Contacts of the helix formed by residues 108 - 129 (chain A) in PDB entry 1EC8
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 THR 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LYS* 3.9 24.3 - - + +
61A ILE* 3.9 22.2 - - + +
64A THR* 3.7 26.7 - - - +
94A ARG* 4.3 20.7 + - + -
95A ASP* 2.9 14.9 + - - +
106A LEU 4.4 4.2 + - - -
107A ARG* 1.3 76.1 + - - +
109A THR* 1.3 60.7 + - - +
110A ILE 3.4 1.8 - - - -
111A HIS* 3.2 6.9 + - - +
112A VAL* 2.9 29.3 + - - +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 4.6 0.3 - - - +
87A VAL* 4.5 1.3 - - + +
88A ARG* 4.0 33.4 - - + +
91A PHE* 2.6 43.8 + - + +
92A ALA* 4.3 3.8 - - - +
94A ARG* 3.2 13.0 - - - +
95A ASP* 2.7 19.1 + - - -
108A THR* 1.3 73.3 - - - +
110A ILE* 1.3 52.1 + - - +
112A VAL* 3.1 10.8 + - + +
113A VAL* 2.8 41.4 + - + +
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Residues in contact with ILE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 3.7 32.5 - - + +
95A ASP* 3.4 6.4 + - - +
107A ARG* 3.8 41.5 - - + +
109A THR* 1.3 74.0 - - - +
111A HIS* 1.3 70.7 + - - +
113A VAL* 3.3 8.7 + - + +
114A THR* 3.0 27.0 + - - -
315A HIS 4.3 0.9 - - - -
316A PHE* 3.5 39.0 - - + +
317A TRP* 4.8 2.0 - - - +
318A THR* 3.6 26.5 - - + -
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Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.3 14.5 - - + +
56A PRO* 3.4 39.6 - - + +
61A ILE* 3.9 15.4 - - + +
105A ASP* 3.7 32.4 - - + +
107A ARG* 2.8 36.8 + - + -
108A THR 3.2 6.1 + - - +
110A ILE* 1.3 78.1 - - + +
112A VAL* 1.3 64.9 + - - +
114A THR* 3.1 1.6 + - - -
115A GLY* 3.0 20.1 + - - -
315A HIS* 3.1 29.4 - - + +
316A PHE* 3.8 18.9 - - + +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.9 20.2 - - + +
64A THR* 3.8 35.2 - - + +
65A LEU* 3.8 33.1 - - + +
68A ALA* 4.8 0.9 - - + -
87A VAL* 4.3 10.3 - - + -
91A PHE* 5.6 0.2 - - + -
108A THR* 2.9 23.5 + - + +
109A THR* 3.1 10.1 + - + +
111A HIS* 1.3 78.5 - - - +
113A VAL* 1.3 63.4 + - - +
115A GLY* 3.3 1.3 + - - +
116A ILE* 3.1 34.8 + - + +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.5 30.9 - - + +
87A VAL* 3.7 26.9 - - + -
88A ARG* 4.0 26.0 - - + +
109A THR* 2.8 24.0 + - + +
110A ILE* 3.6 9.9 - - + +
112A VAL* 1.3 78.1 - - - +
114A THR* 1.4 51.2 + - - +
116A ILE* 3.2 4.8 + - - -
117A GLU* 2.7 34.0 + - + +
318A THR* 4.0 18.6 - - + -
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Residues in contact with THR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 4.2 3.8 - - + -
110A ILE 3.0 15.8 + - - -
111A HIS 3.1 6.9 + - - -
113A VAL* 1.4 76.1 - - - +
115A GLY* 1.4 51.8 + - - +
117A GLU* 2.9 19.0 + - - +
118A ALA* 2.6 35.0 + - - +
314A PRO 3.4 18.8 - - - +
315A HIS* 3.2 20.0 + - - -
318A THR* 3.2 16.7 + - - -
319A MET* 4.2 4.3 - - + -
350A MET* 4.0 23.1 - - + -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.9 25.7 - - - +
53A GLY* 4.0 4.8 - - - -
54A GLU 5.0 0.2 - - - -
55A ILE* 3.5 19.8 - - - +
65A LEU* 5.1 0.2 - - - -
111A HIS 3.0 11.4 + - - -
112A VAL 3.7 2.7 - - - -
114A THR* 1.4 73.1 - - - +
116A ILE* 1.3 64.4 + - - +
118A ALA* 3.4 5.9 + - - +
119A ALA* 3.2 22.5 + - - +
