Contacts of the strand formed by residues 118 - 139 (chain A) in PDB entry 4DEQ
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 VAL 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL 4.0 0.2 - - - +
67A GLY* 3.2 1.7 - - - -
68A THR* 2.9 37.3 + - - +
85A TYR* 5.0 0.9 + - - -
109A GLN* 3.8 15.0 - - + +
110A GLY* 3.6 31.2 - - - +
111A ASN* 3.9 13.9 - - - +
112A THR* 5.1 5.6 - - - +
113A ASN* 6.1 0.4 - - - +
116A ASP* 5.3 5.4 - - + +
117A VAL* 1.3 77.0 - - - +
119A VAL* 1.3 74.8 + - - +
120A ALA 3.9 0.7 + - - -
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Residues in contact with VAL 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 5.2 6.5 - - - -
65A ALA* 4.3 10.8 - - + -
66A VAL 3.5 4.7 - - - +
67A GLY* 4.4 2.2 - - - -
117A VAL* 4.2 10.5 + - + +
118A VAL* 1.3 82.6 - - - +
120A ALA* 1.3 64.2 + - - +
121A VAL* 3.9 24.7 + - + +
149A TYR* 4.4 24.2 - - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.2 2.4 - - - +
66A VAL* 2.7 34.4 + - + +
85A TYR* 3.4 23.8 - - + +
87A ILE* 6.1 0.2 - - + -
108A PHE* 4.0 22.0 - - + -
109A GLN 4.0 17.0 - - - +
118A VAL 3.9 0.6 + - - -
119A VAL* 1.3 74.1 - - - +
121A VAL* 1.3 62.2 + - - +
122A PHE* 3.9 4.3 + - - -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 5.9 4.0 - - - -
3A MET* 3.8 26.9 - - + -
64A THR* 3.7 10.1 - - - +
65A ALA* 3.7 3.4 - - + -
108A PHE* 4.5 6.8 - - - -
119A VAL* 3.9 16.8 + - + +
120A ALA* 1.3 73.9 - - - +
122A PHE* 1.3 75.7 - - - +
123A PRO* 3.7 2.3 - - - +
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Residues in contact with PHE 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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63A VAL* 3.3 42.0 - - + -
64A THR 2.9 16.0 + - - +
65A ALA* 3.9 17.9 - - - -
66A VAL* 3.9 15.3 - - + -
87A ILE* 3.5 33.2 - - + -
89A VAL* 5.0 4.7 - - + -
99A ILE* 3.7 26.2 - - + -
108A PHE* 4.0 12.6 - + - -
120A ALA 4.2 2.2 - - - -
121A VAL* 1.3 87.1 - - - +
123A PRO* 1.3 73.1 - - + +
124A LYS* 3.2 15.0 + - - +
126A LEU* 4.3 12.3 - - + -
128A THR* 6.1 0.2 - - + -
131A VAL* 5.2 2.0 - - + -
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Residues in contact with PRO 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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99A ILE* 3.9 26.5 - - + -
100A LYS 4.5 9.6 - - - +
101A GLU* 3.4 25.8 - - - +
106A VAL* 4.7 10.1 - - + -
108A PHE* 4.6 7.9 - - + -
121A VAL 3.7 2.2 - - - +
122A PHE* 1.3 87.6 - - + +
124A LYS* 1.3 66.3 + - + +
126A LEU* 6.4 0.2 - - + -
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Residues in contact with LYS 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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64A THR* 5.5 0.7 - - - -
122A PHE* 3.2 18.0 - - - +
123A PRO* 1.3 87.0 - - + +
125A PRO* 1.3 78.7 - - + +
126A LEU* 3.5 22.1 + - + +
162A SER* 2.8 38.7 + - - +
164A SER 3.2 27.0 + - - +
165A PRO* 5.6 0.2 - - - -
166A CYS 5.7 0.4 + - - -
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Residues in contact with PRO 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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2A CYS* 5.7 0.4 - - - -
62A PHE* 4.5 17.8 - - + -
63A VAL 3.8 8.7 - - - +
64A THR* 3.9 26.2 - - + -
124A LYS* 1.3 94.9 - - + +
126A LEU* 1.3 61.5 + - - +
127A ILE 4.4 0.2 - - - -
156A TYR* 4.1 27.1 - - + +
160A SER* 5.3 5.8 - - - +
162A SER 4.2 0.9 - - - +
163A GLY* 3.6 17.0 - - - -
