Contacts of the helix formed by residues 66 - 79 (chain B) in PDB entry 5TKM
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 HIS 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLN 3.3 18.4 - - - +
59B VAL 3.6 13.1 + - - -
60B TYR* 3.0 14.0 + - - -
61B PHE 2.9 24.3 + - - -
62B LYS 3.3 11.8 + - - -
63B PRO* 2.9 23.1 + - + +
64B GLN 3.3 0.4 - - - -
65B TYR* 1.3 80.5 - - - +
67B ALA* 1.3 66.4 + - - +
68B GLU* 3.2 13.5 - - - +
69B MET* 3.2 4.4 + - - +
70B CYS* 2.9 24.0 + - - -
97B CYS* 3.5 13.0 - - + -
100B CYS* 3.6 4.0 - - - -
401B ZN 2.0 35.7 - - - -
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Residues in contact with ALA 67 (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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33B THR* 3.6 41.0 - - + +
35B LEU* 3.9 19.6 - - + +
55B PHE* 4.4 5.8 - - + +
56B ARG 4.4 2.0 - - - -
57B GLY* 3.7 16.9 - - - +
58B GLN 4.3 2.0 + - - -
66B HIS* 1.3 72.4 - - - +
68B GLU* 1.3 58.9 + - - +
70B CYS* 3.2 8.7 + - - +
71B PHE* 2.8 30.0 + - - +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.1 16.6 + - - +
35B LEU* 4.0 9.8 - - + +
58B GLN 5.2 0.3 - - - +
66B HIS* 3.5 18.7 - - - +
67B ALA* 1.3 85.6 + - - +
69B MET* 1.3 71.8 + - + +
71B PHE* 3.5 3.3 + - - +
72B LEU* 3.0 26.5 + - - +
90B TRP* 3.5 35.7 - - + -
92B VAL* 5.5 2.0 - - + +
94B TRP 4.2 1.9 - - - +
95B THR 4.0 4.7 - - - +
96B PRO* 3.4 37.4 - - + +
97B CYS 4.7 0.8 + - - -
100B CYS* 4.1 8.5 - - + -
104B LEU* 4.3 2.0 - - + +
401B ZN 4.0 3.6 - - - -
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Residues in contact with MET 69 (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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63B PRO* 3.2 33.4 - - + +
64B GLN* 4.6 8.7 - - - +
66B HIS 3.2 3.7 + - - +
68B GLU* 1.3 84.5 - - + +
70B CYS* 1.3 61.6 + - - +
71B PHE 3.2 0.2 - - - -
72B LEU* 3.9 24.1 - - + +
73B SER* 2.9 32.6 + - - -
100B CYS* 3.7 32.3 - - + +
103B LYS* 3.9 33.4 - - + -
104B LEU* 4.4 4.0 - - + -
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Residues in contact with CYS 70 (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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7B ASN* 4.8 4.5 + - - +
55B PHE* 3.7 24.2 - - + -
56B ARG 4.4 13.5 - - - -
57B GLY* 5.0 0.2 - - - -
64B GLN 4.7 8.9 + - - -
65B TYR* 4.6 6.5 - - - -
66B HIS 2.9 23.2 + - - -
67B ALA* 3.3 12.3 - - - +
69B MET* 1.3 76.4 - - - +
71B PHE* 1.3 61.6 + - - +
73B SER* 4.0 3.4 - - - -
74B TRP* 3.1 24.6 + - - +
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Residues in contact with PHE 71 (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 LEU* 4.2 5.6 - - + -
37B TYR* 3.5 48.5 - + + -
39B VAL* 4.3 2.5 - - + -
55B PHE* 3.8 18.1 - + + -
67B ALA 2.8 15.8 + - - +
68B GLU 3.7 3.8 - - - +
70B CYS* 1.3 78.6 - - - +
72B LEU* 1.3 68.7 + - + +
74B TRP* 3.3 9.8 + + - +
75B PHE* 2.8 52.9 + + + +
88B ILE* 3.7 32.1 - - + -
90B TRP* 3.5 34.1 - + + -
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Residues in contact with LEU 72 (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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68B GLU 3.0 16.1 + - - +
69B MET* 3.3 31.1 + - + +
71B PHE* 1.3 88.6 - - + +
73B SER* 1.3 58.2 + - - +
75B PHE* 3.8 2.5 - - + +
76B CYS* 3.0 39.3 + - - -
103B LYS* 4.3 17.5 - - + +
104B LEU* 4.1 17.9 - - + -
107B PHE* 3.8 46.2 - - + -
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Residues in contact with SER 73 (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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69B MET 2.9 17.3 + - - -
70B CYS* 4.0 4.0 - - - -
72B LEU* 1.3 78.7 - - - +
74B TRP* 1.3 62.3 + - - +
76B CYS* 4.1 3.8 - - - +
77B GLY* 3.1 19.2 + - - -
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Residues in contact with TRP 74 (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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7B ASN* 4.4 12.7 - - + +
8B PRO* 3.9 23.0 - - + +
37B TYR* 3.6 39.3 - + - -
39B VAL* 4.4 1.3 - - + -
51B ASP* 4.1 14.1 - - + -
55B PHE* 3.5 19.7 - + + -
70B CYS 3.1 18.6 + - - +
71B PHE* 3.9 21.3 - + - -
73B SER* 1.3 77.4 - - - +
75B PHE* 1.3 79.4 + + + +
78B ASN* 2.9 67.1 + - + +
79B GLN* 3.5 39.3 - - + -
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Residues in contact with PHE 75 (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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39B VAL* 4.2 17.3 - - + -
71B PHE* 2.8 48.2 + + + +
72B LEU* 3.8 4.3 - - + +
74B TRP* 1.3 82.7 - + + +
76B CYS* 1.3 61.6 + - - +
79B GLN* 2.8 56.5 + - + +
80B LEU* 3.2 32.0 + - + -
86B PHE* 4.0 26.0 - + + -
88B ILE* 3.9 19.5 - - + -
107B PHE* 3.8 27.6 - + - -
114B VAL* 4.5 4.0 - - + -
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Residues in contact with CYS 76 (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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72B LEU* 3.0 25.4 + - - +
73B SER* 4.2 4.0 - - - +
75B PHE* 1.3 77.5 - - - +
77B GLY* 1.3 58.0 + - - +
80B LEU* 3.0 38.3 - - + +
107B PHE* 4.0 29.6 - - - -
111B HIS* 5.6 1.8 - - - -
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Residues in contact with GLY 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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73B SER 3.1 15.5 + - - -
74B TRP 3.8 1.8 - - - -
76B CYS* 1.3 77.4 - - - +
78B ASN* 1.3 69.8 + - - +
80B LEU 4.0 5.8 - - - +
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Residues in contact with ASN 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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74B TRP* 2.9 63.2 + - + +
77B GLY* 1.3 86.8 - - - +
79B GLN* 1.3 68.8 + - - +
80B LEU 3.7 1.6 - - - -
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Residues in contact with GLN 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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39B VAL* 4.6 4.0 - - + -
50B TRP* 3.6 23.5 + - - -
51B ASP* 2.4 39.8 + - - -
74B TRP* 3.5 22.3 - - + -
75B PHE* 2.8 48.0 + - + +
78B ASN* 1.3 83.4 + - - +
80B LEU* 1.3 62.3 + - - +
81B PRO 4.1 0.5 - - - +
82B ALA* 3.4 21.7 - - - +
86B PHE* 3.8 11.8 - - + -
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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
------------------------------------------------------------
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