Contacts of the helix formed by residues 96 - 115 (chain D) in PDB entry 1JPM
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 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D ASP* 3.3 21.0 + - - +
61D SER* 4.0 15.8 - - - +
65D ALA* 3.8 12.2 - - - +
93D LEU* 3.3 32.1 - - + +
94D THR 2.9 21.8 + - - -
95D GLY* 1.3 71.0 - - - +
97D MET* 1.3 64.2 + - - +
98D SER 3.3 3.1 - - - -
99D ALA* 3.2 12.4 + - + +
100D LYS* 3.1 22.4 + - + +
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Residues in contact with MET 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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55D THR* 5.3 4.3 - - + -
57D ASP* 3.7 5.7 + - - +
90D GLN* 4.5 6.3 - - - +
95D GLY* 3.1 21.5 - - - +
96D ASN* 1.3 77.4 - - - +
98D SER* 1.3 55.5 + - - +
100D LYS* 3.4 16.3 + - - -
101D ALA* 2.8 26.3 + - - +
248D PHE* 5.0 8.1 - - + -
249D THR* 3.7 25.4 - - + -
270D MET 3.1 19.1 - - - +
271D LYS* 3.2 24.0 - - - +
272D ALA 3.6 20.0 - - - +
273D GLY* 3.2 13.5 - - - +
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Residues in contact with SER 98 (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 ALA* 3.3 12.9 - - - +
49D PRO 4.1 3.7 + - - -
51D THR* 4.1 6.1 + - - -
55D THR* 3.7 11.8 + - - +
57D ASP* 2.6 35.9 + - - +
62D ILE* 3.9 14.8 - - - -
97D MET* 1.3 73.7 - - - +
99D ALA* 1.3 64.2 + - - +
101D ALA* 3.3 1.9 + - - +
102D ALA 3.0 18.9 + - - -
270D MET* 3.7 27.5 + - - +
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Residues in contact with ALA 99 (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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62D ILE* 3.8 31.3 - - + +
65D ALA* 3.8 28.9 - - + -
66D ILE* 4.1 7.2 - - + +
70D LEU* 4.1 5.6 - - + -
96D ASN* 3.2 13.0 + - + +
98D SER* 1.3 75.4 - - - +
100D LYS* 1.3 66.7 + - + +
102D ALA* 3.4 2.6 + - - +
103D VAL* 3.3 28.1 + - - +
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Residues in contact with LYS 100 (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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70D LEU* 4.2 5.8 - - + -
89D ILE* 3.4 40.7 - - + +
90D GLN* 3.2 29.4 + - - +
93D LEU* 2.9 36.6 + - + -
94D THR* 4.1 1.0 - - - +
95D GLY 2.7 34.1 + - - +
96D ASN* 3.1 8.8 + - + +
97D MET* 3.6 20.8 - - - +
99D ALA* 1.3 78.7 - - + +
101D ALA* 1.3 62.1 + - - +
103D VAL* 3.4 2.4 + - - +
104D GLU* 3.0 25.8 + - - +
273D GLY* 3.4 12.5 - - - +
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Residues in contact with ALA 101 (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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97D MET 2.8 15.7 + - - +
98D SER 3.5 2.0 - - - +
99D ALA 3.2 0.2 - - - -
100D LYS* 1.3 77.2 - - - +
102D ALA* 1.3 62.5 + - - +
104D GLU* 3.2 3.3 + - - +
105D MET* 3.0 28.1 + - - +
269D LEU* 3.3 25.8 - - + +
270D MET* 3.3 28.3 - - + -
273D GLY 3.3 10.2 + - - -
274D GLY* 3.6 5.3 - - - +
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Residues in contact with ALA 102 (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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32D VAL* 5.0 0.7 - - + +
34D VAL* 3.8 23.9 - - + +
46D GLY* 3.3 11.5 - - - -
47D GLU 3.7 19.4 + - - +
48D ALA* 3.6 26.0 - - + -
66D ILE* 4.5 3.8 - - + -
98D SER 3.0 8.8 + - - +
99D ALA* 3.8 5.2 - - - +
100D LYS 3.4 0.2 - - - -
101D ALA* 1.3 74.9 - - - +
103D VAL* 1.3 62.9 + - - +
105D MET* 3.2 9.7 + - - -
106D ALA* 3.3 11.4 + - - +
