Contacts of the helix formed by residues 58 - 69 (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 THR 58 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 6.0 0.9 - - + -
84A LEU* 4.4 9.4 - - + +
105A ASP* 3.5 27.9 + - - +
57B SER* 1.3 76.6 - - - +
59B ASN* 1.3 66.1 + - - +
60B HIS* 3.7 9.0 - - + +
61B ALA* 2.9 41.5 + - + +
62B ILE* 3.1 9.0 + - - +
113B CYS 3.3 3.6 + - - -
114B ARG* 3.8 40.7 + - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.0 4.0 - - - +
104A GLN* 2.8 40.1 + - - +
105A ASP* 3.3 6.0 + - + +
106A MET* 3.7 12.1 - - - -
57B SER 3.7 1.0 + - - -
58B THR* 1.3 71.8 + - - +
60B HIS* 1.3 65.4 - - - +
62B ILE* 2.9 19.4 + - - +
63B VAL* 3.0 10.7 + - - +
2C ILE* 3.1 27.6 - - + +
3C THR* 3.2 41.0 + - - +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.9 1.3 - - + +
38A TYR* 4.6 0.9 - - - -
40A ALA* 3.8 11.8 - - + +
41A MET 2.7 28.3 + - - -
42A TYR* 4.3 2.9 - - + -
81A PRO* 4.3 9.6 - - + +
84A LEU* 3.9 12.6 - - + -
105A ASP 2.8 21.2 + - - +
106A MET* 3.3 24.9 - - - +
108A VAL* 3.2 26.9 - - + +
58B THR* 3.3 5.3 - - + +
59B ASN* 1.3 73.4 - - - +
61B ALA* 1.3 64.1 + - - +
63B VAL* 3.1 9.1 + - + +
64B GLN* 2.8 51.4 + - + +
114B ARG* 4.7 1.6 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER* 4.1 7.4 - - - +
58B THR* 2.9 30.6 + - + +
60B HIS* 1.3 75.9 + - - +
62B ILE* 1.3 58.4 + - - +
64B GLN* 3.1 4.7 + - - +
65B THR* 2.9 33.4 + - - +
77B ALA* 3.9 22.7 - - + +
113B CYS 3.5 19.1 - - - +
114B ARG* 4.0 5.8 - - - -
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TRP* 4.5 1.1 - - + -
51B LEU* 4.0 32.3 - - + -
57B SER* 3.8 35.2 - - - +
58B THR 3.1 6.9 + - - +
59B ASN* 2.9 9.4 + - - +
61B ALA* 1.3 73.1 - - - +
63B VAL* 1.3 68.3 + - - +
65B THR* 3.1 15.4 + - - -
66B LEU* 3.2 24.0 + - + +
1C LEU* 3.4 25.8 - - + +
2C ILE* 3.8 23.1 - - + -
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 6.2 0.2 - - + -
21A VAL* 3.9 38.1 - - + -
23A PHE* 5.5 0.4 - - + -
26A VAL* 5.7 2.5 - - + -
28A TRP* 4.1 27.6 - - + -
38A TYR* 4.0 21.3 - - + +
40A ALA* 5.0 2.7 - - + -
106A MET* 4.1 17.5 - - + -
59B ASN 3.0 13.2 + - - +
60B HIS* 3.1 9.4 + - + +
62B ILE* 1.3 79.9 - - - +
64B GLN* 1.3 63.7 + - - +
66B LEU* 3.1 5.2 + - - +
67B VAL* 3.1 22.1 + - + +
2C ILE* 4.5 1.8 - - + -
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Residues in contact with GLN 64 (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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19A LEU* 5.7 3.4 - - + -
42A TYR* 3.6 18.3 - - + +
43A CYS 4.8 4.8 + - - -
81A PRO* 5.5 1.9 - - - +
60B HIS* 2.8 46.7 + - + +
61B ALA* 3.1 6.0 + - - +
63B VAL* 1.3 74.6 - - - +
65B THR* 1.3 62.8 + - - +
67B VAL* 3.8 7.0 - - - +
68B ASN* 3.1 22.2 + - - +
74B ILE* 4.1 12.5 - - + +
75B PRO* 3.0 39.2 + - - +
76B LYS 3.5 14.8 + - - -
77B ALA* 4.2 9.0 - - - +
114B ARG* 5.3 3.6 - - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B CYS* 4.7 8.6 + - - +
48B PRO 3.7 24.8 + - - +
49B PHE* 3.9 19.6 - - + +
51B LEU* 3.7 20.7 - - + +
61B ALA 2.9 19.0 + - - -
62B ILE 3.1 6.2 + - - -
64B GLN* 1.3 81.0 - - - +
66B LEU* 1.3 64.1 + - + +
68B ASN* 3.3 8.5 + - - +
69B SER* 3.1 19.2 + - - -
76B LYS* 5.4 2.8 - - + +
77B ALA* 4.1 18.1 + - - +
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Residues in contact with LEU 66 (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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26A VAL* 4.3 31.7 - - + +
28A TRP* 3.3 39.3 - - + +
49B PHE* 3.7 29.6 - - + -
51B LEU* 5.1 4.5 - - + -
62B ILE* 3.2 25.2 + - + +
63B VAL 3.1 6.8 + - - +
65B THR* 1.3 78.4 - - + +
67B VAL* 1.3 61.1 + - - +
69B SER* 2.4 27.6 + - - +
70B VAL* 3.7 4.2 + - - +
1C LEU* 4.7 9.4 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.4 12.8 - - + -
20A TYR 6.0 0.2 - - - +
21A VAL* 4.2 25.8 - - + -
26A VAL* 4.6 13.9 - - + +
63B VAL* 3.1 18.7 + - + +
64B GLN* 3.9 7.6 - - - +
65B THR 3.3 0.2 - - - -
66B LEU* 1.3 74.3 - - - +
68B ASN* 1.3 52.9 + - - +
70B VAL* 2.8 12.4 + - + +
71B ASN* 2.7 40.5 + - + +
74B ILE* 3.8 31.2 - - + -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 5.8 3.4 - - - +
64B GLN 3.1 16.1 + - - +
65B THR* 3.5 8.4 + - - +
67B VAL* 1.3 79.1 - - - +
69B SER* 1.3 60.9 + - - +
70B VAL 2.9 5.2 + - - -
71B ASN 3.4 20.6 + - - -
72B SER* 3.7 15.8 + - - +
74B ILE* 2.7 25.7 + - - +
75B PRO* 3.7 5.4 - - - +
76B LYS* 3.5 51.4 + - - +
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Residues in contact with SER 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 3.8 38.6 - - - -
65B THR 3.1 10.3 + - - -
66B LEU* 2.4 27.7 + - - +
67B VAL 3.0 0.2 - - - -
68B ASN* 1.3 80.2 - - - +
70B VAL* 1.3 66.3 + - - +
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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