Contacts of the strand formed by residues 76 - 92 (chain B) in PDB entry 4EFV
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 TRP 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.7 31.0 - + - -
69A ARG* 5.3 5.6 - - + -
70A GLY* 3.7 34.3 - - - -
71B ILE* 4.1 14.8 - - + +
72B ASP* 3.0 29.5 + - + +
73B SER* 3.6 15.4 - - - +
74B LYS 3.8 0.4 - - - -
75B HIS* 1.3 93.6 - - + +
77B ASN* 1.3 63.8 + - - +
78B SER 4.1 0.9 + - - -
112B LEU* 4.0 20.0 - - + -
113B SER 3.5 5.8 - - - -
114B LYS* 3.5 60.6 - - + -
115B LYS* 3.4 16.2 + - - +
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Residues in contact with ASN 77 (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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76B TRP* 1.3 74.8 - - - +
78B SER* 1.3 59.7 + - - +
79B TYR* 5.7 0.7 - - - -
112B LEU* 3.4 2.3 - - - -
113B SER* 2.6 58.3 + - - +
114B LYS 4.6 1.0 + - - -
115B LYS* 3.3 41.7 + - - +
116B ALA* 4.5 3.2 - - - +
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Residues in contact with SER 78 (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 SER 4.5 0.2 + - - -
67B GLY* 2.9 19.9 - - - -
68B CYS* 2.7 25.1 + - - -
71B ILE* 4.0 15.6 - - - +
76B TRP 4.0 0.9 + - - -
77B ASN* 1.3 77.1 - - - +
79B TYR* 1.3 67.7 + - - +
110B CYS* 3.6 22.2 - - - -
111B VAL 3.2 7.0 - - - -
112B LEU* 3.8 10.5 - - - -
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Residues in contact with TYR 79 (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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11A GLU* 2.7 39.1 + - + -
61B PRO* 4.5 4.0 - - + +
62B ASN* 6.1 0.2 - - - +
67B GLY* 4.2 5.2 - - - -
68B CYS* 3.5 6.9 - - - -
77B ASN* 5.7 0.9 - - + -
78B SER* 1.3 79.7 - - - +
80B CYS* 1.3 64.9 + - - +
81B THR* 3.5 31.2 + - + +
111B VAL* 3.0 54.5 + - + +
113B SER* 5.8 4.9 - - - -
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Residues in contact with CYS 80 (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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15B CYS* 2.0 56.8 - - - -
58B CYS* 3.9 6.5 - - - +
60B ASP 4.0 9.2 - - - +
61B PRO* 3.6 24.4 + - - +
63B PRO* 4.0 21.3 - - - -
68B CYS* 3.7 8.7 - - - -
79B TYR* 1.3 75.2 - - - +
81B THR* 1.3 60.8 + - - +
108B CYS* 3.7 12.1 - - - -
109B VAL 3.6 0.2 - - - -
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Residues in contact with THR 81 (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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58B CYS* 3.5 8.7 - - - -
79B TYR* 3.5 19.0 + - + +
80B CYS* 1.3 74.6 - - - +
82B THR* 1.3 74.6 + - - +
83B THR* 4.0 3.1 + - + -
108B CYS* 3.2 2.1 - - - -
109B VAL* 2.8 41.6 + - + +
111B VAL* 3.7 28.7 - - + -
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Residues in contact with THR 82 (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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56B THR 4.4 2.7 - - - +
57B LYS* 4.3 13.5 - - + -
58B CYS* 3.8 32.1 - - + +
81B THR* 1.3 86.6 + - - +
83B THR* 1.3 63.9 + - - +
84B HIS* 5.3 2.8 - - - -
105B ASP* 3.5 31.5 + - - +
107B ALA 3.1 10.3 - - - +
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Residues in contact with THR 83 (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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106A THR 4.9 3.1 + - - -
107A ALA* 4.4 6.6 - - - +
81B THR* 5.2 3.6 - - + -
82B THR* 1.3 76.9 - - - +
84B HIS* 1.3 67.2 + - - +
105B ASP* 3.6 4.9 - - - -
106B THR* 2.9 23.5 + - - -
107B ALA* 2.9 26.2 + - - +
109B VAL* 3.9 29.0 - - + +
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Residues in contact with HIS 84 (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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54A PHE* 4.4 11.2 - + - -
56A THR* 5.5 0.7 + - - -
106A THR* 5.3 4.2 - - - +
82B THR 5.3 2.0 - - - -
83B THR* 1.3 84.4 - - - +
85B THR* 1.3 61.6 + - - +
86B PHE* 4.0 26.0 - + - -
103B ARG* 3.4 45.6 + - + +
104B ILE 3.4 11.9 - - - +
