Contacts of the strand formed by residues 78 - 92 (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 CYS 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A CYS* 2.0 50.9 - - - -
79A CYS 5.0 1.6 - - - +
80A VAL* 3.8 15.5 - - + -
47B CYS* 4.0 2.9 - - - -
76B LYS 4.7 2.9 - - - +
77B ALA* 1.3 74.5 - - - +
79B CYS* 1.3 68.1 + - - +
80B VAL* 3.5 5.5 + - - +
113B CYS* 3.6 0.2 - - - -
114B ARG 3.0 28.9 + - - +
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Residues in contact with CYS 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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78A CYS* 4.9 1.0 - - - +
14B CYS* 2.0 51.6 - - + -
15B LYS 4.1 0.7 - - - -
43B CYS* 3.9 29.0 - - - +
44B HIS* 3.9 10.9 - - - -
45B GLY 3.3 24.2 + - - +
47B CYS* 3.9 5.8 - - - -
78B CYS* 1.3 77.1 - - - +
80B VAL* 1.3 67.6 + - - +
111B CYS* 4.3 0.4 - - - -
112B GLY 3.5 4.3 - - - -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A CYS* 3.5 29.2 - - + -
80A VAL* 3.8 15.7 - - + -
114A ARG* 4.2 18.6 - - + +
43B CYS* 3.5 7.9 - - - -
78B CYS 3.9 2.9 - - - +
79B CYS* 1.3 81.2 - - - +
81B PRO* 1.3 80.6 - - + +
82B THR* 3.3 0.3 + - - +
111B CYS* 3.3 1.9 - - - -
112B GLY 2.9 31.7 + - - +
114B ARG* 3.6 35.0 - - + -
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Residues in contact with PRO 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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60A HIS* 4.2 12.3 - - + +
64A GLN* 5.3 2.5 - - - +
114A ARG* 3.2 30.7 - - + +
43B CYS* 3.4 18.8 - - + +
80B VAL* 1.3 94.2 - - + +
82B THR* 1.3 61.2 + - - +
84B LEU* 3.8 23.6 - - + +
108B VAL* 3.7 31.6 - - + -
110B GLY 3.5 3.8 - - - +
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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 ASN* 4.1 4.1 + - - -
80B VAL 3.5 5.4 - - - +
81B PRO* 1.3 73.8 - - - +
83B GLU* 1.3 84.4 + - - +
84B LEU* 4.3 2.9 - - - -
110B GLY 2.7 11.0 + - - -
111B CYS 3.4 14.9 + - - -
112B GLY* 3.3 23.6 - - - +
114B ARG* 3.5 47.8 + - + +
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Residues in contact with GLU 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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56B ASN* 4.6 5.0 - - - +
82B THR* 1.3 112.2 + - - +
84B LEU* 1.3 61.3 + - - +
108B VAL* 3.7 1.9 - - - +
109B GLU* 2.8 38.2 + - + -
110B GLY* 3.0 26.3 + - - +
111B CYS 4.9 0.7 - - - +
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Residues in contact with LEU 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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58A THR* 4.6 14.1 - - + +
60A HIS* 4.1 17.7 - - + -
114A ARG* 6.2 0.7 - - - -
81B PRO* 3.8 21.8 - - + +
82B THR 5.5 1.1 - - - -
83B GLU* 1.3 78.4 - - - +
85B SER* 1.3 61.4 + - - +
105B ASP* 3.7 43.3 - - + +
107B VAL 3.1 18.6 - - - +
108B VAL* 3.8 25.1 - - + -
109B GLU* 4.2 4.3 - - - +
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Residues in contact with SER 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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84B LEU* 1.3 74.4 - - - +
86B ALA* 1.3 64.7 + - - +
104B GLN* 5.8 0.2 - - - -
105B ASP 4.3 3.6 - - - +
106B MET 3.1 6.9 + - - -
107B VAL* 2.8 42.8 + - - +
109B GLU* 2.8 31.0 + - - -
