Contacts of the helix formed by residues 116 - 138 (chain A) in PDB entry 3DEW
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 ILE 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 3.9 20.9 - - + +
57A LEU* 4.0 15.5 - - + +
58A GLN* 3.8 28.7 - - + +
61A PHE* 3.9 29.6 - - + -
112A CYS* 3.0 14.5 + - + +
114A ALA 3.5 0.2 - - - -
115A ALA* 1.3 88.4 - - + +
117A VAL* 1.3 67.1 + - + +
118A SER 3.6 0.7 - - - -
119A PRO* 3.7 3.8 - - - +
120A ALA* 3.3 24.4 + - - +
205A BME 3.7 24.9 - - - -
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Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.0 14.6 - - + -
61A PHE* 3.7 38.4 - - + -
102A TYR* 4.9 1.8 - - - +
105A GLU* 3.9 28.5 - - + -
106A LEU* 4.8 3.4 - - + -
112A CYS 3.4 3.3 + - - +
113A PHE* 3.1 26.2 + - + +
116A ILE* 1.3 76.6 - - - +
118A SER* 1.3 66.6 + - - +
120A ALA* 3.2 2.8 + - - +
121A ILE* 3.0 45.8 + - + +
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 2.8 48.7 + - - -
114A ALA* 4.3 5.6 - - - -
117A VAL* 1.3 73.9 - - - +
119A PRO* 1.3 64.9 - - - +
121A ILE* 3.9 4.1 - - - +
122A ALA* 2.9 32.4 + - - +
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ALA 3.2 22.0 - - - +
115A ALA 3.6 21.5 - - - +
116A ILE* 3.7 7.0 - - - +
117A VAL 3.7 1.8 - - - -
118A SER* 1.3 90.4 - - - +
120A ALA* 1.3 55.9 + - - +
122A ALA* 3.9 6.6 - - + +
123A SER* 2.9 32.1 + - - -
126A ARG* 5.1 2.4 + - - +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.9 16.6 - - + +
64A PHE* 3.5 39.6 - - + -
116A ILE 3.3 19.0 + - - +
117A VAL 3.2 4.0 + - - +
118A SER 3.2 0.8 - - - -
119A PRO* 1.3 75.4 - - - +
121A ILE* 1.3 63.6 + - - +
123A SER* 2.7 23.6 + - - -
124A VAL 3.4 3.8 + - - -
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 4.8 1.8 - - + -
64A PHE* 4.5 7.6 - - + -
102A TYR* 3.7 42.6 - - + +
106A LEU* 3.9 24.0 - - + -
117A VAL* 3.0 40.5 + - + +
118A SER* 3.9 3.8 - - - +
120A ALA* 1.3 76.9 - - - +
122A ALA* 1.3 64.1 + - - +
124A VAL* 3.1 6.3 + - - +
125A ILE* 3.0 35.5 + - + +
152A LEU* 6.0 1.3 - - + -
209A ACY 4.5 5.4 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A SER* 2.9 19.2 + - - +
119A PRO* 3.9 5.6 - - + +
121A ILE* 1.3 78.5 - - - +
123A SER* 1.3 57.2 + - - +
125A ILE* 4.0 6.0 - - - +
126A ARG* 2.9 63.4 + - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE 4.1 6.2 + - - -
67A LEU* 4.1 18.8 - - - +
71A ARG* 4.9 9.6 + - - -
119A PRO 2.9 15.3 + - - -
120A ALA* 2.7 22.7 + - - -
122A ALA* 1.3 77.3 - - - +
124A VAL* 1.3 57.2 + - - +
126A ARG* 3.7 13.0 - - - +
127A LEU* 3.1 27.4 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.6 31.0 - - + -
67A LEU* 4.2 15.0 - - + -
70A ILE* 5.5 2.7 - - + -
84A TYR* 3.6 35.9 - - + -
87A TRP* 3.9 14.6 - - + -
120A ALA 3.7 2.0 - - - +
121A ILE 3.1 8.3 + - - +
123A SER* 1.3 82.4 + - - +
125A ILE* 1.3 65.3 + - - +
127A LEU* 3.1 8.7 + - + +
128A LEU* 3.0 27.6 + - + +
209A ACY 3.7 16.2 - - + -
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.0 32.6 + - + +
122A ALA* 4.0 5.8 - - - +
124A VAL* 1.3 75.2 - - - +
126A ARG* 1.3 59.4 + - + +
128A LEU* 3.3 8.2 + - + +
129A ALA* 2.9 27.7 + - - +
148A VAL* 4.1 23.6 - - + -
151A ALA* 3.8 16.5 - - + +
152A LEU* 3.8 31.0 - - + -
155A ALA* 3.7 29.6 - - + -
209A ACY 3.9 10.5 - - + -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 5.1 2.6 + - - +
122A ALA* 2.9 50.1 + - + +
123A SER* 3.7 11.2 - - - +
125A ILE* 1.3 77.7 - - + +
127A LEU* 1.3 56.1 + - - +
129A ALA* 3.1 6.4 + - - +
130A GLU* 2.8 48.9 + - + +
148A VAL* 6.0 2.7 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.1 20.0 - - + -
70A ILE* 3.6 36.1 - - + -
71A ARG* 3.5 50.9 - - + +
74A ALA* 6.2 2.5 - - + -
80A VAL* 4.9 4.6 - - + +
123A SER 3.1 14.3 + - - +
124A VAL* 3.1 7.6 + - + +
126A ARG* 1.3 80.0 - - - +
