Contacts of the helix formed by residues 91 - 113 (chain D) in PDB entry 2JC2
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 GLY 91 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B PHE* 3.7 4.7 - - - -
47B GLY 4.6 1.8 - - - -
48B GLN* 3.4 17.9 + - - -
90D MET* 1.3 79.9 - - - +
92D PHE* 1.3 64.5 + - - -
93D ASN 3.5 2.2 - - - -
94D GLU* 2.8 18.6 + - - -
95D PHE* 3.2 19.1 + - - +
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Residues in contact with PHE 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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33B ASP* 3.7 21.3 - - + -
35B LEU* 4.0 6.7 - - + -
36B TYR* 3.6 53.2 - + + -
39B PHE* 3.5 42.1 - + + -
47B GLY 4.9 1.0 + - - -
91D GLY* 1.3 69.2 - - - -
93D ASN* 1.3 78.5 + - - +
95D PHE* 3.2 4.7 + + - +
96D LYS* 3.0 51.4 + - + +
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Residues in contact with ASN 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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91D GLY 3.5 0.4 - - - -
92D PHE* 1.3 90.3 - - - +
94D GLU* 1.3 65.2 + - + +
96D LYS* 3.3 11.2 + - - +
97D GLU* 3.1 23.3 + - - +
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Residues in contact with GLU 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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48B GLN* 4.7 1.4 - - - +
82D LEU* 2.9 47.5 - - + +
83D ASP* 4.5 0.8 - - - -
84D ARG* 4.0 13.7 + - - +
85D ASP* 4.7 6.2 - - - +
89D THR 4.5 2.3 - - - +
90D MET* 3.5 20.1 - - + -
91D GLY* 2.8 31.7 + - - +
92D PHE 3.3 0.4 - - - -
93D ASN* 1.3 76.5 - - + +
95D PHE* 1.3 59.9 + - - +
97D GLU* 3.2 12.3 + - - +
98D LEU 2.8 24.3 + - - -
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Residues in contact with PHE 95 (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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35B LEU* 4.1 32.8 - - + -
39B PHE* 3.9 22.9 - + + -
49B ILE* 4.1 4.5 - - + -
54B LEU* 3.7 31.2 - - + -
57B CYS* 3.5 29.2 - - + -
58B LEU* 3.9 15.0 - - + -
61B SER* 3.9 15.7 - - - -
90D MET* 3.8 11.4 - - - -
91D GLY 3.2 13.7 + - - +
92D PHE* 3.2 16.9 + + - +
94D GLU* 1.3 73.4 - - - +
96D LYS* 1.3 60.0 + - - +
98D LEU* 3.2 5.7 + - + +
99D TRP* 2.9 37.5 + + + +
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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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33B ASP* 2.8 30.6 + - - +
34B PRO* 5.9 0.2 - - - +
35B LEU* 4.2 22.5 - - + +
92D PHE* 3.0 41.4 + - + +
93D ASN* 3.4 13.5 - - - +
95D PHE* 1.3 75.8 - - - +
97D GLU* 1.3 62.6 + - - +
99D TRP* 3.4 2.9 + - - +
100D ALA* 3.2 24.1 + - - +
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Residues in contact with GLU 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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82D LEU* 4.1 21.0 - - + +
93D ASN 3.1 13.9 + - - +
94D GLU* 3.4 13.9 - - - +
95D PHE 3.2 0.2 - - - -
96D LYS* 1.3 75.3 - - - +
98D LEU* 1.3 61.3 + - - +
100D ALA* 3.7 5.0 + - - +
101D VAL* 3.3 33.8 + - + +
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Residues in contact with LEU 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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54B LEU* 3.8 35.7 - - + -
58B LEU* 4.7 3.1 - - + -
78D MET* 3.9 24.7 - - + -
81D MET* 3.8 28.3 - - + -
82D LEU* 3.4 16.5 - - + +
90D MET* 3.8 17.3 - - + -
94D GLU 2.8 8.1 + - - +
95D PHE* 3.2 9.6 + - + +
97D GLU* 1.3 75.0 - - - +
99D TRP* 1.3 58.5 - - - +
