in PDB entry 1ZXN
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 VAL 78 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D SER 3.5 2.2 - - - +
54D VAL* 3.4 35.4 - - - +
55D GLU 3.8 12.3 - - - +
56D LEU* 3.9 9.6 - - + +
77D PHE* 1.3 85.0 - - - +
79D PRO* 1.3 66.1 - - - +
80D GLY 3.7 4.3 - - - +
81D LEU* 3.0 22.8 + - + +
82D TYR 3.2 9.0 + - - -
226D PHE* 3.6 38.8 - - + +
228D MET* 3.8 17.8 - - + +
235D ILE* 5.3 0.3 - - - +
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Residues in contact with PRO 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE 4.2 3.1 - - - +
52D GLY 4.8 0.7 - - - -
53D SER* 3.4 30.7 - - - +
55D GLU 3.2 17.7 - - - +
57D VAL* 3.7 23.1 - - + -
59D GLN* 5.8 0.7 - - - +
77D PHE* 3.6 21.7 - - + +
78D VAL* 1.3 81.9 - - - +
80D GLY* 1.3 61.4 + - - +
82D TYR* 3.3 8.5 + - + +
83D LYS* 3.0 21.5 + - - +
377D THR* 5.2 13.2 - - + -
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Residues in contact with GLY 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 3.3 32.7 + - - +
53D SER 2.8 19.0 + - - -
78D VAL* 3.1 3.1 - - - +
79D PRO* 1.3 71.5 - - - +
81D LEU* 1.3 64.8 + - - +
83D LYS* 3.0 11.9 + - - +
84D ILE* 3.1 18.4 + - - +
226D PHE* 3.9 7.4 - - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D VAL* 3.0 14.9 + - + +
80D GLY* 1.3 74.6 - - - +
82D TYR* 1.3 63.4 + - - +
84D ILE* 3.2 26.5 - - + +
85D PHE* 3.4 9.4 + - + +
221D PRO* 4.0 20.6 - - + -
223D LEU* 4.4 8.3 - - + -
226D PHE* 3.6 40.9 - - + -
228D MET* 3.4 31.0 - - + -
231D LEU* 5.6 5.4 - - + -
235D ILE* 3.8 29.8 - - + +
239D MET* 5.8 3.8 - - + -
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D PHE* 4.1 21.3 - + + -
78D VAL 3.2 7.6 + - - +
79D PRO* 3.4 11.4 - - + +
80D GLY 3.1 0.4 - - - -
81D LEU* 1.3 80.4 - - - +
83D LYS* 1.3 60.3 + - + +
85D PHE* 3.4 11.7 + + - +
86D ASP* 2.9 45.6 + - + +
235D ILE* 4.4 12.3 - - + +
238D LEU* 3.2 40.6 - - + +
239D MET* 5.3 1.6 - - + -
241D ARG* 4.9 1.4 + - - -
242D ARG* 3.1 37.3 + - + -
318D ALA* 4.1 10.7 + - - +
377D THR* 5.4 8.3 - - - -
379D GLU* 6.6 0.2 - - + -
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Residues in contact with LYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D TYR 3.4 20.9 - - - -
51D ILE* 3.4 33.4 - - + +
79D PRO 3.0 13.3 + - - +
80D GLY* 3.0 10.4 + - - +
82D TYR* 1.3 79.3 - - + +
84D ILE* 1.3 60.8 + - - +
86D ASP* 3.0 8.4 + - + +
87D GLU* 2.7 63.1 + - + +
169D LEU* 4.3 6.5 - - - -
377D THR* 5.0 19.1 - - - +
378D LYS* 4.0 24.0 - - - +
908D SO4 4.5 3.5 + - - -
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 4.3 16.6 - - + -
80D GLY 3.1 8.7 + - - +
81D LEU* 3.2 22.0 - - + +
83D LYS* 1.3 76.7 - - - +
85D PHE* 1.3 68.2 + - - +
87D GLU* 3.5 11.9 + - + +
88D ILE* 3.6 18.0 + - - +
169D LEU* 4.0 10.3 - - + +
170D CYS* 3.7 37.8 - - + +
173D PHE* 4.0 20.0 - - + +
174D SER* 5.0 1.3 - - - +
219D PHE* 5.1 2.5 - - + -
221D PRO* 4.7 7.9 - - + -
226D PHE* 3.5 32.8 - - + -
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 3.7 9.6 - - + +
82D TYR* 3.4 13.9 + + - +
83D LYS 3.1 0.4 - - - -
84D ILE* 1.3 86.4 - - + +
86D ASP* 1.3 69.1 + - + +
88D ILE* 3.2 12.1 + - - +
89D LEU* 3.3 40.4 + - + +
107D VAL* 4.6 12.6 - - + -
109D ILE* 4.5 6.3 - - + -
116D ILE* 3.9 31.4 - - + -
