Contacts of the strand formed by residues 98 - 114 (chain B) in PDB entry 3BK3
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 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B VAL* 5.3 6.3 - - + -
90B LEU* 3.6 35.2 - - + -
91B MET 3.7 8.5 - - - +
92B LEU* 5.0 10.1 - - + -
96B GLU 3.9 9.4 - - - +
97B LYS* 1.3 76.7 - - - +
99B VAL* 1.3 62.5 + - - +
100B LEU 4.3 0.3 + - - -
37D GLU* 4.6 13.0 - - - +
38D CYS 3.7 32.5 + - - +
39D LYS* 5.5 1.8 - - - -
40D GLN* 5.4 14.6 - - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.5 4.8 - - - +
91B MET* 2.8 66.0 + - + +
93B ASP* 4.3 11.0 - - + +
97B LYS* 4.0 13.0 - - + +
98B VAL* 1.3 78.3 - - - +
100B LEU* 1.3 65.0 + - - +
101B LYS* 4.0 14.1 - - + -
6D GLU* 3.5 35.4 - - + +
37D GLU* 5.9 1.8 - - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B SER* 4.1 21.8 - - - +
89B MET 3.5 21.1 - - - +
90B LEU* 3.8 16.6 - - + +
98B VAL 4.3 0.4 + - - -
99B VAL* 1.3 74.4 - - - +
101B LYS* 1.3 61.3 + - - +
102B ASN* 5.4 0.2 - - - +
6D GLU* 3.7 7.5 - - - +
7D ALA* 3.0 45.8 + - + +
18D ILE* 3.4 29.8 - - + -
21D ILE* 4.2 17.0 - - + -
36D ALA* 3.8 29.1 + - + +
38D CYS* 4.4 3.1 - - - -
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Residues in contact with LYS 101 (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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88B SER* 3.5 4.5 + - - -
89B MET 3.0 31.1 + - - +
91B MET* 3.5 36.5 - - + +
99B VAL* 4.0 10.2 + - + +
100B LEU* 1.3 74.7 - - - +
102B ASN* 1.3 64.2 + - - +
103B TYR* 3.6 31.6 - - + +
4D GLY* 4.1 20.4 - - - +
5D THR* 3.1 21.3 - - - +
6D GLU* 3.6 13.5 - - - +
7D ALA 4.2 0.4 - - - +
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.4 3.8 - - + -
87B ILE 3.4 6.9 + - - +
88B SER* 2.8 28.9 + - - -
100B LEU* 5.3 0.2 - - - +
101B LYS* 1.3 75.2 - - - +
103B TYR* 1.3 61.1 + - - +
104B GLN* 4.1 14.9 + - - +
4D GLY* 3.2 1.7 - - - -
5D THR* 2.8 42.8 + - - +
6D GLU 4.6 1.2 - - - +
7D ALA* 3.7 28.8 - - - +
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Residues in contact with TYR 103 (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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59A ASN* 3.8 2.5 - - - +
31B TRP* 3.7 18.5 - + - -
86B ALA* 3.2 4.0 - - - +
87B ILE* 2.9 31.2 + - + +
89B MET* 3.6 39.7 - - + -
91B MET* 3.9 10.6 - - - +
101B LYS* 3.6 40.9 - - + +
102B ASN* 1.3 75.0 - - - +
104B GLN* 1.3 64.4 + - - +
106B MET* 3.5 21.3 - - + +
2D ILE* 3.4 33.0 - - + -
3D THR 3.4 20.6 - - - -
4D GLY* 3.3 19.1 - - - -
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Residues in contact with GLN 104 (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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59A ASN* 2.8 24.7 + - - +
85B SER 5.8 0.2 - - - -
86B ALA* 3.7 21.0 - - - +
102B ASN* 4.1 14.3 + - - +
103B TYR* 1.3 74.8 - - - +
105B ASP* 1.3 83.3 + - - +
106B MET* 3.1 2.1 + - - +
3D THR 4.4 2.0 + - - +
5D THR* 5.9 7.2 - - + +
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Residues in contact with ASP 105 (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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58A THR* 4.0 24.0 - - - +
59A ASN* 4.3 4.4 + - - +
60A HIS* 2.9 27.2 + - - +
84B LEU* 3.7 40.0 - - + +
85B SER* 4.0 7.7 + - - +
104B GLN* 1.3 82.8 + - - +
106B MET* 1.3 59.3 + - - +
107B VAL 3.8 0.7 - - - -
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASN* 3.5 23.3 - - - -
60A HIS* 3.4 17.6 + - - -
63A VAL* 4.3 11.4 - - + -
23B PHE* 4.9 2.5 - - + -
