Contacts of the helix formed by residues 103 - 124 (chain B) in PDB entry 2E9V
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 PRO 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B MET* 1.3 85.9 - - + +
104B GLU* 1.3 59.9 + - - +
105B PRO* 3.1 11.9 - - + -
106B ASP* 2.8 47.0 + - - +
107B ALA 3.1 8.7 + - - -
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Residues in contact with GLU 104 (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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102B MET 3.0 6.3 + - - -
103B PRO* 1.3 70.8 - - - +
105B PRO* 1.3 63.4 - - + +
107B ALA* 3.3 1.6 + - - +
108B GLN* 2.9 26.7 + - - +
202B LEU* 4.0 22.1 - - + +
235B ASP* 3.9 21.8 + - - +
238B PRO* 4.0 11.0 - - - +
264B TRP* 2.7 37.8 + - + +
267B LYS* 5.0 5.2 + - - -
269B LEU* 3.5 16.1 - - + +
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Residues in contact with PRO 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PRO* 3.1 14.1 - - + -
104B GLU* 1.3 95.7 - - + +
106B ASP* 1.3 62.4 + - - +
108B GLN* 3.5 4.6 + - + +
109B ARG* 3.2 21.7 + - - +
269B LEU* 3.9 43.1 - - + +
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B MET* 4.0 12.6 - - + -
103B PRO* 2.8 39.9 + - + +
105B PRO* 1.3 78.5 - - - +
107B ALA* 1.3 61.6 + - - +
108B GLN 3.2 0.2 - - - -
109B ARG* 3.3 10.4 + - - +
110B PHE* 3.0 43.0 + - + -
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Residues in contact with ALA 107 (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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102B MET* 3.6 23.8 - - + -
103B PRO 3.1 6.0 + - - +
104B GLU 3.3 6.9 + - - +
106B ASP* 1.3 77.0 - - - +
108B GLN* 1.3 58.8 + - - +
111B PHE* 3.0 28.9 + - - +
198B LEU* 4.7 2.0 - - + +
201B MET* 3.8 29.9 - - + +
202B LEU* 3.8 23.1 - - + -
264B TRP* 4.3 2.3 - - + -
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Residues in contact with GLN 108 (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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104B GLU 2.9 17.2 + - - +
105B PRO 3.7 6.6 - - - +
106B ASP 3.2 0.2 - - - -
107B ALA* 1.3 76.1 - - - +
109B ARG* 1.3 62.5 + - - +
111B PHE* 3.4 2.8 + - - +
112B HIS* 3.1 50.0 + - + +
264B TRP* 2.7 54.2 + - + +
265B TYR 3.2 10.9 + - - -
267B LYS 2.8 26.4 + - - +
269B LEU* 3.7 23.5 + - + +
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Residues in contact with ARG 109 (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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105B PRO 3.2 10.7 + - - +
106B ASP* 3.6 13.7 - - - +
107B ALA 3.3 0.2 - - - -
108B GLN* 1.3 76.8 + - - +
110B PHE* 1.3 77.9 + - - +
112B HIS* 3.3 15.6 + - + +
113B GLN* 3.2 41.4 + - - +
141B ARG 3.7 8.7 + - - -
142B ASP* 3.2 25.8 + - - +
143B ASN* 2.5 28.5 + - - -
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Residues in contact with PHE 110 (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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92B LEU* 4.0 8.1 - - + -
95B ARG* 5.1 8.3 - - + -
102B MET* 3.5 31.9 - - + -
106B ASP* 3.0 32.7 + - + +
107B ALA 4.0 0.4 - - - +
108B GLN 3.4 0.2 - - - -
109B ARG* 1.3 84.4 - - - +
111B PHE* 1.3 52.5 + - - +
113B GLN* 3.3 17.7 + - - +
114B LEU* 2.8 34.2 + - - +
138B LEU* 3.8 35.7 - - + -
142B ASP* 3.5 26.0 - - + -
144B LEU* 3.8 16.0 - - + +
201B MET* 3.8 17.0 - - - -
