Contacts of the helix formed by residues 119 - 140 (chain B) in PDB entry 3E6D
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 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 2.7 39.2 + - - +
116A PHE* 5.8 2.6 - - + +
117A ARG* 3.0 49.8 + - - +
115B PHE 3.3 10.3 + - - +
116B ARG 5.4 0.2 - - - -
117B THR 4.3 0.2 - - - -
118B ASP* 1.3 73.2 + - - +
120B ASP* 1.3 63.4 + - - +
122B ILE* 3.1 37.9 + - + +
123B PHE* 3.8 6.7 - - + -
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Residues in contact with ASP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 2.9 35.8 + - - -
118B ASP* 3.1 15.2 + - - +
119B GLU* 1.3 77.1 - - - +
121B MET* 1.3 56.9 + - - +
122B ILE 3.1 0.2 - - - -
123B PHE* 3.0 11.3 + - - +
124B GLU* 2.9 31.8 + - + +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 4.8 3.8 - - + -
23B LYS* 4.0 14.6 - - + -
24B LEU* 3.4 44.4 - - + +
27B TYR* 3.6 33.9 - - + -
114B VAL* 4.0 17.5 - - + -
115B PHE* 3.6 5.9 - - + -
118B ASP* 3.1 23.9 + - + +
119B GLU 3.1 0.8 - - - -
120B ASP* 1.3 75.3 - - - +
122B ILE* 1.3 66.4 + - - +
124B GLU* 3.8 25.0 - - + +
125B ILE* 3.2 30.7 + - + +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PHE* 3.8 36.6 - - + -
123A ILE* 3.4 31.9 - - + -
115B PHE* 3.5 38.5 - - + +
119B GLU* 3.1 31.7 + - + +
121B MET* 1.3 79.6 - - - +
123B PHE* 1.3 62.2 + - + +
125B ILE* 3.4 2.8 + - - +
126B PHE* 3.1 44.2 + - + -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.0 9.4 - - + -
88A TYR* 3.1 27.9 + - - +
109A GLU* 3.7 23.6 - - + +
112A LEU* 4.0 21.8 - - + -
113A ARG* 3.6 53.8 - - + +
116A PHE* 3.9 25.6 - + - -
119B GLU* 3.8 16.8 - - + -
120B ASP* 3.0 9.2 + - + +
122B ILE* 1.3 81.3 - - + +
124B GLU* 1.3 59.2 + - - +
126B PHE* 3.6 10.1 - + - +
127B LYS* 3.0 30.5 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.5 34.0 - - + +
23B LYS* 4.3 22.5 + - + +
120B ASP* 2.9 20.5 + - + +
121B MET* 3.8 27.8 - - + +
122B ILE 3.3 0.2 - - - -
123B PHE* 1.3 77.4 - - - +
125B ILE* 1.3 61.3 + - - +
127B LYS* 3.8 18.3 + - - +
128B ASN* 3.2 17.2 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 3.4 38.4 - - + -
21B ILE* 4.7 6.3 - - + -
24B LEU* 5.0 11.7 - - + -
52B MET* 6.2 0.4 - - + -
82B LEU* 4.6 17.0 - - + -
111B LEU* 4.4 19.7 - - + -
114B VAL* 6.3 0.2 - - + -
115B PHE* 3.8 30.7 - - + -
121B MET* 3.2 19.5 + - + +
122B ILE 3.8 4.0 - - - +
124B GLU* 1.3 74.2 - - - +
126B PHE* 1.3 66.9 + - + +
128B ASN* 3.4 5.5 + - - +
129B TYR* 3.1 28.4 + - + +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 6.4 0.9 - - + -
87A LEU* 4.5 10.8 - - + -
88A TYR* 5.2 0.2 - - + -
112A LEU* 4.8 4.5 - - + -
116A PHE* 3.6 35.4 - + - -
123A ILE* 4.0 17.0 - - + -
126A ILE* 3.4 37.7 - - + -
127A PHE* 4.5 17.5 - + + -
130A TYR* 5.6 1.2 - + - -
122B ILE* 3.1 25.8 + - + +
123B PHE* 3.6 26.7 - + + +
124B GLU 3.3 0.4 - - - -
125B ILE* 1.3 78.1 - - + +
127B LYS* 1.3 57.0 + - - +
129B TYR* 3.0 6.4 + - - +
130B LEU* 2.8 46.6 + - + +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.6 40.8 - - + -
89A PRO 5.9 2.2 - - - +
123B PHE 3.0 18.2 + - - +
124B GLU* 3.8 20.3 + - - +
126B PHE* 1.3 74.8 - - - +
128B ASN* 1.3 64.5 + - - +
130B LEU* 3.7 5.1 - - - +
131B THR* 2.9 37.6 + - - +
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Residues in contact with ASN 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 2.9 37.2 + - - +
20B PRO 4.1 7.9 + - - -
21B ILE* 4.2 19.4 - - + +
82B LEU* 4.6 3.1 - - + +
124B GLU 3.2 12.0 + - - +
125B ILE* 3.5 12.3 - - + +
127B LYS* 1.3 80.8 - - - +
129B TYR* 1.3 67.0 + - + +
131B THR* 3.5 5.5 + - - -
132B LYS* 2.8 57.1 + - - +
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Residues in contact with TYR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.4 30.7 - + + -
130A TYR* 4.0 22.9 - - + -
131A LEU* 3.5 26.5 - - + +
134A VAL* 3.7 29.4 - - + -
52B MET* 3.1 22.2 - - + +
82B LEU* 3.6 25.1 + - + -
83B ILE* 4.7 0.7 - - - -
84B GLY 4.4 3.3 + - - -