101D VAL* 3.2 5.7 + - + +
102D LEU* 2.9 53.6 + - + +
164D VAL* 5.5 0.4 - - + -
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Residues in contact with TRP 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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35B LEU* 3.8 37.8 - - + +
58B LEU* 4.4 10.3 - - + -
61B SER* 3.4 45.3 - - - -
63B ILE* 3.4 26.8 - - + +
95D PHE* 2.9 21.2 + + + +
96D LYS 3.8 4.9 - - - +
98D LEU* 1.3 76.2 - - - +
100D ALA* 1.3 63.1 + - + +
102D LEU* 3.4 6.6 + - - +
103D ASN* 2.9 62.7 + - + +
106D ARG* 4.8 4.0 - - - -
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Residues in contact with ALA 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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96D LYS 3.2 14.2 + - - +
97D GLU* 3.9 7.2 - - - +
99D TRP* 1.3 86.7 - - + +
101D VAL* 1.3 57.6 + - + +
103D ASN* 3.7 3.3 + - - +
104D GLY* 3.1 22.7 + - - -
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Residues in contact with VAL 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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81D MET* 5.2 9.6 - - + -
97D GLU* 3.3 22.2 + - + +
98D LEU* 3.2 7.5 + - + +
100D ALA* 1.3 76.5 - - + +
102D LEU* 1.3 60.9 + - + +
104D GLY* 3.3 2.7 + - - -
105D TRP* 3.0 68.8 + - + +
167D ARG* 4.2 15.5 - - - +
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Residues in contact with LEU 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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58B LEU* 3.8 26.5 - - + -
63B ILE* 4.0 16.9 - - + +
70D PHE* 4.7 7.0 - - + -
78D MET* 3.9 17.7 - - + -
98D LEU* 2.9 45.4 + - + +
99D TRP 3.9 3.6 - - - +
101D VAL* 1.3 76.4 - - - +
103D ASN* 1.3 58.1 + - - +
105D TRP* 3.3 14.8 + - + +
106D ARG* 2.8 29.9 + - - +
156D PHE* 5.1 3.2 - - + -
160D ILE* 3.8 38.4 - - + +
164D VAL* 4.9 1.3 - - + -
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Residues in contact with ASN 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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63B ILE* 4.3 3.7 - - + +
99D TRP* 2.9 47.1 + - + +
100D ALA* 3.9 4.7 - - - +
102D LEU* 1.3 73.1 - - - +
104D GLY* 1.3 61.5 + - - +
106D ARG* 3.0 37.4 - - - +
107D GLN* 2.8 60.4 + - - +
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Residues in contact with GLY 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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100D ALA 3.1 16.2 + - - -
101D VAL* 3.3 3.8 + - - -
102D LEU 3.3 0.2 - - - -
103D ASN* 1.3 77.0 + - - +
105D TRP* 1.3 63.5 + - - +
107D GLN* 3.5 8.5 + - - +
108D HIS* 3.2 21.3 + - - +
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Residues in contact with TRP 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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81D MET* 4.9 3.6 - - + -
101D VAL* 3.0 40.1 + - + +
102D LEU* 3.8 11.0 - - + +
104D GLY* 1.3 74.6 - - - +
106D ARG* 1.3 60.0 + - - +
108D HIS* 3.4 7.8 + - + +
109D PHE* 2.9 29.2 + - - +
132D MET* 3.6 24.0 - - + +
156D PHE* 4.9 1.1 - - - -
159D TYR* 4.0 25.0 - + + -
160D ILE* 4.2 21.3 - - + -
163D CYS* 3.9 27.5 - - + -
164D VAL* 3.7 28.3 - - + -
167D ARG* 3.6 29.3 - - - +
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Residues in contact with ARG 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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62B GLY 2.7 30.9 + - - -
63B ILE* 3.4 28.7 - - + +
64B ALA 4.5 1.0 - - - +
116B ARG* 4.0 13.1 - - - +