28B TRP* 5.8 0.9 - - + -
38B TYR* 2.7 53.2 + - + +
40B ALA* 3.9 0.7 - - - +
85B SER 3.1 7.1 + - - +
87B ILE* 4.1 25.6 - - + +
89B MET* 4.2 20.6 - - + -
103B TYR* 3.5 20.6 - - + +
104B GLN 3.2 14.6 - - - +
105B ASP* 1.3 75.9 - - - +
107B VAL* 1.3 62.3 + - + +
2D ILE* 4.0 14.1 - - + -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 5.6 1.3 - - - +
38B TYR* 3.4 32.1 - - + -
39B HIS 3.8 13.7 - - - +
40B ALA 4.1 2.5 - - - +
41B MET* 4.9 3.6 - - + -
84B LEU* 3.1 7.6 - - - -
85B SER* 2.8 43.2 + - - +
87B ILE* 3.9 18.2 - - + -
106B MET* 1.3 77.5 - - - +
108B VAL* 1.3 69.2 + - - +
109B GLU* 3.2 19.5 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 3.4 33.0 - - + +
16B ARG* 3.1 42.8 + - + -
40B ALA 3.2 13.4 + - - +
41B MET* 4.0 10.1 - - + +
42B TYR* 4.5 2.2 - - - -
43B CYS* 3.8 21.5 - - - -
81B PRO* 3.7 24.7 - - + -
83B GLU 3.8 3.4 - - - -
84B LEU* 3.8 2.9 - - + -
107B VAL* 1.3 73.2 - - - +
109B GLU* 1.3 59.2 + - - +
110B GLY 3.8 13.0 - - - +
111B CYS* 4.1 0.4 - - - -
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 4.0 18.6 + - - +
83B GLU* 2.8 23.2 + - + +
84B LEU 4.2 2.7 - - - +
85B SER* 2.8 41.7 + - - +
107B VAL* 3.2 12.2 + - - +
108B VAL* 1.3 76.1 - - - +
110B GLY* 1.3 55.8 + - - +
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG* 5.0 2.5 - - - -
81B PRO* 3.5 4.9 - - - +
82B THR* 2.7 32.4 + - - -
83B GLU* 3.0 23.0 + - - +
108B VAL* 3.6 3.5 - - - +
109B GLU* 1.3 79.5 - - - +
111B CYS* 1.3 60.6 + - - -
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Residues in contact with CYS 111 (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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14B CYS* 4.1 14.1 - - - +
15B LYS* 3.8 6.5 - - - -
16B ARG* 3.5 30.2 - - - +
43B CYS* 2.0 54.1 - - + -
56B ASN* 4.7 7.3 + - - +
80B VAL 3.3 5.4 - - - +
82B THR* 3.4 10.9 + - - -
83B GLU* 4.9 0.5 - - - +
108B VAL* 4.1 1.3 - - - -
110B GLY* 1.3 74.3 - - - -
112B GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 112 (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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14B CYS* 4.0 6.7 - - - -
55B LEU* 6.2 1.6 - - - -
56B ASN* 3.5 14.8 - - - -
79B CYS* 3.5 2.1 - - - -
80B VAL* 2.9 34.5 + - - +
82B THR* 3.3 14.0 - - - +
111B CYS* 1.3 76.3 - - - +
113B CYS* 1.3 66.3 + - - -
114B ARG* 3.8 1.4 + - - -
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Residues in contact with CYS 113 (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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14B CYS* 4.2 4.3 - - - -
47B CYS* 2.1 55.6 - - + -
48B PRO* 5.3 0.2 - - - -
55B LEU* 3.9 22.2 - - - -
56B ASN 2.9 7.1 + - - -
57B SER* 3.3 22.0 - - - +
58B THR 3.3 16.3 + - - -
61B ALA* 3.5 2.7 - - - +
77B ALA* 4.2 7.0 - - + -
78B CYS 3.6 0.7 - - - -
112B GLY* 1.3 75.0 - - - -
114B ARG* 1.3 72.3 + - - +
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Residues in contact with ARG 114 (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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80A VAL* 4.0 18.7 - - + +
81A PRO* 3.2 35.7 - - + +
84A LEU* 6.3 1.3 - - - -
56B ASN* 2.7 51.7 + - - +
58B THR* 3.8 33.0 + - + +
60B HIS* 4.7 2.6 + - - -
61B ALA* 4.0 14.6 + - - +
64B GLN* 5.3 3.1 - - - +
77B ALA* 3.6 5.7 - - - +
78B CYS* 3.0 30.1 + - - +
80B VAL* 3.6 29.8 - - + -
82B THR* 3.5 29.8 + - + +
113B CYS* 1.3 87.4 + - - +
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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