Contacts of the helix formed by residues 115 - 136 (chain A) in PDB entry 2E8A
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 TYR 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ASP* 3.1 23.1 + - - -
100A LYS* 4.1 29.3 - - + +
101A PRO 3.9 7.0 - - - -
102A LYS* 3.6 38.9 + - + -
114A PHE* 1.3 76.8 - - - +
116A PRO* 1.3 73.7 - - + +
117A GLU* 3.5 27.8 - - - +
118A GLU* 2.8 43.4 + - + +
119A ILE* 3.2 11.3 + - - +
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Residues in contact with PRO 116 (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 ALA* 4.1 8.0 - - + +
73A LEU* 3.7 33.2 - - + +
74A ILE* 3.7 30.5 - - + +
75A GLY 5.3 0.9 - - - +
101A PRO* 3.2 30.7 - - + +
102A LYS* 5.5 0.2 - - - -
103A VAL* 5.8 2.2 - - + -
114A PHE 4.4 0.7 - - - +
115A TYR* 1.3 87.6 - - + +
117A GLU* 1.3 64.1 + - - +
119A ILE* 3.1 10.8 + - + +
120A SER* 2.9 30.8 + - - -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.0 11.1 - - + +
75A GLY 5.3 1.4 + - - -
100A LYS* 4.8 11.8 + - - +
115A TYR* 3.5 28.4 - - + +
116A PRO* 1.3 83.2 - - - +
118A GLU* 1.3 61.7 + - + +
120A SER 3.8 0.2 - - - -
121A SER* 2.8 28.9 + - - -
157A ALA* 3.4 38.0 - - - +
160A ASP* 4.5 15.0 - - + +
161A ALA* 3.5 12.2 - - - +
164A ILE* 4.6 6.9 - - + +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LYS* 4.5 1.7 + - - -
113A ALA 4.4 2.1 - - - +
114A PHE* 3.3 25.9 - - + -
115A TYR* 2.8 51.7 + - + +
117A GLU* 1.3 80.2 - - + +
119A ILE* 1.3 64.8 + - - +
121A SER* 2.6 25.0 + - - -
122A MET* 3.1 16.4 + - + +
164A ILE* 5.4 9.2 - - + -
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Residues in contact with ILE 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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40A SER 5.9 2.2 - - - +
42A VAL* 3.8 16.7 - - + +
44A PHE* 4.0 20.0 - - + -
67A VAL* 4.1 29.4 - - + +
68A PHE* 5.9 0.4 - - - -
70A ALA* 3.7 22.0 - - + -
103A VAL* 4.8 7.9 - - + -
114A PHE* 3.8 18.8 - - + +
115A TYR 3.6 12.3 - - - +
116A PRO* 3.1 8.4 + - + +
118A GLU* 1.3 77.2 - - - +
120A SER* 1.3 63.1 + - - +
122A MET* 3.1 38.8 + - + +
123A VAL* 3.4 11.1 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.0 22.5 - - - +
70A ALA* 3.8 17.4 - - - +
71A LYS* 4.7 2.6 + - - +
74A ILE* 3.8 12.5 - - - +
116A PRO 2.9 15.5 + - - -
119A ILE* 1.3 77.4 - - - +
121A SER* 1.3 57.8 + - - +
123A VAL* 3.1 10.7 + - - +
124A LEU* 2.8 31.0 + - - +
161A ALA* 4.0 17.5 - - - -
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Residues in contact with SER 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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117A GLU 2.8 18.4 + - - -
118A GLU* 2.6 21.1 + - - +
120A SER* 1.3 75.2 - - - +
122A MET* 1.3 60.6 + - - +
124A LEU* 4.3 1.3 - - - -
125A THR* 2.8 33.9 + - - -
161A ALA* 3.2 26.4 - - - +
164A ILE* 3.4 29.0 - - - +
165A ALA* 3.6 3.9 - - - +
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Residues in contact with MET 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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42A VAL* 3.7 28.0 - - + -
44A PHE* 3.9 16.2 - - + -
49A ARG* 5.0 11.0 - - - +
51A ILE* 3.6 25.4 - - + +
114A PHE* 4.4 14.1 - - + -
118A GLU* 3.1 23.6 - - + +
119A ILE* 3.1 40.7 + - + +
121A SER* 1.3 79.2 + - - +
