Contacts of the helix formed by residues 108 - 127 (chain D) in PDB entry 2BKU
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 GLU 108 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.8 31.5 - - + +
58D ARG* 5.7 0.4 - - - +
106D SER* 3.0 19.4 + - - +
107D ILE* 1.3 81.4 - - + +
109D PRO* 1.4 82.6 - - - +
110D ARG* 4.2 12.1 + - - +
111D ILE* 3.4 25.3 + - + -
112D ALA 3.3 14.0 + - - -
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Residues in contact with PRO 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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113C GLU* 6.0 2.7 - - - +
106D SER 4.9 1.3 - - - +
107D ILE 3.4 9.8 - - - +
108D GLU* 1.4 93.3 - - - +
110D ARG* 1.3 62.9 + - + +
112D ALA* 3.1 4.1 + - + +
113D ASN* 2.8 40.3 + - - +
153D ARG* 3.6 25.4 - - - +
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Residues in contact with ARG 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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81C ILE* 4.8 2.8 - - - +
82C GLN* 2.8 51.8 - - - +
111C VAL* 3.9 22.6 + - - +
113C GLU* 5.8 8.7 - - - +
55D LEU* 4.1 18.0 - - + +
56D GLU* 5.3 0.2 - - - +
59D ILE* 3.3 46.2 - - + +
108D GLU* 3.5 13.5 + - - +
109D PRO* 1.3 80.0 - - + +
111D ILE* 1.3 60.0 + - - +
113D ASN* 3.8 11.9 - - - +
114D ALA* 3.3 20.8 + - - +
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.1 11.8 - - + +
55D LEU* 3.5 28.0 - - + -
58D ARG* 3.3 53.6 - - + +
59D ILE* 4.6 5.2 - - + +
103D ALA* 3.8 19.1 - - + +
106D SER* 3.8 16.8 - - - +
108D GLU* 3.4 24.1 + - + +
109D PRO 3.2 0.2 - - - -
110D ARG* 1.3 77.9 - - - +
112D ALA* 1.3 61.0 + - - +
114D ALA* 3.4 6.2 + - - +
115D ALA* 2.9 26.3 + - - +
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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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103D ALA 3.4 13.0 - - - +
104D LEU* 3.3 29.6 - - - +
106D SER 4.2 7.4 - - - +
108D GLU 3.3 9.3 + - - +
109D PRO* 3.1 9.3 + - + +
111D ILE* 1.3 76.4 - - - +
113D ASN* 1.3 56.7 + - - +
115D ALA* 3.3 2.3 + - - +
116D ALA* 2.7 34.0 + - - +
150D ASN* 6.6 0.2 - - + -
153D ARG* 4.1 7.0 - - - +
154D ALA* 3.9 12.1 - - + -
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Residues in contact with ASN 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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110C ARG 4.5 16.0 - - - +
113C GLU* 5.3 5.5 - - - +
109D PRO* 2.8 29.7 + - - +
110D ARG* 3.8 12.3 - - - +
111D ILE 3.3 0.2 - - - -
112D ALA* 1.3 73.7 - - - +
114D ALA* 1.3 62.8 + - - +
116D ALA* 3.2 9.4 + - - +
117D GLN* 3.2 26.4 + - - +
153D ARG* 3.2 34.3 + - - +
154D ALA* 5.5 0.2 - - - +
157D LEU* 3.3 16.6 - - + +
161D TYR* 4.4 3.0 - - - +
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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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48D LEU* 5.2 0.2 - - + -
59D ILE* 4.1 16.6 - - + +
62D ALA* 3.7 24.2 - - + +
63D LEU* 4.1 14.6 - - + +
110D ARG 3.3 15.2 + - - +
111D ILE* 3.7 5.4 - - - +
112D ALA 3.3 0.4 - - - -
113D ASN* 1.3 79.7 - - - +
115D ALA* 1.3 57.5 + - - +
117D GLN* 3.1 16.8 + - - +
118D LEU* 3.0 26.2 + - - +