118D ILE* 4.5 8.3 - - + +
219D PHE* 4.2 12.1 - + + -
239D MET* 3.4 65.7 - - + -
242D ARG* 4.1 7.6 - - + -
243D ALA* 6.3 0.4 - - + -
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Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D TYR* 2.9 38.6 + - + +
83D LYS* 3.4 9.4 - - + +
85D PHE* 1.3 84.0 - - - +
87D GLU* 1.3 60.1 + - + +
89D LEU* 3.2 5.1 + - - +
90D VAL* 2.8 45.0 + - - +
242D ARG* 2.9 38.9 + - - -
317D ILE* 4.8 10.4 - - - +
318D ALA 5.3 0.6 + - - -
378D LYS* 6.1 0.3 - - - +
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Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LYS* 2.7 68.0 + - + +
84D ILE* 3.7 9.6 - - - +
85D PHE 3.2 0.4 - - - -
86D ASP* 1.3 75.5 - - - +
88D ILE* 1.3 58.1 + - + +
90D VAL* 3.9 8.0 - - - +
91D ASN* 3.0 33.8 + - - +
160D GLY 5.7 0.7 - - - +
166D GLY* 3.7 35.0 - - - +
169D LEU* 5.7 2.2 - - + -
378D LYS* 3.7 6.5 + - - -
906D MG 4.1 7.3 - - - -
908D SO4 3.2 21.4 + - - -
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Residues in contact with ILE 88 (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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84D ILE 3.6 14.1 - - - +
85D PHE 3.2 5.9 + - - +
87D GLU* 1.3 74.1 - - + +
89D LEU* 1.3 68.1 + - - +
91D ASN* 2.9 22.5 + - + +
92D ALA* 3.0 12.6 + - - +
118D ILE* 3.7 29.4 - - + +
142D PHE* 5.0 2.5 - - + -
167D ALA* 4.1 20.9 - - + -
170D CYS* 3.9 29.4 - - + -
177D PHE* 4.2 12.6 - - + -
217D ILE* 4.0 23.8 - - + -
219D PHE* 3.9 10.5 - - + -
907D ADP 5.6 0.2 + - - -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D PHE* 3.3 28.4 + - + +
86D ASP* 3.2 9.8 + - - +
88D ILE* 1.3 78.3 - - - +
90D VAL* 1.3 63.4 + - - +
92D ALA* 3.1 12.8 + - - +
93D ALA* 3.2 13.0 + - - +
105D ILE* 4.3 15.0 - - + -
107D VAL* 3.8 25.8 - - + -
118D ILE* 4.4 12.9 - - + +
242D ARG* 3.8 33.0 - - + +
243D ALA* 4.3 3.8 - - - +
246D ILE* 3.5 36.9 - - + +
255D VAL* 6.4 0.4 - - + -
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ASP* 2.8 46.4 + - - +
87D GLU* 3.9 9.9 - - - +
89D LEU* 1.3 68.8 - - - +
91D ASN* 1.3 54.5 + - - +
93D ALA* 3.2 7.8 + - + +
94D ASP* 2.6 55.3 + - - +
160D GLY* 4.0 22.4 - - - +
242D ARG* 4.1 11.0 - - - +
246D ILE* 5.4 1.3 - - - -
315D ASN 4.2 5.6 - - - +
316D SER 4.3 3.8 - - - +
317D ILE* 4.1 21.1 - - + -
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Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D GLU 3.0 27.0 + - - -
88D ILE* 2.9 18.7 + - + +
90D VAL* 1.3 75.6 - - - +
92D ALA* 1.3 62.9 + - - +
94D ASP* 3.0 22.7 - - - +
95D ASN 3.4 3.8 + - - -
142D PHE* 5.1 0.8 - - - -
167D ALA* 4.0 17.6 - - - +
906D MG 2.5 21.7 - - - -
907D ADP 2.7 66.3 + - - +
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Residues in contact with ALA 92 (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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88D ILE 3.0 10.3 + - - +
89D LEU 3.3 9.4 - - - +
90D VAL 3.1 0.2 - - - -
91D ASN* 1.3 74.0 - - - +
93D ALA* 1.3 68.9 + - - +
95D ASN* 2.9 21.8 + - - +
102D MET* 3.5 10.9 - - - +
105D ILE* 3.6 24.5 - - + -
118D ILE* 3.9 20.4 - - + -
120D ASN* 4.1 9.0 - - + +
246D ILE* 6.2 0.2 - - + -
907D ADP 4.0 10.7 + - - +