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Residues in contact with ILE 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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13A MET* 3.9 12.1 - - + -
41A VAL* 4.5 1.3 - - + +
43A ILE* 4.2 13.0 - - + -
65A LEU* 3.8 13.9 - - + -
68A ALA* 4.0 12.1 - - + -
72A VAL* 4.2 15.3 - - + -
83A VAL* 4.7 5.6 - - + -
84A LEU* 3.9 13.7 - - + -
87A VAL* 3.9 35.4 - - + -
112A VAL* 3.1 24.1 + - + +
113A VAL* 3.6 5.6 - - - +
115A GLY* 1.3 75.6 - - - +
117A GLU* 1.3 65.6 + - - +
119A ALA* 3.2 2.3 + - - +
120A MET* 2.9 41.8 + - + +
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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
----------------------------------------------------------
84A LEU* 3.6 21.7 - - + +
113A VAL* 2.7 19.6 + - + +
114A THR* 2.9 8.9 + - - +
116A ILE* 1.3 73.6 - - - +
118A ALA* 1.3 64.2 + - - +
120A MET* 3.3 3.0 + - - +
121A LEU* 2.8 40.6 + - + +
318A THR* 3.4 14.2 - - - -
319A MET* 2.7 37.2 + - - +
320A GLN* 2.4 52.4 + - - +
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Residues in contact with ALA 118 (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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52A VAL 3.5 4.7 - - - +
53A GLY* 3.7 18.8 - - - -
114A THR 2.6 17.9 + - - +
115A GLY 3.7 4.9 - - - +
117A GLU* 1.3 73.9 - - - +
119A ALA* 1.3 59.9 + - - +
121A LEU* 3.7 2.4 - - - +
122A ASP* 2.8 30.5 + - - +
319A MET* 3.7 24.0 - - - -
350A MET* 3.9 19.5 - - + -
398A LEU* 4.2 4.6 - - + +
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Residues in contact with ALA 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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41A VAL* 4.1 5.8 - - + -
43A ILE* 3.4 28.7 - - + -
51A GLY* 3.6 19.5 - - - +
52A VAL* 3.2 19.7 + - - +
115A GLY 3.2 11.4 + - - +
116A ILE 3.2 0.4 + - - -
118A ALA* 1.3 81.6 - - - +
120A MET* 1.4 56.0 + - - +
122A ASP* 3.2 4.7 + - - +
123A LEU* 2.9 31.4 + - - +
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.9 31.4 - - + -
43A ILE* 3.9 17.0 - - + -
72A VAL* 4.5 7.6 - - + -
75A LYS* 5.9 1.1 - - + -
76A THR 4.6 3.6 - - - +
77A LEU* 4.1 23.4 - - + +
80A TYR* 3.8 37.9 - - + -
83A VAL* 5.5 8.3 - - + -
84A LEU* 5.3 2.9 - - + -
116A ILE* 2.9 39.0 + - + +
117A GLU* 3.7 5.2 - - - +
119A ALA* 1.4 68.6 - - - +
121A LEU* 1.4 56.8 + - - +
123A LEU* 3.1 7.4 + - - +
124A LEU* 2.6 37.1 + - - +
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Residues in contact with LEU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.7 33.4 - - + +
117A GLU* 2.8 44.2 + - + +
118A ALA* 3.7 3.6 - - - +
120A MET* 1.4 68.9 - - - +
122A ASP* 1.4 58.8 + - - +
124A LEU* 3.1 4.2 + - + +
125A GLY* 2.8 33.3 + - - -
132A VAL* 4.0 21.0 - - + +
135A LEU* 3.9 26.1 - - + +
136A LEU* 4.0 23.1 - - + -
319A MET* 3.9 18.8 - - - -
320A GLN* 4.6 4.3 - - - +
398A LEU* 6.0 0.2 - - + -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR 4.2 1.2 - - - +
51A GLY* 3.4 6.7 - - - -
52A VAL* 3.0 24.7 + - - +
118A ALA 2.8 14.7 + - - +
119A ALA 3.2 9.4 - - - +
120A MET 3.1 0.2 - - - -
121A LEU* 1.4 78.4 - - - +
123A LEU* 1.3 62.9 + - - +
126A GLN* 2.9 43.7 + - - +
132A VAL* 4.2 8.7 - - - +
396A PRO 4.9 0.2 - - - +
