Contacts of the helix formed by residues 58 - 78 (chain Z) in PDB entry 6F0X
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 ASP 58 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Q LYS* 4.4 2.0 - - - +
38Z TYR* 6.0 3.8 - - + -
43Z PHE* 4.7 5.9 - - + -
56Z THR* 3.0 12.8 + - - +
57Z THR* 1.3 74.4 + - - +
59Z LEU* 1.3 53.5 + - - +
60Z GLU* 3.0 28.3 - - - +
61Z LEU* 2.3 52.3 + - + +
62Z ILE* 2.4 38.8 + - - +
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Residues in contact with LEU 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Z THR 2.7 15.4 + - - +
58Z ASP* 1.3 70.0 + - - +
60Z GLU* 1.3 60.2 + - + +
62Z ILE* 3.6 21.8 - - + -
63Z LYS* 2.9 55.8 + - - +
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Residues in contact with GLU 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136Q LYS* 3.3 43.8 + - + +
137Q PRO 4.3 7.6 - - - +
58Z ASP* 2.9 18.8 + - - +
59Z LEU* 1.3 78.9 - - + +
61Z LEU* 1.3 58.8 + - - +
63Z LYS* 3.4 4.3 + - - +
64Z TYR* 2.9 27.2 + - - +
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Residues in contact with LEU 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135Q GLY* 6.3 1.1 - - - -
136Q LYS* 3.7 13.7 - - + +
29Z ASN* 5.9 0.2 - - - +
32Z LEU* 5.0 5.6 - - + -
38Z TYR* 3.5 35.7 - - + +
43Z PHE* 6.2 0.2 - - + -
56Z THR* 5.1 11.9 - - + +
58Z ASP* 2.3 40.2 + - + +
60Z GLU* 1.3 66.1 - - - +
62Z ILE* 1.3 65.3 + - - +
64Z TYR* 4.1 11.4 - - + -
65Z LEU* 2.8 66.8 + - + +
151Z PHE* 4.0 21.5 - - + -
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Residues in contact with ILE 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Z THR* 3.9 19.0 - - + +
57Z THR* 3.3 34.5 - - - +
58Z ASP 2.4 36.6 + - - +
59Z LEU* 3.4 25.8 - - + +
61Z LEU* 1.3 69.2 - - - +
63Z LYS* 1.3 59.5 + - + +
65Z LEU* 3.8 3.0 - - - +
66Z ASN* 2.6 53.4 + - - +
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Residues in contact with LYS 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Z LEU* 2.9 46.2 + - - +
60Z GLU* 3.9 2.9 - - - +
62Z ILE* 1.3 77.7 - - + +
64Z TYR* 1.3 58.8 + - - +
66Z ASN* 3.2 10.7 + - - +
67Z ASN* 2.7 40.6 + - - +
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Residues in contact with TYR 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q LEU* 3.2 53.5 + - + +
134Q SER* 3.2 23.7 - - - -
135Q GLY* 4.8 3.9 + - - -
136Q LYS* 2.7 32.3 - - + +
60Z GLU 2.9 8.3 + - - +
61Z LEU* 3.5 9.4 - - + +
63Z LYS* 1.3 78.0 - - - +
65Z LEU* 1.3 72.7 + - + +
67Z ASN* 3.1 13.7 + - - +
68Z VAL* 3.0 35.8 + - + +
151Z PHE* 5.9 0.4 - + - -
152Z ASP* 5.4 0.9 + - - -
153Z LEU* 3.3 36.9 - - + +
167Z TRP* 4.3 4.5 - - - -
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Residues in contact with LEU 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Z SER* 5.5 6.5 - - - +
28Z ILE* 4.3 31.6 - - + -
29Z ASN* 4.4 15.3 - - - +
32Z LEU* 5.6 0.2 - - + -
56Z THR* 5.8 1.3 - - + -
61Z LEU* 2.8 49.4 + - + +
62Z ILE* 4.0 3.1 - - - +
64Z TYR* 1.3 88.6 - - + +
66Z ASN* 1.3 61.6 + - - +
68Z VAL* 3.5 10.6 - - + +
69Z VAL* 2.7 38.2 + - + +
151Z PHE* 5.9 0.4 - - + -
153Z LEU* 4.0 19.1 - - + -
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Residues in contact with ASN 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Z SER* 5.6 1.6 + - - -
62Z ILE* 2.6 51.8 + - - +
63Z LYS* 3.2 9.4 + - - +
65Z LEU* 1.3 75.0 - - - +
67Z ASN* 1.3 65.6 + - - +
69Z VAL* 3.2 9.6 + - - +
70Z GLU* 2.9 25.1 + - - +
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Residues in contact with ASN 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q LEU* 5.8 7.9 - - + +
63Z LYS* 2.7 33.7 + - - +
64Z TYR* 3.2 13.8 - - - +
66Z ASN* 1.3 77.4 - - - +
68Z VAL* 1.3 63.6 + - + +
70Z GLU* 3.3 3.4 + - - +
71Z GLN* 2.9 26.7 + - - +
167Z TRP* 5.7 2.7 - - + -
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Residues in contact with VAL 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133Q LEU* 5.5 0.2 - - + -
28Z ILE* 6.0 5.6 - - + -
64Z TYR* 3.0 35.0 + - + +
65Z LEU* 3.5 17.0 - - + +
67Z ASN* 1.3 75.8 - - + +
69Z VAL* 1.3 58.1 + - + +
71Z GLN* 3.7 5.5 - - - +
72Z LEU* 2.8 57.5 + - + +
84Z LEU* 5.7 5.2 - - + -
153Z LEU* 4.9 5.6 - - + -
155Z ILE* 6.2 2.2 - - + -
167Z TRP* 3.9 30.5 - - + -
