Contacts of the helix formed by residues 103 - 123 (chain D) in PDB entry 1XS2
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 ASN 103 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B PRO* 3.6 8.7 - - + +
64B GLU* 2.9 29.5 + - - +
66B THR* 5.2 4.8 - - - +
64D GLU* 4.5 7.1 + - - -
65D GLU* 3.4 31.6 + - - +
69D GLY* 5.3 9.5 + - - -
70D ALA* 5.4 0.8 - - - +
73D LEU* 3.4 31.9 - - + +
78D PHE* 5.2 1.1 - - + -
100D TYR* 6.5 0.2 - - + -
101D ARG 3.0 16.4 - - - +
102D GLY* 1.3 73.4 - - - +
104D ARG* 1.3 64.5 + - - +
105D MET 3.4 2.5 - - - -
106D ALA* 3.5 2.1 + - + +
107D ARG* 3.1 22.0 + - - +
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU* 5.2 0.8 + - - -
65D GLU* 3.3 5.3 + - - +
102D GLY* 4.1 16.8 - - - +
103D ASN* 1.3 76.0 - - - +
105D MET* 1.3 61.1 + - - +
107D ARG* 3.2 15.5 + - - +
108D ALA* 2.8 29.6 + - - +
249D ALA* 3.2 32.3 + - - +
250D SER* 3.9 17.3 - - - -
271D ALA 3.6 2.7 - - - -
272D ARG 3.8 15.7 - - - +
273D VAL 3.0 21.1 + - - -
274D GLY* 3.5 14.5 - - - +
278D GLU* 4.1 15.0 + - - +
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Residues in contact with MET 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D GLY* 5.3 0.3 - - - -
55D THR* 3.3 27.9 + - - +
56D MET* 3.6 35.0 - - + +
62D TYR* 4.0 30.3 - - + -
63D ARG* 4.7 11.2 - - + -
65D GLU* 3.0 26.4 + - - +
104D ARG* 1.3 75.7 - - - +
106D ALA* 1.3 61.9 + - - +
108D ALA* 3.3 4.4 + - - +
109D MET* 3.2 24.8 + - - +
271D ALA* 3.5 17.2 - - + +
272D ARG* 4.0 24.0 - - + +
298D MET* 4.6 5.8 - - - -
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Residues in contact with ALA 106 (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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56D MET* 3.9 7.7 - - - +
65D GLU* 3.0 9.7 + - - +
70D ALA* 3.7 28.9 - - + +
73D LEU* 3.9 22.4 - - + -
74D LEU* 4.1 5.1 - - + +
78D PHE* 4.0 6.5 - - + -
103D ASN* 3.7 8.5 - - + +
104D ARG 3.3 0.2 - - - -
105D MET* 1.3 73.6 - - - +
107D ARG* 1.3 65.6 + - - +
109D MET* 3.2 21.4 + - - +
110D VAL* 3.7 8.8 + - - +
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PHE* 3.6 27.4 - - + -
94D SER* 3.9 24.2 + - - -
97D LEU* 4.2 20.8 + - + +
98D GLY 2.5 35.8 + - - +
99D SER* 4.4 0.8 - - - +
100D TYR* 4.0 19.2 + - - +
102D GLY 4.1 12.6 + - - -
103D ASN 3.1 19.6 + - - +
104D ARG* 3.5 22.7 - - - +
106D ALA* 1.3 76.0 - - - +
108D ALA* 1.3 57.1 + - - +
110D VAL* 3.1 6.4 + - - +
111D GLU* 2.9 28.8 + - + +
274D GLY* 4.5 7.0 - - - +
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Residues in contact with ALA 108 (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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104D ARG 2.8 15.9 + - - +
105D MET 3.4 6.5 - - - +
106D ALA 3.1 0.4 - - - -
107D ARG* 1.3 76.8 - - - +
109D MET* 1.3 63.6 + - - +
111D GLU* 4.2 1.6 - - - -
112D MET* 2.8 37.3 + - - +
271D ALA* 3.6 30.1 - - + +
274D GLY 3.7 22.0 - - - -
275D GLY* 3.8 1.8 - - - +
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Residues in contact with MET 109 (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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15D ILE* 5.8 0.7 - - + -
39D PRO* 3.9 28.7 - - + +
40D LEU 4.2 4.0 - - - +
41D LEU* 3.4 31.7 - - + +
52D ALA* 3.4 12.0 - - + +
53D GLU 4.3 3.1 - - - +
54D GLY* 3.6 30.7 - - - +
56D MET* 3.9 19.1 - - - +
70D ALA* 5.2 1.1 - - - -
71D LEU* 4.6 5.6 - - + -
74D LEU* 3.8 26.7 - - + -
105D MET 3.2 10.5 + - - +
106D ALA* 3.2 10.5 + - - +
108D ALA* 1.3 74.4 - - - +