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Residues in contact with ALA 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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48D LEU* 4.6 4.0 - - + -
62D ALA* 4.3 4.4 - - - +
100D ALA* 3.5 24.5 - - - +
103D ALA* 3.6 9.4 - - + -
104D LEU* 3.5 13.9 - - - +
111D ILE 2.9 18.4 + - - +
112D ALA 3.4 5.2 - - - +
114D ALA* 1.3 72.4 - - - +
116D ALA* 1.3 60.6 + - - +
118D LEU* 3.8 7.6 - - - +
119D ILE* 2.8 37.9 + - - +
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Residues in contact with ALA 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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104D LEU* 4.0 16.1 - - + +
112D ALA 2.7 17.1 + - - +
113D ASN 3.2 11.0 - - - +
115D ALA* 1.3 74.0 - - - +
117D GLN* 1.3 56.3 + - - +
119D ILE* 3.6 2.8 + - - +
120D ALA* 3.1 28.9 + - - +
154D ALA 4.4 0.4 - - - +
157D LEU* 3.9 23.1 - - + -
158D ALA* 4.2 16.9 - - - +
161D TYR* 3.9 11.9 - - + -
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77C ASP* 4.4 10.9 - - - +
107C ASP 5.6 0.2 - - - +
110C ARG* 3.7 45.3 + - - +
111C VAL* 4.6 4.4 - - - +
63D LEU* 3.3 27.2 - - + +
66D LYS* 3.9 24.0 + - + +
113D ASN 3.4 16.9 + - - +
114D ALA* 3.1 10.2 + - - +
116D ALA* 1.3 75.0 - - - +
118D LEU* 1.3 60.0 + - - +
120D ALA* 3.4 6.7 + - - +
121D ALA* 3.0 28.6 + - - +
161D TYR* 3.9 19.5 - - + -
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Residues in contact with LEU 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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44D SER 6.3 0.2 - - - -
45D SER* 5.6 3.6 - - - -
48D LEU* 4.3 17.0 - - + -
62D ALA* 4.2 23.1 - - + +
65D LEU* 3.7 28.3 - - + -
66D LYS* 4.3 9.7 - - - +
69D LEU* 3.4 29.6 - - + -
96D ILE* 5.1 4.3 - - + +
100D ALA* 4.5 12.1 - - + -
114D ALA 3.0 12.5 + - - +
115D ALA* 3.8 8.1 - - - +
117D GLN* 1.3 77.0 - - - +
119D ILE* 1.3 63.1 + - - +
121D ALA* 3.2 5.2 + - - +
122D ILE* 3.0 37.0 + - + +
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Residues in contact with ILE 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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100D ALA* 3.7 40.2 - - + +
101D LEU* 3.9 9.6 - - + -
104D LEU* 3.7 30.7 - - + -
115D ALA 2.8 24.6 + - - +
116D ALA* 3.9 4.5 - - - +
118D LEU* 1.3 72.2 - - - +
120D ALA* 1.3 63.5 + - - +
122D ILE* 3.3 2.2 + - - -
123D ALA* 3.0 21.3 + - - +
132D TRP* 3.6 29.1 - - + -
135D LEU* 4.1 16.6 - - + -
139D MET* 5.0 2.0 - - - -
158D ALA* 5.2 1.6 - - + -
162D MET* 4.1 15.3 - - + -
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Residues in contact with ALA 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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116D ALA 3.1 18.3 + - - +
117D GLN* 3.6 6.5 - - - +
119D ILE* 1.3 75.5 - - - +
121D ALA* 1.3 64.0 + - - +
123D ALA* 3.2 3.3 + - - +
124D ASP* 3.0 29.9 + - - +
158D ALA 4.8 1.1 - - - +
161D TYR* 3.9 26.9 - - + +
162D MET* 4.2 23.0 - - + +
165D SER* 4.9 2.7 - - - +
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Residues in contact with ALA 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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66D LYS* 3.9 20.0 - - + -
69D LEU* 4.2 20.1 - - + +