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Residues in contact with VAL 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z ALA* 3.6 31.8 - - + +
22Z GLU* 4.6 3.1 - - + +
24Z PHE* 6.1 0.7 - - + -
25Z SER* 3.9 29.4 - - - +
65Z LEU* 2.7 32.0 + - + +
66Z ASN* 3.2 10.3 + - - +
68Z VAL* 1.3 75.2 - - + +
70Z GLU* 1.3 60.1 + - + +
72Z LEU* 3.3 8.1 + - + +
73Z LYS* 2.8 32.3 + - - +
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Residues in contact with GLU 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Z ARG* 5.2 4.7 + - - -
66Z ASN 2.9 15.7 + - - +
67Z ASN* 4.1 3.8 - - - +
69Z VAL* 1.3 77.9 - - - +
71Z GLN* 1.3 57.6 + - - +
73Z LYS* 3.1 42.3 + - - +
74Z ASP* 2.9 31.2 + - + +
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Residues in contact with GLN 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Z ASN 2.9 19.3 + - - +
68Z VAL* 3.7 6.5 - - - +
70Z GLU* 1.3 76.2 - - - +
72Z LEU* 1.3 59.5 + - + +
74Z ASP* 3.2 15.7 + - - +
75Z TRP* 2.8 82.1 + - + +
164Z PRO* 3.4 21.0 - - - +
167Z TRP* 4.6 17.2 + - + +
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Residues in contact with LEU 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z ALA* 5.3 5.6 - - + -
24Z PHE* 5.0 12.8 - - + -
28Z ILE* 6.4 0.9 - - + -
68Z VAL* 2.8 41.6 + - + +
69Z VAL* 3.7 7.0 - - + +
71Z GLN* 1.3 74.5 - - + +
73Z LYS* 1.3 60.1 + - - +
75Z TRP* 3.7 16.3 - - + +
76Z LEU* 2.8 43.5 + - + +
81Z VAL* 4.2 23.1 - - + -
84Z LEU* 4.2 26.5 - - + -
104Z ILE* 6.0 1.3 - - + -
155Z ILE* 5.0 14.1 - - + -
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Residues in contact with LYS 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Z ARG* 4.8 27.7 - - + +
17Z ALA* 3.4 29.1 - - + +
18Z GLU* 3.8 34.0 - - + +
21Z ALA* 4.6 8.2 - - + +
69Z VAL* 2.8 18.1 + - - +
70Z GLU* 3.2 40.7 + - - +
72Z LEU* 1.3 75.8 - - - +
74Z ASP* 1.3 56.6 + - - +
76Z LEU* 4.5 2.2 - - - +
77Z TYR* 2.9 29.7 + - + +
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Residues in contact with ASP 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Z GLU* 2.9 17.0 + - + +
71Z GLN* 3.2 17.7 + - - +
73Z LYS* 1.3 75.0 - - - +
75Z TRP* 1.3 86.8 + - + +
77Z TYR* 2.8 28.6 + - - +
78Z LYS* 2.9 30.9 + - - +
162Z VAL* 5.1 4.7 - - - +
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Residues in contact with TRP 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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131Q LEU* 4.4 15.5 - - + -
71Z GLN* 2.8 54.5 + - + +
72Z LEU* 3.2 15.2 + - + +
74Z ASP* 1.3 98.8 + - - +
76Z LEU* 1.3 51.1 + - - +
78Z LYS* 3.1 1.5 - - + -
79Z CYS 2.5 10.9 + - - -
80Z SER* 2.3 60.2 + - - -
81Z VAL* 4.0 26.0 - - + +
155Z ILE* 4.0 23.3 - - + -
157Z THR* 4.3 9.6 - - + -
162Z VAL* 3.8 24.7 + - + +
163Z VAL* 4.9 0.9 - - - -
164Z PRO* 3.4 23.6 - - + -
167Z TRP* 5.1 11.7 - + - -
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Residues in contact with LEU 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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13Z LEU* 3.4 14.0 - - - +
17Z ALA* 3.5 38.8 - - + +
20Z VAL* 4.5 17.9 - - + -
21Z ALA* 4.7 3.6 - - + +
24Z PHE* 5.7 4.9 - - + -
72Z LEU* 2.8 32.5 + - + +
75Z TRP* 1.3 73.1 - - - +
77Z TYR* 1.3 56.6 + - - +
78Z LYS 2.8 4.4 + - - -
79Z CYS* 2.6 22.3 + - - +
81Z VAL* 4.5 13.7 - - + +
104Z ILE* 4.2 19.5 - - + -
106Z CYS* 3.5 5.2 - - + -
191Z HIS* 3.4 32.8 - - + +
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Residues in contact with TYR 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Z LEU* 3.2 43.4 - - + +
14Z ARG* 3.3 48.0 - - + -
17Z ALA* 4.2 3.7 - - + +
73Z LYS* 2.9 14.4 + - + +
74Z ASP* 2.8 19.2 + - - +
76Z LEU* 1.3 71.0 - - - +
78Z LYS* 1.3 75.9 + - + +
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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
----------------------------------------------------------
74Z ASP* 2.9 28.1 + - - +
75Z TRP* 4.7 1.1 - - + -
76Z LEU 2.8 0.6 - - - -
77Z TYR* 1.3 95.8 - - + +
79Z CYS* 1.3 70.9 + - - +
80Z SER* 3.0 20.5 + - - +
159Z LYS* 3.9 8.0 + - - +
162Z VAL* 5.4 11.9 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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