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Residues in contact with VAL 103 (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 ILE* 5.7 3.1 - - + -
34D VAL* 4.8 8.5 - - + -
36D ILE* 3.9 7.4 - - + +
66D ILE* 4.0 23.1 - - + -
70D LEU* 3.4 24.7 - - + -
74D LEU* 3.4 32.5 - - + -
89D ILE* 3.9 14.1 - - + -
99D ALA 3.3 17.6 + - - +
100D LYS 3.8 3.1 - - - +
102D ALA* 1.3 75.2 - - - +
104D GLU* 1.3 58.6 + - - +
106D ALA* 3.3 7.0 + - - +
107D LEU* 3.0 27.6 + - + +
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Residues in contact with GLU 104 (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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86D LEU* 3.5 26.2 - - + +
89D ILE* 4.3 10.4 - - + +
90D GLN* 3.0 18.9 + - - +
100D LYS 3.0 17.7 + - - +
101D ALA 3.2 4.5 + - - +
103D VAL* 1.3 73.9 - - - +
105D MET* 1.3 61.0 + - - +
107D LEU* 3.1 5.6 + - - -
108D TYR* 2.8 41.5 + - + -
273D GLY 3.6 8.9 - - - +
274D GLY* 3.8 6.1 - - - -
275D ILE* 2.7 31.5 + - - +
276D SER* 2.5 33.1 + - - -
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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
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45D TRP 3.3 12.3 - - - +
46D GLY* 3.6 2.0 - - - -
47D GLU 3.3 25.8 - - - +
101D ALA 3.0 15.1 + - - +
102D ALA 3.2 7.2 + - - +
104D GLU* 1.3 77.6 - - - +
106D ALA* 1.3 56.6 + - - +
108D TYR* 3.8 3.9 - - - +
109D ASP* 2.9 30.5 + - - +
269D LEU* 3.9 25.6 - - + -
270D MET* 3.3 33.9 - - + -
274D GLY* 6.2 0.9 - - - -
275D ILE* 4.9 7.4 - - + +
299D GLU* 4.1 3.6 - - - +
302D LEU* 4.8 2.0 - - - +
303D GLY* 4.0 22.9 - - - +
306D ALA* 3.6 26.5 - - + -
352D LEU* 4.1 4.3 - - + +
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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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34D VAL* 4.4 6.3 - - + -
36D ILE* 3.5 24.7 - - + -
38D TYR* 2.8 21.8 + - - -
44D GLY* 3.5 27.4 - - - +
45D TRP 3.1 19.5 + - - +
46D GLY 3.9 2.9 - - - +
102D ALA 3.3 6.0 + - - +
103D VAL 3.7 3.1 - - - +
104D GLU 3.3 0.2 - - - -
105D MET* 1.3 79.8 - - - +
107D LEU* 1.3 55.1 + - - +
109D ASP* 3.9 0.4 - - - -
110D GLY 3.3 10.6 + - - -
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Residues in contact with LEU 107 (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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3D ILE* 3.7 20.4 - - + -
36D ILE* 4.2 7.4 - - + -
38D TYR* 3.4 7.8 + - - +
74D LEU* 3.8 8.5 - - + -
79D LEU* 3.5 32.3 - - + +
82D TYR* 3.2 17.7 + - + +
85D ILE* 3.6 16.2 - - + -
86D LEU* 5.1 2.7 - - + -
89D ILE* 3.1 35.9 - - + -
103D VAL 3.0 16.6 + - - +
104D GLU* 3.1 7.6 + - + +
106D ALA* 1.3 74.1 - - - +
108D TYR* 1.3 60.2 + - - +
109D ASP 3.1 1.3 - - - -
110D GLY* 3.2 1.9 + - - -
111D TRP* 2.8 29.3 + - - +
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Residues in contact with TYR 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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82D TYR* 3.0 35.9 + + - -
86D LEU* 3.6 19.4 - - + +
104D GLU* 2.8 52.9 + - + +
105D MET 4.0 2.5 - - - +
107D LEU* 1.3 70.0 - - - +
109D ASP* 1.3 65.2 + - - +
111D TRP* 3.7 23.0 - + - +
112D ALA* 2.9 27.0 + - - +
119D LEU* 3.8 23.4 - - + +
123D LEU* 4.1 12.1 - - + -
275D ILE* 3.7 38.8 - - + -
276D SER* 3.7 14.0 - - - -
279D GLU* 4.3 8.2 + - - -
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Residues in contact with ASP 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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44D GLY* 3.5 5.2 - - - -