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Residues in contact with LEU 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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61A ARG 3.1 4.7 - - - +
62A PHE* 4.3 2.5 - - - -
63A VAL* 3.1 31.5 + - + +
89A VAL* 4.8 6.3 - - + -
99A ILE* 4.1 37.2 - - + -
122A PHE* 4.3 8.5 - - + -
123A PRO* 6.4 0.2 - - + -
124A LYS* 3.6 23.6 - - + +
125A PRO* 1.3 75.2 - - - +
127A ILE* 1.3 66.3 + - - +
128A THR* 3.3 12.5 + - + +
163A GLY 3.4 5.2 - - - +
164A SER 3.3 36.1 - - - +
165A PRO* 3.5 19.3 - - + -
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Residues in contact with ILE 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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60A LEU* 3.8 29.3 - - + +
61A ARG 3.4 4.5 - - - +
62A PHE* 3.3 36.1 - - + -
91A SER* 4.9 4.3 + - - -
126A LEU* 1.3 70.4 - - - +
128A THR* 1.3 62.8 + - - +
153A ILE* 4.1 20.2 - - + -
163A GLY* 2.7 30.0 + - - +
165A PRO* 4.8 8.7 - - - +
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Residues in contact with THR 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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57A LEU* 4.3 1.0 - - - +
59A LEU 3.9 0.3 - - - +
60A LEU* 4.0 8.1 - - - -
61A ARG* 2.8 33.7 + - - +
63A VAL* 3.7 29.4 - - + -
89A VAL* 3.5 17.1 - - + +
90A SER* 3.2 17.1 + - - -
91A SER* 5.0 3.6 - - - -
122A PHE* 6.1 0.2 - - + -
126A LEU* 3.7 11.0 - - + +
127A ILE* 1.3 78.2 - - - +
129A ARG* 1.3 66.9 + - - +
130A PHE 3.1 20.2 + - - +
131A VAL* 4.4 7.4 - - + -
165A PRO* 5.8 0.7 - - - -
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Residues in contact with ARG 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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56A ASP* 2.9 36.8 + - - +
57A LEU* 2.9 39.2 + - - +
58A GLY* 3.5 19.3 + - - -
59A LEU* 3.8 30.3 - - - +
60A LEU* 4.3 6.7 - - + +
90A SER 3.2 8.3 + - - +
91A SER* 4.0 15.9 + - - +
128A THR* 1.3 79.5 + - - +
130A PHE* 1.3 81.9 + - + +
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Residues in contact with PHE 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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54A GLN* 3.5 26.5 - - - -
55A VAL 3.6 2.9 - - - +
56A ASP* 3.5 39.5 - - + -
89A VAL* 3.5 1.7 - - - -
90A SER* 2.7 31.8 + - - +
91A SER 4.0 2.0 - - - -
92A ASN* 3.4 28.3 - - - -
93A GLY* 3.5 17.5 - - - -
96A TRP* 3.5 18.6 - - + -
128A THR* 3.1 17.3 + - - -
129A ARG* 1.3 103.1 - - + +
131A VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 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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54A GLN* 3.1 4.0 - - - +
55A VAL* 2.9 43.1 + - + +
57A LEU* 4.2 20.9 - - + -
63A VAL* 4.4 13.0 - - + -
66A VAL* 4.6 18.8 - - + -
87A ILE* 4.0 21.5 - - + -
88A ASP 3.8 4.3 - - - -
89A VAL* 4.4 5.8 - - + -
96A TRP* 4.6 0.4 - - - -
122A PHE* 5.2 1.6 - - + -
128A THR* 4.4 12.1 - - + -
130A PHE* 1.3 80.3 - - - +
132A ARG* 1.3 64.6 - - - +
133A ILE* 4.2 7.8 + - + +
146A PHE* 5.5 1.1 - - + -
148A VAL* 4.6 9.2 - - + -
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Residues in contact with ARG 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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52A TRP* 3.7 63.0 - - + +
53A ILE 3.4 6.3 - - - +
54A GLN* 3.0 29.6 + - + -
87A ILE* 3.5 3.7 - - - -
88A ASP* 2.8 48.7 + - + +
93A GLY 4.8 2.0 + - - -
96A TRP* 3.4 48.8 - - + +
131A VAL* 1.3 75.1 - - - +
133A ILE* 1.3 61.9 + - - +
134A LYS* 3.9 15.9 + - + +