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Residues in contact with PHE 111 (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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107B ALA 3.0 18.7 + - - +
108B GLN* 3.6 8.1 - - - +
109B ARG 3.2 0.2 - - - -
110B PHE* 1.3 75.1 - - - +
112B HIS* 1.3 54.5 + - - +
114B LEU* 3.5 10.3 - - + +
115B MET* 2.8 66.9 + - + +
194B CYS* 4.0 19.5 - - + -
198B LEU* 3.9 29.8 - - + -
201B MET* 4.4 8.9 - - + +
241B LEU* 3.9 17.7 - - + -
245B ILE* 4.3 13.5 - - + -
259B ILE* 3.9 4.5 - - + -
264B TRP* 3.8 13.9 - + + -
265B TYR* 3.4 40.8 - + - -
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Residues in contact with HIS 112 (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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108B GLN* 3.1 44.9 + - + +
109B ARG* 3.5 12.1 - - + +
111B PHE* 1.3 72.9 - - - +
113B GLN* 1.3 64.5 + - + +
115B MET* 3.2 2.4 + - - +
116B ALA* 2.8 30.9 + - - +
265B TYR* 2.9 69.3 + + - +
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Residues in contact with GLN 113 (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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66B ASN* 3.5 30.0 - - - +
109B ARG* 3.2 39.1 + - + +
110B PHE* 3.6 13.2 - - - +
112B HIS* 1.3 81.3 - - + +
114B LEU* 1.3 62.4 + - - +
116B ALA* 3.3 4.8 + - - +
117B GLY* 3.0 19.1 + - - -
143B ASN* 3.0 23.7 - - - +
144B LEU* 3.1 38.0 - - + +
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Residues in contact with LEU 114 (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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110B PHE 2.8 18.1 + - - +
111B PHE* 3.5 12.3 - - + +
113B GLN* 1.3 75.9 - - - +
115B MET* 1.3 68.9 + - + +
117B GLY* 3.3 2.3 + - - -
118B VAL* 3.0 46.3 + - + +
131B ILE* 4.4 4.0 - - + -
136B LEU* 3.8 29.6 - - + -
144B LEU* 3.9 13.6 - - + +
146B ILE* 3.8 7.7 - - + +
194B CYS* 3.7 29.8 - - + +
197B VAL* 4.2 26.0 - - + -
201B MET* 5.5 0.9 - - + -
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Residues in contact with MET 115 (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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111B PHE* 2.8 49.8 + - + +
112B HIS 3.2 0.4 + - - +
114B LEU* 1.3 78.9 - - + +
116B ALA* 1.3 56.0 + - - +
118B VAL* 3.4 6.8 + - + +
119B VAL* 2.8 40.7 + - + +
191B VAL* 5.8 2.2 - - - -
194B CYS* 3.1 45.5 - - + -
256B ILE* 4.5 24.2 - - + -
259B ILE* 4.4 19.7 - - + -
260B LYS* 6.1 2.0 - - + -
265B TYR* 3.4 22.7 - - + +
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Residues in contact with ALA 116 (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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64B HIS* 4.1 8.1 + - + +
66B ASN* 3.3 21.8 - - - +
112B HIS 2.8 17.7 + - - +
113B GLN* 3.5 2.2 - - - +
115B MET* 1.3 75.3 - - - +
117B GLY* 1.3 61.4 + - - +
119B VAL* 3.4 7.7 + - - +
120B TYR* 3.1 22.5 + - - +
265B TYR* 5.0 0.2 + - - -
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Residues in contact with GLY 117 (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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64B HIS* 4.4 1.8 - - - -
66B ASN* 3.7 23.7 - - - +
67B VAL* 4.6 1.7 - - - +
113B GLN 3.0 11.1 + - - -
114B LEU 3.7 2.7 - - - -
116B ALA* 1.3 78.3 - - - +
118B VAL* 1.3 55.0 + - - +
120B TYR* 3.2 9.7 - - - +
121B LEU* 3.1 30.1 + - - +
146B ILE* 4.0 13.5 - - - -