105B ASP* 3.7 11.9 - - - +
106B THR* 4.0 4.7 - - - -
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Residues in contact with THR 85 (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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54A PHE* 3.3 30.5 + - - -
85A THR* 4.6 7.8 - - + +
87A VAL* 5.4 0.9 - - + -
104A ILE* 5.7 0.3 - - - +
106A THR* 3.8 19.9 - - + +
84B HIS* 1.3 76.1 + - - +
86B PHE* 1.3 77.7 + - - +
87B VAL* 3.9 20.9 - - + -
103B ARG* 3.6 5.9 - - - -
104B ILE* 3.0 26.0 + - + +
106B THR* 3.5 25.7 + - + -
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Residues in contact with PHE 86 (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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21A TRP* 4.0 21.5 - + + -
52A TYR 5.7 0.2 - - - +
53A PHE* 5.8 0.3 - - - -
54A PHE* 4.0 43.7 + + + +
87A VAL* 5.4 2.4 - - - +
31B ILE* 3.6 47.6 - - + -
84B HIS* 4.0 26.7 - + - -
85B THR* 1.3 85.6 + - - +
87B VAL* 1.3 63.4 + - - +
101B PHE* 3.9 15.8 - - + -
102B ILE 3.3 17.3 - - - +
103B ARG* 4.1 23.6 - - + -
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Residues in contact with VAL 87 (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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87A VAL* 4.1 31.0 - - + -
88A LYS* 5.5 3.4 - - + +
53B PHE* 4.3 18.4 - - + -
85B THR* 3.9 16.2 - - + -
86B PHE* 1.3 80.3 - - - +
88B LYS* 1.3 77.3 + - - +
89B ALA 3.4 1.0 + - - -
101B PHE* 3.7 3.4 - - - -
102B ILE* 2.9 30.5 + - - +
104B ILE* 3.8 28.7 - - + -
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Residues in contact with LYS 88 (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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44A ILE* 5.7 3.1 - - + -
49A PHE* 3.5 33.7 - - + +
50A LYS 3.3 24.5 + - - +
51A GLN* 5.4 0.4 - - - +
52A TYR* 4.9 3.2 - - - +
51B GLN* 4.9 0.5 - - - +
53B PHE* 4.7 1.4 - - - -
87B VAL* 1.3 84.5 - - - +
89B ALA* 1.3 61.9 + - - +
99B TRP* 4.0 39.7 - - + -
100B ARG* 3.4 10.1 - - - +
101B PHE* 3.5 45.7 - - + -
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Residues in contact with ALA 89 (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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38B VAL* 4.8 0.7 - - + -
51B GLN* 3.6 5.8 - - - +
53B PHE* 3.7 17.7 - - + -
88B LYS* 1.3 77.5 - - - +
90B LEU* 1.3 63.0 + - - +
91B THR* 3.3 10.0 + - + -
99B TRP* 3.2 8.2 - - - -
100B ARG 2.7 34.9 + - - +
102B ILE* 3.5 35.0 - - + -
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Residues in contact with LEU 90 (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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38B VAL* 3.9 0.2 - - - -
39B LEU* 3.2 49.6 + - + -
41B GLU 3.8 8.3 - - - +
42B VAL* 3.7 26.5 - - + -
43B ASN 5.0 3.1 - - - +
51B GLN* 2.8 24.1 + - - +
89B ALA* 1.3 68.5 - - - +
91B THR* 1.3 64.8 + - - +
97B ALA* 4.8 5.6 - - + -
98B ALA* 3.7 22.4 - - - +
99B TRP* 3.5 29.3 - - + +
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Residues in contact with THR 91 (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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36B VAL* 3.8 22.4 - - + -
37B MET 3.2 11.7 - - - +
38B VAL* 4.2 11.0 - - + -
39B LEU* 4.6 2.7 - - - +
89B ALA* 3.7 10.9 + - + +
90B LEU* 1.3 80.0 - - - +
92B MET* 1.3 62.7 + - - +
97B ALA* 3.2 5.0 - - - +
98B ALA 2.8 42.6 + - - -
100B ARG* 3.0 28.1 + - - +
102B ILE* 4.0 16.4 - - + -
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Residues in contact with MET 92 (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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36B VAL* 4.4 0.9 - - - -
37B MET* 2.6 46.5 + - + +
39B LEU* 4.1 22.2 - - + -
91B THR* 1.3 75.4 - - - +
93B ASP* 1.3 66.1 + - - +
94B GLY 3.1 26.0 - - - +
95B LYS* 3.8 20.2 - - - +
96B GLN 3.4 6.3 - - - -
97B ALA* 3.6 31.4 - - + -
100B ARG* 3.7 1.1 - - - -
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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