123A VAL* 1.3 65.7 + - - +
125A THR* 3.2 8.7 + - - -
126A LYS 3.0 17.7 + - - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 12.6 - - + -
16A SER* 3.6 30.7 - - - +
38A THR* 5.9 0.9 - - + -
39A PRO 4.8 4.0 - - - +
40A SER* 4.0 32.1 - - - +
41A TYR 4.3 2.7 - - - +
42A VAL* 4.0 16.2 - - + -
51A ILE* 3.9 8.7 - - + -
119A ILE* 3.8 13.2 - - + +
120A SER* 3.1 11.5 + - - +
122A MET* 1.3 76.4 - - - +
124A LEU* 1.3 62.7 + - - +
126A LYS* 3.1 5.6 + - + +
127A MET* 3.0 25.3 + - + +
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Residues in contact with LEU 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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9A ILE* 3.7 38.5 - - + +
11A LEU* 4.0 29.4 - - + -
120A SER 2.8 14.1 + - - +
121A SER 3.8 4.0 - - - +
123A VAL* 1.3 74.3 - - - +
125A THR* 1.3 60.5 + - - +
127A MET* 3.2 5.7 + - + +
128A LYS* 2.9 29.5 + - - +
144A ILE* 3.9 14.6 - - + -
158A THR 4.4 0.7 - - - +
161A ALA* 3.6 18.2 - - + -
162A GLY* 3.5 33.7 - - - +
165A ALA* 3.9 11.1 - - + +
167A LEU* 4.8 4.7 - - + +
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Residues in contact with THR 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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51A ILE* 5.9 4.9 - - + -
121A SER 2.8 23.7 + - - -
122A MET* 3.4 10.2 - - - +
123A VAL 3.2 0.2 - - - -
124A LEU* 1.3 78.5 - - - +
126A LYS* 1.3 56.8 + - - +
128A LYS* 3.2 15.9 + - - +
129A GLU* 2.9 53.8 + - + +
165A ALA* 3.5 22.3 + - - +
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Residues in contact with LYS 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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31A ASN* 5.3 4.3 - - - +
32A ASP* 2.9 26.7 + - - -
38A THR* 4.4 20.4 - - + -
51A ILE* 3.7 44.1 + - + +
52A GLY* 5.6 0.2 - - - -
53A ASP 6.0 0.9 - - - +
122A MET 3.0 6.4 + - - +
123A VAL* 3.4 9.2 - - + +
125A THR* 1.3 77.7 - - - +
127A MET* 1.3 59.0 + - - +
129A GLU* 3.1 22.0 + - + +
130A ILE* 2.9 53.7 + - + +
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Residues in contact with MET 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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7A ILE* 5.1 0.9 - - - -
9A ILE* 4.2 28.7 - - + -
16A SER* 3.7 35.9 - - - +
17A CYS* 3.7 2.5 - - - +
18A VAL* 3.7 42.2 - - + +
29A ILE 5.8 0.9 - - - +
36A ARG 5.7 0.7 - - - +
37A THR* 5.6 0.9 - - - -
38A THR* 3.9 33.4 - - - +
123A VAL* 3.0 23.6 + - + +
124A LEU* 3.6 7.6 - - - +
126A LYS* 1.3 78.4 - - - +
128A LYS* 1.3 61.3 + - - +
130A ILE* 3.4 10.0 + - + +
131A ALA* 3.2 22.0 + - - +
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Residues in contact with LYS 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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7A ILE* 4.4 10.3 - - - +
9A ILE* 5.0 0.2 - - - +
124A LEU 2.9 14.0 + - - +
125A THR* 3.4 20.4 - - - +
127A MET* 1.3 75.2 - - - +
129A GLU* 1.3 61.5 + - - +
131A ALA* 3.2 4.0 + - - +
132A GLU* 2.9 60.2 + - - +
139A VAL* 3.8 14.6 - - + +
165A ALA 2.7 29.9 + - - +
166A GLY* 4.2 8.1 + - - +
167A LEU* 3.7 31.0 - - + -
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Residues in contact with GLU 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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51A ILE* 6.1 0.5 - - - +
