Contacts of the strand formed by residues 47 - 67 (chain A) in PDB entry 1TVG
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 GLN 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A THR* 2.7 31.2 + - - +
20A SER* 2.7 24.2 + - - -
39A TRP* 4.1 4.4 - - + -
41A THR* 3.4 32.1 - - + +
43A GLY* 3.4 28.1 - - - +
44A MET 2.8 25.3 + - - +
45A PHE* 3.8 13.7 - - + -
46A PRO* 1.3 74.6 - - - +
48A GLU* 1.3 64.2 + - - +
118A ILE* 3.4 3.1 - - - +
119A ILE* 2.8 33.8 + - + +
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Residues in contact with GLU 48 (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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17A LEU* 4.7 5.6 - - - +
18A ALA* 3.3 2.6 - - - +
19A THR* 2.8 47.4 + - + -
39A TRP* 4.1 4.6 - - - -
46A PRO* 5.7 2.1 - - - +
47A GLN* 1.3 77.1 - - - +
49A PHE* 1.3 68.3 + - - +
50A ILE* 4.4 13.3 - - - +
116A ARG* 2.7 50.9 + - + +
117A PHE 3.1 16.6 - - - +
118A ILE* 3.9 11.3 - - + +
119A ILE* 4.6 0.7 - - - +
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Residues in contact with PHE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.9 15.0 - - + -
17A LEU 3.8 8.5 - - - -
18A ALA* 3.9 18.4 - - + -
30A ILE* 3.7 37.7 - - + -
39A TRP* 3.6 21.1 - + - -
48A GLU* 1.3 79.1 - - - +
50A ILE* 1.3 67.4 + - - +
51A ILE* 4.0 12.8 - - + -
72A LEU* 6.1 0.7 - - + -
116A ARG* 4.4 0.3 - - - +
117A PHE* 2.8 67.7 + + + -
119A ILE* 5.2 3.8 - - + -
129A VAL* 3.9 21.3 - - + -
132A VAL* 4.0 14.6 - - + -
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.3 5.2 - - - +
16A ILE* 2.8 48.4 + - + +
17A LEU* 3.9 28.0 - - + -
48A GLU* 4.4 11.2 - - - +
49A PHE* 1.3 81.5 - - - +
51A ILE* 1.3 75.6 + - - +
82A PRO* 4.2 4.0 - - + +
85A PHE* 3.9 22.4 - - + -
114A TYR* 3.8 26.9 - - + -
115A LEU 3.2 9.4 - - - +
116A ARG* 4.0 18.4 - - + -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A CYS* 4.0 14.8 - - + +
13A SER* 4.4 10.1 - - - -
14A GLU 3.5 7.2 - - - +
15A VAL* 4.4 9.6 - - + -
31A ILE* 4.2 11.0 - - + -
49A PHE* 4.0 17.5 - - + -
50A ILE* 1.3 75.7 - - - +
52A CYS* 1.3 65.4 + - - +
53A PHE* 3.9 24.2 + - + -
114A TYR* 3.2 7.1 - - - +
115A LEU* 2.8 39.8 + - + +
117A PHE* 3.8 11.9 - - + -
132A VAL* 3.5 36.8 - - + -
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Residues in contact with CYS 52 (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 SER* 3.2 3.6 - - - -
14A GLU* 2.7 43.5 + - + +
16A ILE* 4.1 13.9 - - + -
50A ILE 3.9 0.6 + - - -
51A ILE* 1.3 73.8 - - - +
53A PHE* 1.3 60.2 + - - +
54A HIS* 3.6 46.0 + - + -
113A THR 4.6 0.7 - - - -
114A TYR* 3.4 41.3 - - + -
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Residues in contact with PHE 53 (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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6A LEU* 3.5 24.2 - - + -
7A CYS* 3.8 21.8 - - - -
12A GLY 4.1 2.6 - - - +
13A SER* 3.5 21.6 + - - -
51A ILE* 4.3 7.4 - - + -
52A CYS* 1.3 71.8 - - - +
54A HIS* 1.3 72.0 - - - +
55A LYS* 3.2 40.5 + - + +
57A VAL* 3.6 34.1 - - + -
59A ILE* 4.1 8.7 - - + -
112A ALA* 4.0 5.4 - - + -
113A THR 3.1 27.7 + - - +
114A TYR* 4.2 2.2 - - - -
115A LEU* 3.9 37.5 - - + -
134A ALA* 4.5 1.6 - - + -
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLY* 3.1 22.4 + - - +
14A GLU* 3.0 40.2 + - + +