110D VAL* 1.3 61.1 + - - +
112D MET* 5.5 0.2 - - - -
113D ALA* 3.2 26.2 + - - +
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Residues in contact with VAL 110 (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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41D LEU* 3.5 12.6 - - + -
43D LEU* 3.9 4.8 - - + +
74D LEU* 3.3 32.3 - - + -
78D PHE* 4.1 15.9 - - + -
79D LEU* 4.7 3.1 - - + -
82D ILE* 3.9 26.9 - - + -
93D VAL* 4.2 11.9 - - + -
97D LEU* 4.2 20.6 - - + -
106D ALA 4.0 4.5 - - - +
107D ARG 3.1 6.4 + - - +
109D MET* 1.3 77.3 - - - +
111D GLU* 1.3 58.1 + - - +
114D ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 111 (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 PRO* 4.7 5.4 - - - +
93D VAL* 5.5 2.7 - - - -
94D SER* 3.1 29.7 + - - +
97D LEU* 5.5 1.8 - - + +
107D ARG* 2.9 16.6 + - + +
108D ALA 4.0 2.0 - - - +
110D VAL* 1.3 76.9 - - - +
112D MET* 1.3 60.7 + - - +
114D ALA* 3.3 8.0 + - - +
115D TRP* 2.9 61.0 + - + -
274D GLY 3.9 13.7 - - - +
275D GLY* 3.3 7.8 - - - -
276D HIS 2.9 23.4 + - - -
277D ALA* 3.1 23.4 + - - +
278D GLU 4.6 0.6 + - - -
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Residues in contact with MET 112 (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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52D ALA* 3.8 12.8 - - + -
53D GLU 5.3 9.0 - - - +
108D ALA* 2.8 34.6 + - - +
111D GLU* 1.3 86.4 - - - +
113D ALA* 1.3 66.8 + - - +
115D TRP* 3.1 2.8 + - - +
116D ASP 3.0 18.0 + - - -
270D VAL* 3.6 39.5 - - + -
271D ALA* 4.4 7.2 - - + -
275D GLY* 3.9 6.3 - - - -
276D HIS* 4.0 12.1 - - + +
304D GLY* 5.6 2.9 - - - +
307D HIS* 3.4 48.6 - - + +
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Residues in contact with ALA 113 (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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41D LEU* 4.1 6.5 - - + +
43D LEU* 3.7 23.3 - - + -
50D GLY* 3.5 26.1 - - - +
51D VAL 4.2 1.8 - - - -
52D ALA* 3.5 15.6 - - - +
109D MET 3.2 20.8 + - - +
112D MET* 1.3 76.2 - - - +
114D ALA* 1.3 57.2 + - - +
116D ASP* 3.1 4.3 + - - +
117D LEU* 2.9 25.8 + - - +
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Residues in contact with ALA 114 (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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8D PHE* 4.6 5.7 - - + -
10D ILE* 5.4 0.7 - - + -
43D LEU* 3.7 10.9 - - + +
90D PRO* 4.1 8.4 - - + +
93D VAL* 4.2 32.5 - - + -
110D VAL 3.0 18.5 + - - +
111D GLU* 3.4 7.4 - - - +
112D MET 3.2 0.2 - - - -
113D ALA* 1.3 76.9 - - - +
115D TRP* 1.3 57.1 + - - +
117D LEU* 3.3 7.2 + - - +
118D TRP* 3.0 31.3 + - - +
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Residues in contact with TRP 115 (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 PRO* 3.6 28.1 - - + +
91D GLU* 3.6 27.6 - - - -
111D GLU* 2.9 57.0 + - - -
112D MET 3.1 7.2 + - - +
114D ALA* 1.3 72.1 - - - +
116D ASP* 1.3 67.6 + - - +
118D TRP* 3.7 25.1 - + - +
119D ALA* 2.9 27.8 + - - +
126D LEU* 3.7 27.6 - - + -
129D LEU* 4.3 19.1 - - + -
130D LEU* 3.9 25.4 - - + -
276D HIS* 3.6 20.7 - + + +
277D ALA* 3.7 4.6 - - + +
280D ARG* 4.3 9.9 - - - -
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Residues in contact with ASP 116 (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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49D GLN 4.0 0.7 - - - +
50D GLY* 3.3 7.2 - - - -
51D VAL* 2.9 33.3 + - - +
112D MET 3.0 12.6 + - - +
113D ALA* 3.1 8.9 + - - +
115D TRP* 1.3 77.1 - - - +