125A THR* 2.9 36.5 + - + +
126A LYS* 3.1 26.5 + - + +
128A LYS* 1.3 79.9 - - - +
130A ILE* 1.3 58.4 + - + +
132A GLU* 3.2 15.4 + - - +
133A ALA* 2.8 32.2 + - - +
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Residues in contact with ILE 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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18A VAL* 4.0 7.9 - - + -
29A ILE* 3.6 25.3 - - + +
30A ALA 3.4 23.3 - - - +
31A ASN* 3.3 32.8 - - + -
32A ASP* 4.1 8.1 - - - +
38A THR* 4.9 0.9 - - - +
126A LYS* 2.9 51.3 + - + +
127A MET* 3.4 19.1 - - + +
129A GLU* 1.3 78.1 - - + +
131A ALA* 1.3 62.8 + - - +
133A ALA* 3.4 6.6 + - - +
134A TYR 3.3 14.7 + - - -
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Residues in contact with ALA 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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7A ILE* 3.9 25.8 - - + -
18A VAL* 4.2 5.2 - - + -
29A ILE* 3.6 26.9 - - + -
127A MET 3.2 10.4 + - - +
128A LYS 3.6 7.0 - - - +
130A ILE* 1.3 78.1 - - - +
132A GLU* 1.3 59.5 + - - +
134A TYR* 3.2 2.4 + - - +
135A LEU* 2.9 36.9 + - + +
139A VAL* 4.2 6.5 - - + -
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Residues in contact with GLU 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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128A LYS* 2.9 42.1 + - - +
129A GLU* 3.2 17.6 + - - +
131A ALA* 1.3 76.5 - - - +
133A ALA* 1.3 56.2 + - - +
136A GLY* 2.8 30.5 + - - -
137A TYR 3.5 25.7 + - - +
138A PRO* 3.4 10.7 - - + +
139A VAL* 2.9 39.1 + - + +
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Residues in contact with ALA 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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32A ASP* 5.7 5.2 - - - +
129A GLU 2.8 16.1 + - - +
130A ILE* 3.6 9.0 - - - +
131A ALA 3.2 0.2 - - - -
132A GLU* 1.3 77.1 - - - +
134A TYR* 1.3 62.5 + - - +
136A GLY* 4.0 4.9 + - - -
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Residues in contact with TYR 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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20A VAL* 4.7 1.6 - - + -
22A GLN* 4.3 13.1 + - - -
25A LYS* 5.6 0.2 + - - -
27A GLU* 2.3 43.6 + - + +
29A ILE* 3.5 41.5 - - + -
130A ILE 3.3 1.2 + - - +
131A ALA 3.2 5.0 + - - +
133A ALA* 1.3 82.9 - - - +
135A LEU* 1.3 72.3 + - + +
136A GLY* 3.6 0.5 + - - -
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Residues in contact with LEU 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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5A ALA* 4.8 2.2 - - + +
7A ILE* 4.7 1.8 - - + -
20A VAL* 4.2 26.9 - - + -
22A GLN* 3.7 37.4 - - - +
131A ALA* 2.9 26.1 + - + +
134A TYR* 1.3 89.3 - - + +
136A GLY* 1.3 59.9 + - - +
137A TYR* 3.3 45.4 - - + +
139A VAL* 3.9 24.5 - - + -
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Residues in contact with GLY 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 GLU 2.8 12.8 + - - -
133A ALA 4.0 4.7 + - - -
134A TYR 3.4 2.8 - - - -
135A LEU* 1.3 76.8 - - - +
137A TYR* 1.3 62.1 + - - +
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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