52A CYS* 3.3 29.8 + - - -
53A PHE* 1.3 79.3 - - - +
55A LYS* 1.3 66.4 + - - +
113A THR 4.3 1.6 + - - -
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Residues in contact with LYS 55 (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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6A LEU* 5.6 4.0 - - - -
11A GLU* 3.4 28.2 + - - -
12A GLY* 4.7 4.0 - - - -
13A SER* 5.4 2.7 - - - -
53A PHE* 3.2 40.6 + - + +
54A HIS* 1.3 82.2 + - - +
56A HIS* 1.3 68.9 + - - +
57A VAL* 4.0 6.5 - - + -
113A THR* 3.7 17.2 + - - +
138A VAL* 3.5 42.2 - - + -
139A VAL 5.5 0.2 - - - +
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Residues in contact with HIS 56 (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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55A LYS* 1.3 79.3 - - - +
57A VAL* 1.3 59.9 + - - +
78A THR* 4.0 13.5 + - - -
79A SER 5.6 1.1 - - - -
80A LYS* 6.2 2.2 - - - +
112A ALA 3.8 4.8 + - - +
113A THR* 3.3 25.9 - - + +
138A VAL* 3.5 3.8 - - - +
139A VAL* 2.7 55.3 + - + +
140A SER 5.1 7.2 - - - -
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Residues in contact with VAL 57 (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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6A LEU* 3.9 27.6 - - + -
53A PHE* 3.6 38.4 - - + -
55A LYS* 4.0 22.4 - - + -
56A HIS* 1.3 80.9 - - - +
58A ARG* 1.3 64.3 + - - +
59A ILE* 4.0 13.2 - - + -
111A SER* 3.3 4.9 - - - -
112A ALA 3.0 40.7 + - - +
137A THR 3.3 9.4 - - - +
138A VAL* 4.3 1.6 - - + -
139A VAL* 4.3 2.4 - - - +
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Residues in contact with ARG 58 (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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6A LEU* 4.2 0.2 - - - +
57A VAL* 1.3 73.4 - - - +
59A ILE* 1.3 61.7 + - - +
60A GLU* 5.3 0.3 - - - +
108A HIS* 2.9 36.3 + - + +
110A GLY 3.7 2.9 - - - -
111A SER* 3.3 24.9 - - - +
136A GLY* 3.1 5.7 - - - -
137A THR* 2.8 41.7 + - - +
139A VAL* 3.6 22.2 - - + +
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Residues in contact with ILE 59 (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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6A LEU* 4.3 9.4 - - + -
53A PHE* 4.1 15.0 - - + -
57A VAL* 4.0 12.6 - - + -
58A ARG* 1.3 75.3 - - - +
60A GLU* 1.3 63.3 + - - +
61A ARG 3.6 24.2 - - - +
62A LEU* 3.8 14.1 - - + -
88A TRP* 4.1 17.0 - - + -
107A ALA 3.9 2.0 - - - +
108A HIS* 3.0 31.4 - - - -
110A GLY 2.8 22.5 + - - +
112A ALA* 4.5 3.8 - - + -
115A LEU* 3.9 38.1 - - + -
134A ALA* 4.3 2.9 - - + -
135A GLU 3.5 5.4 - - - +
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Residues in contact with GLU 60 (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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58A ARG 4.1 0.4 + - - +
59A ILE* 1.3 73.3 - - - +
61A ARG* 1.3 65.2 + - + +
106A VAL* 3.9 12.6 - - + +
107A ALA 3.3 23.7 + - - +
108A HIS* 4.4 9.4 - - + +
135A GLU* 2.8 26.0 + - - +
136A GLY* 4.9 5.3 - - - -
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Residues in contact with ARG 61 (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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59A ILE* 3.6 5.5 - - - +
60A GLU* 1.3 84.8 - - + +
62A LEU* 1.3 71.1 - - - +
63A VAL* 3.3 27.5 - - - +
104A GLU* 2.7 37.7 + - + +