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Residues in contact with VAL 118 (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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114B LEU* 3.0 35.2 + - + +
115B MET* 3.9 6.1 - - + +
117B GLY* 1.3 74.1 - - - +
119B VAL* 1.3 67.6 + - - +
121B LEU* 3.7 8.6 - - + +
122B HIS* 2.9 55.7 + - + +
131B ILE* 4.2 8.3 - - + -
146B ILE* 3.8 9.2 - - + -
190B ASP* 4.3 9.2 - - + -
191B VAL* 5.7 0.2 - - + -
194B CYS* 3.9 15.5 - - - -
256B ILE* 3.9 12.1 - - + -
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Residues in contact with VAL 119 (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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115B MET 2.8 26.6 + - - +
116B ALA* 3.7 7.9 - - - +
118B VAL* 1.3 75.2 - - - +
120B TYR* 1.3 53.4 + - - +
122B HIS* 3.7 3.2 - - - +
123B GLY* 2.7 34.0 + - - -
256B ILE* 3.3 36.8 - - + -
260B LYS* 3.6 19.7 - - - +
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Residues in contact with TYR 120 (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 ARG 5.1 4.7 + - - -
61B MET 3.8 5.5 + - - -
62B LEU* 4.7 2.9 - - + -
63B ASN* 3.1 33.7 + - - +
64B HIS* 3.3 49.6 - + + -
67B VAL* 4.0 8.7 - - + -
116B ALA 3.1 11.8 + - - +
117B GLY 3.2 8.1 - - - +
119B VAL* 1.3 80.2 - - - +
121B LEU* 1.3 77.2 + - + +
123B GLY* 3.0 11.9 + - - -
124B ILE* 3.1 52.6 + - + +
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Residues in contact with LEU 121 (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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62B LEU* 4.1 17.7 - - + -
67B VAL* 4.4 7.0 - - + -
117B GLY 3.1 15.5 + - - +
118B VAL* 3.3 12.1 + - + +
120B TYR* 1.3 90.7 - - + +
122B HIS* 1.3 63.1 + - + +
124B ILE* 3.0 12.4 + - - +
126B ILE* 2.7 49.4 + - + +
128B HIS* 4.4 19.7 - - + +
131B ILE* 6.1 0.2 - - + -
146B ILE* 4.4 16.8 - - + -
149B PHE* 3.9 33.4 - - + -
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Residues in contact with HIS 122 (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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118B VAL* 2.9 38.4 + - + +
119B VAL* 4.0 3.1 - - - +
121B LEU* 1.3 77.1 - - + +
123B GLY* 1.3 62.9 + - - +
125B GLY* 3.2 9.4 + - - -
126B ILE 3.3 16.4 - - - -
127B THR* 4.7 0.2 - - - -
155B PHE* 4.0 13.5 - + - -
156B ARG* 3.3 20.9 + - - -
187B GLU* 3.5 58.1 + - + +
190B ASP* 2.6 30.1 + - + +
191B VAL 4.8 0.7 - - - -
256B ILE* 4.0 14.4 - - + +
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Residues in contact with GLY 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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140A GLU 5.6 0.7 - - - +
119B VAL* 2.7 16.4 + - - -
120B TYR* 3.3 7.0 - - - -
121B LEU 3.0 0.4 - - - -
122B HIS* 1.3 78.9 - - - +
124B ILE* 1.3 59.4 + - - +
125B GLY 3.4 1.8 + - - -
156B ARG* 5.7 1.2 - - - -
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Residues in contact with ILE 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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140A GLU* 4.4 8.5 - - - +
141A ARG* 2.6 84.2 + - + +
61B MET 4.4 4.0 - - - +
62B LEU* 4.2 4.9 - - + -
120B TYR* 3.1 54.0 + - + +
121B LEU* 3.0 16.1 + - - +
123B GLY* 1.3 81.0 - - - +
125B GLY* 1.3 50.8 + - - +
126B ILE* 3.5 14.1 - - + -
156B ARG 4.6 1.0 - - - +
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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