397A GLY* 3.5 3.1 - - - -
398A LEU* 2.9 43.2 + - + +
399A GLY 4.7 0.7 + - - -
400A VAL* 4.4 6.9 - - - +
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Residues in contact with LEU 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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10A VAL* 4.4 2.0 - - + -
43A ILE* 3.4 35.0 - - + +
44A LYS 4.4 5.4 - - - -
45A ASP* 3.6 25.3 - - - +
49A HIS* 3.7 19.7 + - + +
50A THR 3.4 8.3 - - - +
51A GLY 3.2 25.1 - - - +
77A LEU* 3.9 21.0 - - + +
119A ALA 2.9 15.8 + - - +
120A MET* 3.4 12.6 - - - +
122A ASP* 1.3 78.9 - - - +
124A LEU* 1.3 58.1 - - - +
126A GLN* 3.1 8.2 + - - +
127A HIS* 2.9 27.2 + - - +
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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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77A LEU* 4.0 33.0 - - + +
80A TYR* 3.6 37.2 - - + +
120A MET 2.6 20.8 + - - +
121A LEU* 3.7 6.7 - - + +
123A LEU* 1.3 73.5 - - - +
125A GLY* 1.4 51.8 + - - +
127A HIS* 3.0 5.2 + - + +
128A LEU* 2.8 58.9 + - + +
135A LEU* 4.1 17.0 - - + -
128C LEU* 4.5 21.5 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU 2.8 17.4 + - - -
124A LEU* 1.4 71.2 - - - +
126A GLN* 1.4 56.3 + - - +
128A LEU 3.5 0.2 + - - -
129A GLY 2.9 9.0 + - - -
130A VAL* 2.8 49.1 + - - +
131A ASN 4.9 0.4 - - - -
135A LEU* 3.5 16.2 - - - +
396A PRO* 3.4 1.9 - - - +
397A GLY* 3.6 7.9 - - - -
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Residues in contact with GLN 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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49A HIS* 3.3 46.2 - - + +
50A THR 3.1 25.0 + - - +
122A ASP* 2.9 35.0 + - - +
123A LEU* 3.1 9.1 + - - +
125A GLY* 1.4 76.5 - - - +
127A HIS* 1.3 65.2 + - - +
129A GLY* 3.6 7.1 + - - -
396A PRO* 3.8 17.0 - - + +
397A GLY* 4.1 10.3 - - - -
400A VAL 5.9 1.4 + - - -
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR 3.2 19.1 + - - -
7A THR* 3.7 3.6 + - + -
8A PRO* 3.5 26.7 - - + +
47A SER* 5.5 0.6 + - - -
49A HIS* 4.5 8.8 + - - +
77A LEU* 3.7 24.0 - - + -
123A LEU 2.9 5.8 + - - +
124A LEU* 3.4 7.9 - - + +
126A GLN* 1.3 79.3 - - - +
128A LEU* 1.4 62.5 + - + +
129A GLY* 3.3 2.8 + - - -
5C PHE* 3.0 33.3 + - - +
6C THR* 5.5 0.2 - - - -
7C THR* 3.0 16.3 + - - -
127C HIS* 3.2 28.3 + - - -
128C LEU* 4.1 17.9 - - + -
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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
----------------------------------------------------------
124A LEU* 2.8 47.1 + - + +
125A GLY 4.3 2.0 - - - +
127A HIS* 1.4 80.9 - - + +
129A GLY* 1.3 61.0 + - - +
130A VAL* 3.2 14.8 + - + +
135A LEU* 4.0 17.5 - - + -
7C THR* 3.4 39.9 - - + +
76C THR* 4.2 5.5 + - - +
78C GLY* 3.9 19.5 - - - -
80C TYR* 6.3 0.9 - - + -
124C LEU* 4.4 21.8 - - + -
127C HIS* 4.2 12.1 - - + -
128C LEU* 4.6 4.0 - - + -
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 2.9 6.5 + - - -
126A GLN 3.6 4.2 + - - -
127A HIS 3.3 4.9 + - - -
128A LEU* 1.3 77.8 - - - +
130A VAL* 1.3 61.7 + - - +
394A GLU 5.5 1.0 - - - +
396A PRO* 4.0 22.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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