125B ILE* 3.1 13.3 + - + +
126B PHE* 3.0 5.9 + - - +
128B ASN* 1.3 92.7 - - - +
130B LEU* 1.3 60.5 + - - +
132B LYS* 3.6 18.5 + - + +
133B VAL* 2.9 35.5 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A MET* 4.2 9.2 - - + -
85A GLY 3.7 19.7 - - - +
86A LYS* 4.2 9.4 - - + -
87A LEU* 4.2 22.2 - - + +
88A TYR* 4.6 10.5 - - + +
90A THR* 4.7 11.1 - - + +
130A TYR* 3.5 38.3 - - + +
126B PHE* 2.8 34.2 + - + +
127B LYS* 3.7 9.0 - - - +
129B TYR* 1.3 71.5 - - - +
131B THR* 1.3 63.0 + - - +
133B VAL* 3.8 2.0 - - - +
134B ALA* 3.0 26.1 + - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PRO 4.7 9.5 + - - -
90A THR* 5.1 13.2 - - - +
19B PHE* 3.9 22.4 - - + -
127B LYS* 2.9 32.9 + - - +
128B ASN* 3.6 6.9 - - - -
130B LEU* 1.3 78.0 - - - +
132B LYS* 1.3 61.1 + - - +
134B ALA* 3.4 6.4 + - - +
135B TYR* 3.1 22.9 + - + +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.1 14.4 - - + -
18B PHE 5.0 1.6 - - - -
19B PHE* 3.7 46.6 - - + +
75B TYR* 6.1 3.4 - - - -
82B LEU* 2.9 33.9 + - - +
128B ASN* 2.8 43.6 + - - +
129B TYR* 3.6 28.9 - - + +
131B THR* 1.3 74.2 - - - +
133B VAL* 1.3 65.2 + - - +
135B TYR* 3.2 4.0 + - - +
136B TYR* 3.2 34.9 + - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 5.0 10.5 - - + +
130A TYR* 3.7 24.0 - - + +
133A LYS* 4.0 20.9 - - + +
134A VAL* 3.5 22.9 - - + +
137A TYR* 4.1 23.4 - - + -
129B TYR 2.9 21.2 + - - +
130B LEU* 3.8 4.5 - - - +
132B LYS* 1.3 74.8 - - - +
134B ALA* 1.3 58.2 + - - +
136B TYR* 3.4 5.2 + - - +
137B ALA* 2.9 32.3 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TYR* 5.7 2.5 - - - -
90A THR* 3.8 33.2 - - + +
92A ASN* 3.0 32.4 + - - +
130B LEU 3.0 18.1 + - - +
131B THR* 3.7 4.7 - - - +
132B LYS 3.2 0.2 - - - -
133B VAL* 1.3 77.9 - - - +
135B TYR* 1.3 62.5 + - - +
137B ALA* 4.5 3.6 - - - -
138B ARG* 3.1 13.5 + - - +
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.8 31.0 - + + -
131B THR* 3.1 13.8 + - + +
132B LYS 3.2 7.8 + - - +
134B ALA* 1.3 75.7 - - - +
136B TYR* 1.3 81.1 + + - +
138B ARG* 3.1 13.3 + - - +
139B GLN* 2.7 57.0 + - + +
190B HIS* 5.8 0.9 - - - -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.4 21.8 - - + -
137A TYR* 3.3 29.4 - - + +
138A ALA* 4.1 21.1 - - + -
141A VAL* 4.1 26.1 - - + +
19B PHE* 4.8 16.5 - + - -
74B LEU 5.6 2.9 - - - -
75B TYR* 3.1 34.6 - + + +
132B LYS* 3.2 29.3 + - + +
133B VAL* 4.0 2.5 - - - +
135B TYR* 1.3 92.4 - + - +
137B ALA* 1.3 66.4 + - - +
139B GLN* 3.1 10.1 + - + +
140B VAL* 3.0 24.3 + - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.2 14.3 - - + +
76A TYR* 3.6 34.5 - - + +
92A ASN* 5.1 0.9 - - - +
137A TYR* 4.2 19.1 - - + -
133B VAL* 2.9 20.1 + - + +
134B ALA* 3.9 5.6 - - - +
136B TYR* 1.3 75.3 - - - +
138B ARG* 1.3 59.4 + - - +
140B VAL* 3.0 28.3 + - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.6 19.4 - - + +
66A ILE 5.2 0.8 + - - -
67A PHE* 3.6 40.7 - - + +
68A GLU* 2.7 41.8 + - - -
75A LEU* 4.8 5.6 - - - -
91A GLY 3.7 13.4 + - - -
92A ASN* 3.2 30.6 + - - +
93A ASN 5.1 1.4 - - - +
134B ALA 3.1 19.9 + - - +
135B TYR* 3.1 10.5 + - - +
137B ALA* 1.3 77.4 - - - +
139B GLN* 1.3 72.0 + - - +
140B VAL 3.4 6.6 + - - +
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.4 19.7 - - + -
135B TYR* 2.7 68.1 + - + +
136B TYR* 3.1 11.6 + - + +
138B ARG* 1.3 92.6 - - - +
140B VAL* 1.3 61.6 + - - +
190B HIS* 3.0 48.3 + - + +
191B HIS* 4.7 2.3 - - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 6.2 0.3 - - - +
67A PHE* 5.7 1.7 - - - -
73A LYS* 6.2 0.3 - - - +
74A LEU 4.9 9.8 - - - +
75A LEU* 5.5 10.4 - - - +
137A TYR* 4.7 15.9 - - + -
140A GLN* 4.6 16.6 - - + +
141A VAL* 3.7 28.5 - - + -
136B TYR 3.0 5.9 + - - +
137B ALA* 3.0 23.0 + - - +
138B ARG* 3.5 6.4 - - - +
139B GLN* 1.3 82.4 - - - +
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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
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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