117D LEU* 1.3 61.9 + - - +
119D ALA* 3.7 3.4 - - - +
120D ARG* 2.8 59.5 + - - +
126D LEU* 5.4 2.5 - - - -
307D HIS* 4.3 5.6 - - + -
353D GLY* 3.5 2.1 - - - -
354D THR* 3.2 35.7 + - + -
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Residues in contact with LEU 117 (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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8D PHE* 4.0 26.0 - - + -
10D ILE* 4.4 13.2 - - + -
43D LEU* 4.1 18.2 - - + +
44D HIS 4.6 0.7 - - - -
45D GLY* 3.5 26.0 - - - +
48D VAL* 3.5 37.0 - - + +
49D GLN* 3.8 2.2 - - - -
50D GLY* 3.7 18.8 - - - +
113D ALA 2.9 15.1 + - - +
114D ALA* 3.7 4.9 - - - +
116D ASP* 1.3 78.0 - - - +
118D TRP* 1.3 58.1 + - - +
120D ARG* 3.0 5.1 + - - +
121D THR* 2.9 36.5 + - + +
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Residues in contact with TRP 118 (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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6D ARG 3.8 24.5 - - - -
8D PHE* 3.4 30.1 - + + -
88D ALA 3.4 22.2 - - - -
89D ASN* 4.6 4.4 - - + +
90D PRO* 3.5 32.3 - - + +
114D ALA 3.0 17.9 + - - +
115D TRP* 3.7 21.6 - + - +
117D LEU* 1.3 79.0 - - - +
119D ALA* 1.3 62.2 + - - +
121D THR* 2.5 29.3 + - - -
122D LEU* 3.3 39.3 + - + +
129D LEU* 4.1 15.1 - - + +
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Residues in contact with ALA 119 (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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115D TRP 2.9 17.6 + - - +
118D TRP* 1.3 76.8 - - - +
120D ARG* 1.3 58.8 + - - +
122D LEU* 3.2 2.1 + - - -
123D GLY 3.0 22.3 + - - -
124D VAL 3.1 30.4 + - - +
126D LEU* 4.4 7.9 - - + -
129D LEU* 3.6 25.1 - - + -
353D GLY* 3.7 16.4 - - - -
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Residues in contact with ARG 120 (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 VAL* 3.8 28.1 - - + +
49D GLN* 3.1 25.4 + - - +
116D ASP* 2.8 37.0 + - - +
117D LEU 3.0 7.5 + - - +
119D ALA* 1.3 78.8 - - - +
121D THR* 1.3 59.2 + - - +
123D GLY* 3.5 9.0 + - - -
352D PRO* 3.5 36.5 + - + +
353D GLY 4.0 10.5 - - - +
354D THR* 3.3 15.2 + - - -
355D GLY* 3.8 3.2 - - - +
356D VAL 2.9 29.1 + - - +
357D THR* 5.7 2.4 + - - +
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Residues in contact with THR 121 (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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6D ARG 5.1 3.6 + - - -
8D PHE* 4.4 15.2 - - + -
46D GLU* 4.3 19.7 - - + -
48D VAL* 3.8 18.6 - - + -
117D LEU* 2.9 25.7 + - + +
118D TRP* 2.5 29.3 + - - -
120D ARG* 1.3 75.4 - - - +
122D LEU* 1.3 72.8 + - - +
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Residues in contact with LEU 122 (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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6D ARG 4.8 13.9 - - - +
118D TRP* 3.4 53.6 - - + +
119D ALA 3.2 6.8 + - - +
120D ARG 3.2 0.2 - - - -
121D THR* 1.3 90.7 - - - +
123D GLY* 1.3 60.0 + - - +
124D VAL* 3.6 18.5 + - + +
129D LEU* 4.3 19.7 - - + -
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Residues in contact with GLY 123 (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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119D ALA 3.0 5.5 + - - -
120D ARG 3.5 6.1 + - - -
121D THR 3.5 3.0 - - - -
122D LEU* 1.3 79.0 - - - +
124D VAL* 1.3 60.6 + - - +
125D PRO* 4.1 4.5 - - - +
352D PRO* 3.9 19.5 - - - +
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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