128A LEU* 1.3 64.5 + - + +
130A GLU* 3.4 16.1 + - + +
131A SER* 3.2 20.8 + - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 5.0 3.8 - - + -
80A VAL* 4.4 11.4 - - + -
81A MSE 3.7 24.5 - - - +
84A TYR* 3.6 60.1 - - + -
124A VAL* 3.0 21.9 + - + +
125A ILE* 3.7 12.6 - - + +
127A LEU* 1.3 78.1 - - + +
129A ALA* 1.3 62.8 + - - +
131A SER* 3.2 4.2 + - - -
132A ILE* 3.0 28.5 + - - +
151A ALA* 3.7 27.1 - - + +
154A LEU* 4.6 3.4 - - + -
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE 2.9 18.1 + - - +
126A ARG* 3.5 6.7 - - - +
128A LEU* 1.3 75.4 - - - +
130A GLU* 1.3 58.4 + - + +
132A ILE* 3.3 3.4 + - - +
133A GLU* 2.8 40.1 + - - +
147A ALA* 3.6 13.5 - - + +
148A VAL* 3.8 38.6 - - + +
151A ALA* 3.8 1.5 - - + +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 5.2 3.5 + - - -
126A ARG* 2.8 36.8 + - - +
127A LEU* 3.6 18.3 - - + +
129A ALA* 1.3 73.1 - - + +
131A SER* 1.3 56.1 + - - +
133A GLU* 3.4 17.5 + - - +
134A ALA* 3.0 27.7 + - - +
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 3.2 27.0 - - - +
80A VAL* 3.6 13.7 - - - +
81A MSE 3.3 20.1 - - - +
127A LEU* 3.2 9.8 + - - -
128A LEU 3.2 3.2 + - - -
130A GLU* 1.3 79.0 - - - +
132A ILE* 1.3 58.0 + - - +
134A ALA* 3.3 4.2 + - - +
135A GLY 3.0 22.3 + - - -
204A CL 3.1 27.6 - - - +
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Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A MSE 3.8 17.5 - - + -
128A LEU 3.0 14.7 + - - +
129A ALA 3.6 5.8 - - - +
131A SER* 1.3 73.7 - - - +
133A GLU* 1.3 60.3 + - - +
135A GLY 3.2 1.7 + - - -
136A MSE 2.9 44.0 + - + +
141A PHE* 3.5 20.2 - - + -
147A ALA* 3.8 22.7 - - + +
150A SER* 3.9 8.5 - - - +
151A ALA* 3.5 35.2 - - + +
190A PHE* 3.8 22.2 - - + -
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Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 2.8 28.1 + - - +
130A GLU* 3.5 22.2 - - - +
132A ILE* 1.3 72.7 - - - +
134A ALA* 1.3 56.0 + - - +
136A MSE 3.3 11.3 + - - +
137A THR* 3.0 30.8 + - - -
147A ALA* 3.3 25.1 - - + +
148A VAL* 5.0 5.5 - - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 5.0 1.3 - - + -
130A GLU 3.0 12.8 + - - +
131A SER 3.6 8.1 - - - +
133A GLU* 1.3 72.3 - - - +
135A GLY* 1.3 61.6 + - - +
137A THR* 3.3 8.8 + - - -
138A ARG* 3.0 39.0 + - - +
204A CL 4.2 15.9 - - + -
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.1 10.2 - - - +
131A SER 3.0 11.5 + - - -
132A ILE 3.2 0.6 + - - -
134A ALA* 1.3 78.7 - - - +
136A MSE 1.3 58.2 + - - +
138A ARG* 3.4 4.5 + - - -
139A GLY 3.2 3.3 + - - -
140A LEU* 2.9 34.7 + - - +
141A PHE* 3.2 27.0 + - - -
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Residues in contact with MSE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 2.9 31.3 + - + +
133A GLU* 3.5 14.6 - - - +
134A ALA 3.3 0.2 - - - -
135A GLY* 1.3 72.8 - - - +
137A THR* 1.3 65.4 + - - +
139A GLY* 2.9 12.5 + - - -
141A PHE* 3.6 19.0 - - + +
142A ARG 3.5 13.0 - - - +
143A ARG* 3.1 60.6 + - + +
145A LEU* 3.4 26.9 - - - +
147A ALA* 4.6 8.3 - - - -
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Residues in contact with THR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A GLU 3.0 15.6 + - - -
134A ALA* 3.3 10.6 + - - -
136A MSE 1.3 74.3 - - - +
138A ARG* 1.3 60.7 + - + +
143A ARG* 3.1 20.3 + - - +
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Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLY 3.3 16.3 + - - -
76A ASP* 4.7 0.4 - - - +
77A PRO* 3.3 31.7 - - - +
134A ALA* 3.0 25.8 + - - +
135A GLY* 3.8 5.4 - - - +
136A MSE 3.2 0.4 - - - -
137A THR* 1.3 79.4 - - + +
139A GLY* 1.3 58.6 + - - +
140A LEU* 3.6 33.4 + - + +
143A ARG* 4.4 0.9 - - - -
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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