1199B SO4 4.2 16.1 + - - +
99D TRP* 4.8 5.5 - - - -
102D LEU 2.8 18.1 + - - +
103D ASN* 3.0 33.1 - - - +
104D GLY 3.3 0.2 - - - -
105D TRP* 1.3 76.8 - - - +
107D GLN* 1.3 54.6 + - - +
109D PHE* 3.1 1.0 + - - +
110D ILE* 2.8 59.7 + - + +
156D PHE* 3.8 29.8 - - + -
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Residues in contact with GLN 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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103D ASN* 2.8 45.0 + - - +
104D GLY* 3.7 8.2 - - - +
105D TRP 3.4 0.2 - - - -
106D ARG* 1.3 77.9 - - + +
108D HIS* 1.3 56.8 + - - +
110D ILE* 4.1 9.2 - - + +
111D SER* 3.2 26.7 + - - -
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Residues in contact with HIS 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 GLY 3.2 13.4 + - - +
105D TRP* 3.6 12.8 - - + +
106D ARG 3.2 0.2 - - - -
107D GLN* 1.3 75.7 - - - +
109D PHE* 1.3 61.1 + - - +
111D SER* 3.4 8.6 - - - -
112D LEU* 3.3 58.0 + - + +
124D GLU 5.6 1.4 + - - -
128D ALA* 5.1 9.3 - - + +
159D TYR* 3.3 23.6 - + - +
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Residues in contact with PHE 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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1199B SO4 4.6 7.0 - - - -
105D TRP 2.9 17.4 + - - +
106D ARG 3.1 5.1 + - - +
108D HIS* 1.3 75.6 - - - +
110D ILE* 1.3 63.1 + - + +
112D LEU* 3.0 11.7 + - + +
113D ASP* 2.9 35.3 + - + +
118D GLY* 3.5 34.1 - - - -
120D VAL* 3.6 43.0 - - + +
155D THR 4.0 1.6 - - - -
156D PHE* 3.6 35.0 - + + -
159D TYR* 3.6 42.8 - + + -
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Residues in contact with ILE 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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116B ARG* 6.0 3.4 - - - +
1199B SO4 5.0 16.8 - - - +
106D ARG* 2.8 47.8 + - + +
107D GLN* 4.2 8.3 - - + +
109D PHE* 1.3 73.6 - - + +
111D SER* 1.3 61.9 + - - +
112D LEU 3.4 0.2 + - - -
113D ASP* 3.5 24.2 + - + +
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Residues in contact with SER 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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107D GLN 3.2 20.0 + - - -
108D HIS* 3.4 13.2 - - - -
109D PHE 3.1 0.4 - - - -
110D ILE* 1.3 78.4 - - - +
112D LEU* 1.3 62.4 + - - +
113D ASP 5.0 1.2 - - - +
114D THR* 5.8 0.5 - - - -
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Residues in contact with LEU 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 HIS* 3.3 49.3 + - + +
109D PHE* 3.0 9.6 + - + +
111D SER* 1.3 79.7 - - - +
113D ASP* 1.3 59.5 - - - +
114D THR* 3.0 17.5 + - - -
120D VAL* 4.1 18.4 - - + +
121D ASP* 5.6 1.8 - - - +
124D GLU* 3.5 44.9 - - + +
159D TYR* 5.3 4.3 - - + +
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Residues in contact with ASP 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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67B TYR* 5.7 0.3 - - - -
1199B SO4 5.3 1.9 + - - -
109D PHE* 2.9 24.3 + - + +
110D ILE* 3.5 19.7 + - + +
111D SER 5.0 1.2 - - - +
112D LEU* 1.3 72.2 - - - +
114D THR* 1.3 66.4 + - - +
115D ASP* 3.5 0.7 + - - +
116D ARG* 3.4 14.5 + - - +
117D SER* 2.7 36.2 + - - -
118D GLY* 2.8 28.1 + - - -
119D THR 3.4 8.5 - - - +
120D VAL* 4.2 4.9 - - - +
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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
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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