Contacts of the helix formed by residues 61 - 80 (chain Z) in PDB entry 5WTI
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 SER 61 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Z ALA* 4.0 5.4 - - - -
59Z LYS* 4.4 8.9 + - - +
60Z VAL* 1.3 78.4 - - - +
62Z LYS* 1.3 64.5 + - - +
63Z ALA* 3.7 8.9 + - - +
64Z GLU* 3.3 21.7 + - - +
65Z ILE* 3.1 25.8 + - - +
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Residues in contact with LYS 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Z GLN* 3.4 27.8 + - - +
44Z GLU* 4.0 10.2 - - + +
45Z ALA* 3.8 24.5 - - + +
61Z SER* 1.3 72.7 - - - +
63Z ALA* 1.3 63.1 + - - +
65Z ILE* 3.8 2.0 - - - +
66Z GLN* 3.0 49.4 + - - +
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Residues in contact with ALA 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61Z SER* 3.2 9.4 + - - +
62Z LYS* 1.3 79.7 - - - +
64Z GLU* 1.3 56.4 + - - +
66Z GLN* 3.8 8.4 + - - +
67Z ALA* 3.1 24.3 + - - +
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Residues in contact with GLU 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Z VAL* 3.8 20.9 - - + -
61Z SER* 3.3 18.2 + - - +
62Z LYS 3.3 0.2 - - - -
63Z ALA* 1.3 77.5 - - - +
65Z ILE* 1.3 61.1 + - - +
67Z ALA* 3.1 11.8 + - - +
68Z GLU* 2.7 59.2 + - - +
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Residues in contact with ILE 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Z LYS* 3.6 43.7 - - + +
40Z LEU* 3.6 32.2 - - + +
43Z GLN* 3.9 10.8 - - - +
44Z GLU 3.6 19.3 - - - +
46Z ILE* 4.6 5.6 - - + -
60Z VAL* 3.8 21.3 - - + +
61Z SER 3.1 17.9 + - - +
62Z LYS* 3.8 4.5 - - - +
64Z GLU* 1.3 77.0 - - - +
66Z GLN* 1.3 51.9 + - - +
68Z GLU* 3.1 11.4 + - - +
69Z LEU* 2.7 33.4 + - - +
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Residues in contact with GLN 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43Z GLN* 3.3 38.6 + - + +
62Z LYS* 3.0 48.3 + - - +
63Z ALA* 4.1 6.9 - - - +
65Z ILE* 1.3 76.9 - - - +
67Z ALA* 1.3 56.3 + - - +
69Z LEU* 4.0 7.2 - - - -
70Z TRP* 3.0 23.0 + - - +
88Z LYS* 5.8 0.2 + - - -
92Z PHE* 3.4 46.0 - - + +
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Residues in contact with ALA 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Z ALA 3.1 16.1 + - - +
64Z GLU* 3.1 21.2 + - - +
66Z GLN* 1.3 74.5 - - - +
68Z GLU* 1.3 65.4 + - - +
70Z TRP* 3.2 6.5 + - - +
71Z ASP* 3.0 27.9 + - - +
88Z LYS* 6.3 0.9 - - - +
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Residues in contact with GLU 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Z LYS* 4.3 13.5 + - - -
40Z LEU* 3.7 25.6 - - + +
60Z VAL* 5.2 1.9 - - - +
64Z GLU* 2.7 46.3 + - - +
65Z ILE* 3.6 11.7 - - - +
67Z ALA* 1.3 72.3 - - - +
69Z LEU* 1.3 57.8 + - - +
71Z ASP* 3.4 11.2 + - - +
72Z PHE* 2.9 28.4 + - - +
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Residues in contact with LEU 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Z LEU* 4.0 23.3 - - + +
41Z ILE* 3.8 24.9 - - + -
43Z GLN* 3.4 43.7 - - + +
65Z ILE 2.7 19.4 + - - +
66Z GLN* 3.7 6.3 - - - +
68Z GLU* 1.3 74.5 - - - +
70Z TRP* 1.3 56.6 + - - +
72Z PHE* 3.2 12.1 + - + +
73Z VAL* 2.7 36.2 + - + +
92Z PHE* 3.8 15.5 - - + -
95Z LEU* 3.7 21.3 - - + -
186Z LEU* 6.4 0.7 - - + -
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Residues in contact with TRP 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Z GLN 3.0 17.2 + - - +
67Z ALA* 3.2 6.0 + - - +
69Z LEU* 1.3 74.9 - - - +
71Z ASP* 1.3 67.7 + - - +
73Z VAL* 3.1 27.2 + - + +
74Z LEU* 2.9 71.7 + - + +
77Z GLN* 5.1 3.8 - - - -
85Z GLU* 6.2 1.3 - - + -
86Z VAL 3.4 30.1 - - - -
88Z LYS* 3.6 52.4 - - + +
91Z VAL* 3.9 16.2 - - + -
92Z PHE* 4.1 19.3 - + + -
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Residues in contact with ASP 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Z ALA* 3.0 18.4 + - - +