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Residues in contact with ALA 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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85B SER* 1.3 79.9 + - - +
87B ILE* 1.3 72.7 + - - +
102B ASN* 5.4 3.8 - - + -
103B TYR 3.2 19.1 - - - +
104B GLN* 3.7 32.0 - - - +
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Residues in contact with ILE 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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23B PHE* 5.1 0.4 - - + -
35B PRO* 5.1 6.3 - - + -
38B TYR* 4.2 23.8 - - + -
86B ALA* 1.3 80.7 - - - +
88B SER* 1.3 64.9 + - - +
89B MET* 3.7 33.0 - - + -
101B LYS 4.0 0.2 - - - +
102B ASN* 3.4 5.0 - - - +
103B TYR* 2.9 33.8 + - + +
106B MET* 4.1 24.6 - - + +
107B VAL* 3.9 24.0 - - + -
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Residues in contact with SER 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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35B PRO* 3.9 8.0 - - - +
87B ILE* 1.3 76.1 - - - +
89B MET* 1.3 67.1 + - - +
100B LEU* 4.1 18.1 - - - +
101B LYS 3.5 4.0 - - - -
102B ASN* 2.8 24.7 + - - -
18D ILE* 4.3 17.2 - - - +
19D PRO 5.3 4.2 - - - +
20D ASN* 5.9 0.7 - - - +
21D ILE* 3.7 14.2 - - - +
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Residues in contact with MET 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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23B PHE* 3.7 35.2 - - + -
28B TRP* 5.7 0.7 - - + -
31B TRP* 4.5 0.4 - - + -
32B ILE* 3.7 26.9 - - + -
34B ALA 3.4 9.9 - - - +
35B PRO* 4.2 2.5 - - + -
87B ILE* 3.7 18.8 - - + -
88B SER* 1.3 78.9 - - - +
90B LEU* 1.3 62.9 + - - +
91B MET* 3.7 2.6 + - + +
100B LEU* 3.5 7.1 - - - +
101B LYS* 3.0 31.4 + - - +
103B TYR* 3.6 46.7 - - + +
106B MET* 4.2 7.9 - - + -
2D ILE* 4.3 9.9 - - + -
21D ILE* 4.2 1.3 - - - -
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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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32B ILE* 3.8 1.8 - - - -
33B VAL* 2.9 49.8 + - + +
34B ALA* 2.9 16.9 + - + +
89B MET* 1.3 72.5 - - - +
91B MET* 1.3 58.9 + - - +
98B VAL* 3.6 31.2 - - + -
99B VAL 3.5 10.3 - - - +
100B LEU* 3.8 19.5 - - + +
21D ILE* 4.0 11.1 - - + +
27D ILE* 3.8 33.4 - - + -
38D CYS* 3.7 18.8 - - + -
39D LYS 5.8 1.3 - - - +
40D GLN* 6.2 2.0 - - + -
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Residues in contact with MET 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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31B TRP* 3.2 28.9 - - + +
32B ILE* 4.4 2.2 - - + +
33B VAL* 4.2 3.8 - - - +
89B MET* 3.7 2.8 + - + +
90B LEU* 1.3 75.9 - - - +
92B LEU* 1.3 71.3 + - - +
93B ASP* 3.7 26.7 - - + +
94B GLU* 5.6 0.4 - - - +
98B VAL* 3.7 9.7 - - - +
99B VAL* 2.8 59.1 + - + +
101B LYS* 3.5 37.2 - - + +
103B TYR* 3.9 20.6 - - - +
-1D TRP* 4.9 7.6 - - - -
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Residues in contact with LEU 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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30B ASP 4.4 17.5 - - - +
31B TRP* 3.1 25.5 + - + +
33B VAL* 3.9 20.2 - - + -
91B MET* 1.3 87.4 - - - +
93B ASP* 1.3 69.4 + - - +
96B GLU* 3.0 50.0 - - + +
97B LYS 3.3 6.5 - - - +
98B VAL* 5.0 6.7 - - + -
-1D TRP* 4.9 5.0 + - - -
40D GLN* 6.1 1.8 - - - +
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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