70D VAL* 4.3 13.3 - - + +
117D GLN 3.0 14.1 + - - +
118D LEU* 3.4 9.6 - - - +
120D ALA* 1.3 76.9 - - - +
122D ILE* 1.3 61.6 + - - +
124D ASP* 3.2 27.3 + - - +
125D ILE* 3.5 13.5 + - - +
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Residues in contact with ILE 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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69D LEU* 3.7 17.3 - - + -
84D TRP* 3.7 43.1 - - + +
96D ILE* 4.2 10.5 - - + -
97D LYS* 4.3 11.9 - - + -
100D ALA* 5.1 2.7 - - + -
118D LEU* 3.0 35.4 + - + +
119D ILE* 3.3 0.9 + - - -
121D ALA* 1.3 75.2 - - - +
123D ALA* 1.3 57.7 + - - +
125D ILE* 3.2 11.6 + - - +
126D GLU* 2.9 30.4 + - + +
132D TRP* 3.6 32.8 - - + -
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Residues in contact with ALA 123 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D ILE 3.0 16.2 + - - +
120D ALA 3.2 5.6 + - - +
122D ILE* 1.3 76.4 - - - +
124D ASP* 1.3 65.1 + - - +
126D GLU* 4.4 1.1 - - - +
127D LEU* 3.0 56.1 + - + +
128D PRO* 3.7 0.2 - - - +
132D TRP* 4.2 5.3 - - - -
135D LEU* 3.9 12.8 - - + -
162D MET* 3.8 17.5 - - + -
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Residues in contact with ASP 124 (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 VAL* 3.6 26.9 - - + +
120D ALA 3.0 19.9 + - - +
121D ALA* 3.3 13.0 - - - +
123D ALA* 1.3 78.1 - - - +
125D ILE* 1.3 58.3 + - + +
128D PRO* 3.1 25.3 - - - +
162D MET* 4.6 3.6 - - - +
165D SER* 2.7 43.5 + - - +
166D ALA* 4.4 3.4 + - - +
167D ASP* 3.7 15.2 - - - +
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Residues in contact with ILE 125 (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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69D LEU* 3.5 48.0 - - + +
70D VAL* 6.3 0.7 - - + -
80D PHE 4.2 0.4 - - - +
81D ALA* 3.6 47.7 - - + +
84D TRP* 3.6 26.2 - - + -
85D ILE* 4.0 11.7 - - + +
121D ALA 3.7 12.3 - - - +
122D ILE* 3.2 9.8 + - - +
123D ALA 3.2 0.2 - - - -
124D ASP* 1.3 80.3 - - + +
126D GLU* 1.3 60.2 + - - +
128D PRO* 3.5 2.9 - - - +
129D HIS* 3.4 25.6 + - - -
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Residues in contact with GLU 126 (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 TRP* 3.0 33.5 + - + +
85D ILE* 5.7 3.6 - - + -
93D LYS* 3.4 16.1 - - - +
97D LYS* 2.5 41.2 + - - -
122D ILE* 2.9 18.7 + - - +
123D ALA* 4.7 0.4 - - - +
125D ILE* 1.3 76.6 - - + +
127D LEU* 1.3 64.3 + - - +
128D PRO* 3.3 2.7 - - - -
129D HIS* 3.1 10.5 + - - +
131D ALA* 3.0 43.1 + - + +
132D TRP* 3.1 20.9 + - + +
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Residues in contact with LEU 127 (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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123D ALA* 3.0 36.9 + - + +
126D GLU* 1.3 71.5 - - - +
128D PRO* 1.4 68.4 - - + +
130D GLY* 3.2 11.3 + - - -
131D ALA 3.7 18.2 - - - +
132D TRP* 3.7 16.8 - - + +
133D PRO* 5.7 0.2 - - + -
135D LEU* 4.4 11.4 - - + -
136D MET* 4.1 18.6 - - + -
162D MET* 4.8 4.0 - - + -
170D SER* 2.6 28.9 + - - +
171D GLN* 4.9 1.2 + - - +
172D ALA* 5.1 15.5 + - + +
173D LEU* 3.9 32.3 - - + +
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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