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Residues in contact with ILE 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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52A TRP* 3.3 6.4 - - - +
53A ILE* 2.7 42.0 + - + +
66A VAL* 3.9 21.3 - - + -
68A THR* 4.7 0.2 - - + -
85A TYR* 3.7 28.5 - - + -
86A LYS 3.7 3.4 - - - -
87A ILE* 4.7 8.1 - - + +
131A VAL* 4.8 11.9 - - + +
132A ARG* 1.3 73.9 - - - +
134A LYS* 1.3 63.7 + - - +
135A PRO* 3.8 2.5 - - - +
144A MET* 3.9 27.6 - - + -
146A PHE* 3.6 44.6 - - + -
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Residues in contact with LYS 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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49A TYR 4.8 7.2 - - - +
51A GLU 3.9 6.7 - - - +
52A TRP* 4.2 13.7 - - + -
85A TYR* 4.0 1.3 - - - -
86A LYS* 2.8 59.0 + - + +
88A ASP* 2.8 42.9 + - - +
98A THR* 4.3 6.1 + - - +
132A ARG* 3.9 21.1 - - + +
133A ILE* 1.3 78.5 - - - +
135A PRO* 1.3 69.5 - - - +
136A ALA* 4.5 0.3 - - - +
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Residues in contact with PRO 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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42A TRP* 4.6 6.7 - - + -
48A SER 5.5 0.4 - - - +
49A TYR* 3.5 27.1 - - - +
51A GLU* 3.5 20.0 - - + +
52A TRP* 4.5 1.3 - - - -
82A VAL* 4.1 17.9 - - + -
84A THR 3.9 0.4 - - - +
85A TYR* 3.8 11.0 - - + -
133A ILE 3.8 5.6 - - - +
134A LYS* 1.3 86.8 - - - +
136A ALA* 1.3 58.9 + - - +
138A TRP* 3.9 4.8 - - + -
142A ILE* 4.1 36.3 - - + -
144A MET* 4.4 16.2 - - - -
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Residues in contact with ALA 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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49A TYR* 4.7 8.2 - - - +
84A THR* 2.8 27.7 + - - +
85A TYR* 4.2 3.1 - - - -
86A LYS* 4.9 6.3 - - + +
107A LEU* 3.8 23.6 - - + -
134A LYS 3.6 2.2 + - - +
135A PRO* 1.3 71.3 - - - +
137A THR* 1.3 67.3 + - + +
138A TRP* 3.2 17.3 - - - -
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Residues in contact with THR 137 (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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82A VAL* 3.4 6.8 - - - +
83A LYS* 2.8 32.5 + - - +
84A THR* 2.6 39.1 + - + +
136A ALA* 1.3 83.9 - - + +
138A TRP* 1.3 68.9 + - - +
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Residues in contact with TRP 138 (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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47A ASP* 3.4 34.8 - - + +
48A SER* 3.7 21.5 - - - -
49A TYR* 3.8 5.8 - + + -
81A TYR 3.5 13.7 - - - +
82A VAL* 4.0 9.2 - - + -
83A LYS* 3.9 15.6 + - - +
135A PRO* 3.9 17.5 - - + -
136A ALA 3.2 24.5 - - - -
137A THR* 1.3 99.5 - - - +
139A GLU* 1.3 62.0 + - - +
140A THR 4.2 3.6 + - - -
141A GLY* 3.8 31.2 - - - +
142A ILE* 3.7 21.1 - - + -
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Residues in contact with GLU 139 (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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79A LYS 4.9 0.2 - - - +
80A TYR* 3.8 1.2 - - - -
81A TYR* 3.0 62.3 + - + +
83A LYS* 4.2 20.2 + - + +
138A TRP* 1.3 73.4 - - - +
140A THR* 1.3 71.6 + - - +
141A GLY 2.6 26.2 + - - +
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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
------------------------------------------------------------
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