105A ILE 3.5 11.7 - - - +
106A VAL* 4.5 8.5 - - + -
107A ALA 4.4 1.1 - - - -
133A SER* 6.3 0.2 - - - -
134A ALA* 3.2 4.2 - - - -
135A GLU* 2.8 75.0 + - + +
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Residues in contact with LEU 62 (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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59A ILE* 3.8 14.6 - - + -
61A ARG* 1.3 76.9 - - - +
63A VAL* 1.3 68.5 + - - +
64A ILE* 5.0 5.2 - - + -
74A ILE* 3.8 29.4 - - + -
88A TRP* 3.8 26.7 - - + -
89A ILE* 5.3 1.1 - - + -
103A GLU 3.8 0.7 - - - +
104A GLU* 3.5 0.2 - - - -
105A ILE* 2.8 53.5 + - + +
107A ALA* 5.5 1.3 - - + +
115A LEU* 4.0 17.7 - - + -
117A PHE* 5.0 5.8 - - + -
132A VAL* 5.6 0.9 - - + -
133A SER 3.2 5.4 - - - +
134A ALA* 3.7 26.7 - - + -
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Residues in contact with VAL 63 (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 ARG* 3.3 41.3 - - - +
62A LEU* 1.3 78.8 - - - +
64A ILE* 1.3 71.8 + - - +
65A GLN* 4.3 2.7 - - + -
102A ASN* 5.8 6.1 - - + +
103A GLU 3.3 11.0 - - - +
104A GLU* 4.6 6.5 - - + -
131A SER 4.0 0.7 - - - +
132A VAL* 3.4 2.9 - - - -
133A SER* 2.8 53.0 + - - +
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Residues in contact with ILE 64 (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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62A LEU* 5.0 2.9 - - + -
63A VAL* 1.3 86.0 - - - +
65A GLN* 1.3 68.3 + - - +
66A SER* 4.2 12.2 + - - +
72A LEU* 4.0 20.6 - - + -
74A ILE* 3.9 27.8 - - + -
93A LEU* 5.6 6.4 - - + +
101A GLN 3.6 1.2 - - - +
102A ASN* 3.5 3.6 - - - -
103A GLU* 2.8 44.2 + - + +
105A ILE* 3.9 17.0 - - + -
117A PHE* 4.0 14.4 - - + -
129A VAL* 4.9 4.9 - - + -
131A SER 3.5 8.3 - - - +
132A VAL* 4.2 13.2 - - + -
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Residues in contact with GLN 65 (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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35A PRO* 3.3 44.4 - - - +
63A VAL* 4.3 2.7 - - + -
64A ILE* 1.3 72.5 - - - +
66A SER* 1.3 58.3 + - - +
100A LEU* 4.2 16.5 - - + +
101A GLN 3.1 11.2 - - - +
102A ASN* 3.3 25.9 - - - +
129A VAL* 3.7 2.1 - - - +
130A HIS* 2.7 38.0 + - + +
131A SER* 2.8 29.9 + - - +
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Residues in contact with SER 66 (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 ILE* 4.6 9.0 + - - +
65A GLN* 1.3 77.1 - - - +
67A TYR* 1.3 63.0 + - - +
69A VAL* 3.7 13.7 - - - +
93A LEU* 3.8 9.5 - - - +
100A LEU* 3.6 5.7 - - - +
101A GLN* 2.7 64.2 + - - +
128A SER 3.0 16.6 - - - -
129A VAL* 4.2 6.3 - - - -
130A HIS* 4.1 8.3 - - - +
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Residues in contact with TYR 67 (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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66A SER* 1.3 77.7 - - - +
68A PHE* 1.3 113.9 + + - +
69A VAL 3.1 8.4 + - - -
95A HIS* 3.9 19.5 - + - -
96A THR 4.7 0.7 - - - -
97A GLU* 5.0 1.9 + - - -
98A GLY* 4.7 9.0 + - - -
99A GLN 3.4 30.7 - - - -
100A LEU* 4.2 19.5 - - + -
101A GLN* 3.3 4.9 - - + +
126A PHE* 4.8 8.7 - + - -
128A SER* 2.9 41.4 + - - +
130A HIS* 4.5 4.5 - + + -
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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