45D TRP* 3.0 30.2 + - - +
105D MET 2.9 17.5 + - - +
106D ALA 3.7 6.5 - - - +
108D TYR* 1.3 78.1 - - - +
110D GLY* 1.3 57.7 + - - +
112D ALA 3.5 0.2 + - - -
113D GLN* 2.8 50.7 + - - +
119D LEU* 5.2 0.2 - - - -
350D PRO 4.6 0.2 - - - +
351D GLY* 3.4 4.3 - - - -
352D LEU* 2.9 50.9 + - + +
353D GLY 4.6 1.1 + - - -
354D ILE* 5.1 1.0 + - - +
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Residues in contact with GLY 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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1D MET* 3.0 15.6 - - - +
38D TYR* 3.8 25.6 - - - -
44D GLY* 4.5 0.4 - - - -
79D LEU* 3.6 6.3 - - - -
106D ALA 3.3 5.3 + - - -
107D LEU 3.2 5.7 + - - -
109D ASP* 1.3 79.6 - - - +
111D TRP* 1.3 59.0 + - - +
113D GLN* 3.2 8.1 + - - +
114D MET* 2.8 25.5 + - - +
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Residues in contact with TRP 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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111C TRP* 5.6 2.0 - + - -
117C LEU* 5.3 2.8 - - - +
121C GLN 5.2 4.0 + - - -
122C MET* 3.8 25.0 + - + +
79D LEU* 3.3 16.5 + - + +
82D TYR* 3.9 40.2 - + + +
107D LEU 2.8 20.6 + - - +
108D TYR* 3.7 33.2 - + - +
110D GLY* 1.3 72.2 - - - +
112D ALA* 1.3 62.9 + - - +
114D MET* 3.4 31.1 - - + +
115D CYS* 3.3 28.4 + - - -
119D LEU* 4.8 2.0 - - + -
122D MET* 3.3 53.2 - - + -
123D LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 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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108D TYR 2.9 17.1 + - - +
111D TRP* 1.3 76.6 - - - +
113D GLN* 1.3 65.0 + - - +
115D CYS* 3.2 3.4 + - - +
116D GLY 3.0 16.8 + - - -
117D LEU* 3.1 27.8 + - - +
119D LEU* 3.8 22.4 - - + -
122D MET* 4.4 15.7 - - + -
351D GLY* 3.6 13.5 - - - -
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Residues in contact with GLN 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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1D MET* 4.6 5.4 - - + -
42D ALA* 3.3 26.1 - - + +
43D VAL 3.1 25.5 + - - +
109D ASP* 2.8 42.9 + - - +
110D GLY* 3.2 6.9 + - - +
112D ALA* 1.3 74.7 - - - +
114D MET* 1.3 59.9 + - - +
116D GLY* 2.9 19.4 + - - -
350D PRO* 3.8 33.8 + - + +
351D GLY* 3.9 0.4 - - - -
353D GLY 6.0 0.2 - - - +
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Residues in contact with MET 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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115C CYS 4.8 5.3 - - - +
117C LEU* 3.6 38.4 - - + -
1D MET* 3.5 43.2 - - + +
79D LEU* 4.1 17.0 - - + +
80D ALA* 5.1 2.7 - - - +
110D GLY 2.8 18.0 + - - +
111D TRP* 3.4 36.1 - - + +
112D ALA 3.2 0.2 - - - -
113D GLN* 1.3 77.5 - - - +
115D CYS* 1.3 63.1 + - - +
116D GLY 3.4 0.7 + - - -
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Residues in contact with CYS 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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114C MET* 5.0 3.5 - - - +
115C CYS* 4.0 38.5 - - - -
117C LEU* 4.1 8.1 - - - -
122C MET* 5.7 0.4 - - - -
111D TRP* 3.3 19.9 + - - +
112D ALA 3.2 7.4 + - - +
114D MET* 1.3 94.7 - - - +
116D GLY* 1.3 63.3 + - - +
117D LEU* 3.9 8.6 - - + +
122D MET* 3.7 35.4 - - - -
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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
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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