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Residues in contact with ALA 93 (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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89D LEU 3.2 6.8 + - - +
90D VAL* 3.7 7.4 - - - +
92D ALA* 1.3 78.0 - - - +
94D ASP* 1.3 64.1 + - - +
96D LYS* 2.8 24.4 + - - +
97D GLN* 4.1 2.4 + - - +
102D MET* 4.3 9.0 - - - -
105D ILE* 4.5 0.8 - - - +
246D ILE* 4.0 11.1 - - + +
250D THR* 3.9 15.7 - - + -
315D ASN 5.3 0.2 - - - +
316D SER* 3.7 34.3 - - - +
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Residues in contact with ASP 94 (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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90D VAL* 2.6 43.9 + - - +
91D ASN* 3.0 19.5 - - - +
93D ALA* 1.3 76.0 - - - +
95D ASN* 1.3 60.9 + - - +
97D GLN* 2.9 26.6 + - - +
98D ARG* 3.5 3.5 + - - +
150D ASN* 4.5 3.1 + - - -
159D THR* 3.7 15.3 - - + +
160D GLY 3.3 14.5 + - - +
161D GLY* 3.3 23.9 + - - -
315D ASN 4.8 1.6 - - - +
907D ADP 4.1 8.2 + - + -
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Residues in contact with ASN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ASN 3.4 1.4 + - - -
92D ALA 2.9 13.6 + - - +
94D ASP* 1.3 78.5 - - - +
96D LYS* 1.3 56.5 + - - +
98D ARG* 2.6 48.0 + - - +
99D ASP* 2.7 15.4 + - - +
102D MET* 3.6 10.5 - - - +
120D ASN* 3.5 18.7 - - - +
121D ASN 3.6 10.7 + - - -
122D GLY* 3.9 7.9 - - - -
123D LYS 3.4 19.8 + - - +
907D ADP 3.3 30.7 + - - +
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Residues in contact with LYS 96 (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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93D ALA* 2.8 19.6 + - - +
95D ASN* 1.3 77.4 - - - +
97D GLN* 1.3 69.1 + - - +
99D ASP 3.6 20.1 - - - +
100D PRO* 3.6 10.3 - - - +
102D MET* 3.8 20.3 - - + -
250D THR* 5.2 8.7 - - + -
251D LYS 5.8 2.9 - - - +
253D VAL* 5.0 10.1 - - + -
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Residues in contact with GLN 97 (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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93D ALA 4.8 2.0 - - - +
94D ASP* 2.9 16.2 + - - +
96D LYS* 1.3 85.2 - - - +
98D ARG* 1.3 65.5 + - - +
99D ASP 3.2 0.8 + - - -
100D PRO* 4.4 7.8 - - - +
157D LYS* 6.4 0.2 - - + -
158D VAL* 3.1 44.7 - - + +
159D THR* 4.6 14.8 - - + -
367D LEU* 4.0 22.5 - - - +
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Residues in contact with ARG 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 5.8 5.3 - - - +
34C TYR* 3.5 25.5 + - - -
94D ASP 3.5 1.9 + - - +
95D ASN* 2.6 35.9 + - - +
97D GLN* 1.3 75.5 - - - +
99D ASP* 1.3 58.8 + - + +
100D PRO* 4.3 2.4 - - - +
123D LYS* 2.8 42.2 + - + +
124D GLY 3.3 19.1 + - - -
125D ILE* 5.1 0.2 - - - -
126D PRO* 3.7 9.9 - - - +
149D SER* 6.0 1.3 - - - -
159D THR* 6.1 0.2 - - - +
907D ADP 4.4 16.3 + - - -
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Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ASN* 2.7 10.4 + - - +
96D LYS 3.6 5.6 - - - +
97D GLN 3.2 0.6 - - - -
98D ARG* 1.3 81.5 - - + +
100D PRO* 1.3 61.8 - - - +
101D LYS* 2.7 43.3 + - - +
102D MET* 2.9 18.9 + - - +
122D GLY* 3.8 5.7 - - - -
123D LYS* 3.2 38.4 + - + +
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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