68Z GLU* 3.6 12.4 - - - +
70Z TRP* 1.3 77.3 - - - +
72Z PHE* 1.3 57.1 + - - +
74Z LEU* 3.3 13.3 + - - +
75Z LYS* 2.9 29.3 + - - +
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Residues in contact with PHE 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z TYR* 5.5 5.4 - + - -
37Z ILE* 4.5 25.6 - - + -
40Z LEU* 4.0 18.8 - - + -
41Z ILE* 5.9 2.5 - - + -
68Z GLU 2.9 14.3 + - - +
69Z LEU* 3.2 20.6 + - + +
71Z ASP* 1.3 76.3 - - - +
73Z VAL* 1.3 65.6 + - + +
75Z LYS* 3.4 31.1 + - + +
76Z MET* 3.0 37.3 + - + +
183Z LEU* 6.3 0.2 - - + -
186Z LEU* 3.4 37.0 - - + -
187Z PHE* 3.8 18.8 - - + -
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Residues in contact with VAL 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Z LEU* 2.7 27.3 + - + +
70Z TRP* 3.1 34.7 + - + +
72Z PHE* 1.3 77.6 - - + +
74Z LEU* 1.3 58.4 + - - +
76Z MET* 3.3 2.9 + - - +
77Z GLN* 2.9 48.2 + - - +
91Z VAL* 4.2 7.9 - - + -
95Z LEU* 4.0 26.9 - - + -
183Z LEU* 3.8 22.7 - - + +
186Z LEU* 5.9 1.3 - - + -
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Residues in contact with LEU 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Z TRP* 2.9 64.3 + - + +
71Z ASP* 3.9 13.5 - - - +
73Z VAL* 1.3 73.3 - - - +
75Z LYS* 1.3 65.4 + - - +
77Z GLN* 3.4 21.3 - - - +
78Z LYS* 3.0 26.3 + - - +
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Residues in contact with LYS 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Z TYR* 5.7 7.1 + - - -
71Z ASP 2.9 17.6 + - - +
72Z PHE* 3.6 33.0 - - + +
74Z LEU* 1.3 77.6 - - - +
76Z MET* 1.3 66.3 + - + +
78Z LYS* 3.9 4.7 - - - +
79Z CYS* 3.0 29.0 + - + +
188Z ILE* 6.0 4.3 - - - -
195Z GLU* 5.0 9.7 + - - -
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Residues in contact with MET 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Z PHE* 3.0 36.8 + - + +
73Z VAL 3.8 3.1 - - - +
75Z LYS* 1.3 86.1 - - + +
77Z GLN* 1.3 62.1 + - - +
79Z CYS* 3.7 11.1 - - + +
80Z ASN* 2.9 50.3 + - - +
182Z GLY 4.3 0.7 - - - -
183Z LEU* 4.1 13.7 - - + -
185Z PRO* 3.3 29.2 - - + +
186Z LEU 3.3 24.2 - - - +
187Z PHE* 3.9 15.3 - - - +
188Z ILE* 4.4 18.6 - - + -
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Residues in contact with GLN 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Z TRP* 5.1 3.5 - - - -
73Z VAL* 2.9 30.4 + - - +
74Z LEU* 3.4 31.0 - - - +
76Z MET* 1.3 76.8 - - - +
78Z LYS* 1.3 61.8 + - - +
80Z ASN 3.2 6.2 + - - -
82Z PHE* 3.1 52.2 + - + +
84Z HIS 5.3 3.1 + - - +
85Z GLU* 5.7 1.6 - - - -
86Z VAL* 4.0 18.2 - - - +
91Z VAL* 5.4 0.8 - - - +
181Z TYR* 3.0 30.8 + - - +
182Z GLY 4.0 9.4 - - - +
183Z LEU* 4.2 4.4 - - + +
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Residues in contact with LYS 78 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Z LEU 3.0 16.8 + - - +
75Z LYS* 3.9 4.7 - - - +
77Z GLN* 1.3 76.1 - - - +
79Z CYS* 1.3 65.3 + - - +
81Z SER* 3.1 14.8 + - - +
82Z PHE 5.1 1.8 - - - +
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Residues in contact with CYS 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Z LYS* 3.0 21.5 + - + +
76Z MET* 3.7 17.5 - - + +
77Z GLN 3.3 0.2 - - - -
78Z LYS* 1.3 80.4 - - - +
80Z ASN* 1.3 60.8 + - - +
81Z SER* 3.3 4.5 + - - -
188Z ILE* 3.8 29.2 - - - -
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Residues in contact with ASN 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Z MET* 2.9 24.2 + - - +
77Z GLN 3.8 2.5 - - - +
78Z LYS 3.1 0.4 - - - -
79Z CYS* 1.3 79.4 - - - +
81Z SER* 1.3 71.4 + - - +
82Z PHE* 3.2 4.8 + - + +
182Z GLY* 2.8 30.1 + - - +
183Z LEU* 4.2 0.2 - - - +
184Z ILE 4.0 3.8 - - - +
185Z PRO* 3.1 52.8 + - - +
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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