Contacts of the helix formed by residues 66 - 83 (chain Z) in PDB entry 6P59
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 PRO 66 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94W SER* 3.6 16.2 - - - +
23Z SER* 4.1 1.3 - - - -
24Z SER* 3.3 17.4 - - - +
25Z ASP* 4.3 0.7 - - - +
64Z GLU 3.8 7.9 - - - +
65Z ILE* 1.3 92.2 - - + +
67Z SER* 1.3 62.0 + - - +
68Z HIS* 3.4 10.5 - - + -
69Z VAL* 3.5 11.5 + - + -
70Z LEU* 2.8 25.6 + - - +
102Z GLU* 3.7 22.9 - - + +
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Residues in contact with SER 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93W PHE* 3.6 10.0 - - - -
94W SER* 2.9 24.8 + - - -
23Z SER* 3.8 13.0 - - - -
25Z ASP* 2.8 36.0 + - - -
27Z HIS* 3.8 19.4 - - - -
29Z PHE* 3.7 5.3 - - - -
66Z PRO* 1.3 74.4 - - - +
68Z HIS* 1.3 59.5 + - - +
71Z SER* 2.8 32.2 + - - -
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Residues in contact with HIS 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93W PHE* 4.1 11.2 - - + -
94W SER* 2.8 43.5 + - - +
95W SER 4.2 2.2 - - - -
96W PRO* 3.2 43.8 - - + +
66Z PRO* 4.1 6.7 - - + +
67Z SER* 1.3 81.8 + - - +
69Z VAL* 1.3 79.1 + - + +
71Z SER* 2.7 19.4 + - - -
72Z LYS* 3.5 14.4 + - - +
99Z ILE* 4.2 20.4 - - + +
102Z GLU* 3.4 20.8 + - - +
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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
----------------------------------------------------------
65Z ILE* 3.8 7.0 - - + -
66Z PRO* 3.5 13.3 + - + +
67Z SER 3.1 0.4 - - - -
68Z HIS* 1.3 103.6 + - + +
70Z LEU* 1.3 66.2 + - - +
71Z SER 3.1 0.2 - - - -
72Z LYS* 3.1 7.7 + - - +
73Z VAL* 2.9 20.7 + - + +
99Z ILE* 4.6 5.8 - - + -
102Z GLU* 3.6 30.1 - - + +
103Z LEU* 3.9 17.3 - - + -
106Z ALA* 3.5 31.9 - - + -
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Residues in contact with LEU 70 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z LEU* 4.0 19.5 - - + +
22Z ILE 4.1 3.8 - - - +
23Z SER* 3.7 26.7 - - - +
29Z PHE* 3.7 27.8 - - + -
62Z PHE* 4.5 15.9 - - + -
65Z ILE* 3.7 19.9 - - + +
66Z PRO 2.8 19.1 + - - +
67Z SER* 3.9 3.1 - - - +
69Z VAL* 1.3 76.4 - - - +
71Z SER* 1.3 56.9 + - - +
73Z VAL* 3.3 16.8 + - + -
74Z CYS* 3.0 36.8 + - - -
77Z PHE* 6.2 0.2 - - + -
110Z LEU* 5.1 3.8 - - + -
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Residues in contact with SER 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W PHE* 3.8 6.7 - - - -
93W PHE* 3.5 29.9 - - - -
29Z PHE* 3.7 18.5 - - - -
67Z SER 2.8 15.1 + - - -
68Z HIS* 2.7 27.2 + - - -
70Z LEU* 1.3 75.0 - - - +
72Z LYS* 1.3 63.5 + - - +
74Z CYS 3.5 1.1 + - - +
75Z MET* 3.2 35.3 + - - +
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Residues in contact with LYS 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70W GLN 4.8 5.3 + - - -
68Z HIS 3.5 11.2 + - - +
69Z VAL* 3.1 9.5 + - - +
71Z SER* 1.3 81.0 + - - +
73Z VAL* 1.3 66.1 + - - +
75Z MET* 3.2 20.9 + - + +
76Z TYR* 3.0 17.4 + - - -
93Z PHE* 3.8 18.5 - - + -
94Z PRO* 2.7 46.2 + - - +
95Z ILE* 4.7 4.2 - - - +
96Z ALA* 5.1 3.7 - - - +
99Z ILE* 4.4 30.7 - - + -
103Z LEU* 4.2 19.5 - - + -
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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
----------------------------------------------------------
152F LEU* 4.2 13.2 - - + -
69Z VAL 2.9 21.2 + - - +
70Z LEU* 3.6 17.0 - - + +
71Z SER 3.3 0.2 - - - -
72Z LYS* 1.3 77.1 - - - +
74Z CYS* 1.3 61.7 + - - +
76Z TYR* 3.0 19.4 + - - +
77Z PHE* 3.1 39.8 + - + -
103Z LEU* 3.6 20.6 - - + -
106Z ALA* 4.2 16.8 - - + -
110Z LEU* 3.8 20.9 - - + -
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Residues in contact with CYS 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15W PHE* 3.5 28.5 - - + -
21Z LEU* 4.2 15.3 - - - -
29Z PHE* 4.0 20.2 - - - -
31Z VAL* 3.6 25.4 - - + +
70Z LEU* 3.0 26.4 + - - +
71Z SER 3.9 0.2 - - - +
72Z LYS 3.3 0.2 - - - -
73Z VAL* 1.3 72.7 - - - +
75Z MET* 1.3 67.0 + - - +
77Z PHE* 3.2 21.8 + - - +
78Z THR* 3.4 15.6 + - - +
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Residues in contact with MET 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W MET* 3.8 21.3 - - + -
15W PHE* 3.6 15.3 - - + -
69W PRO 3.6 11.7 - - - +
70W GLN 3.6 20.9 - - - +
71W ALA* 4.9 1.3 - - - -
72W PRO* 3.8 21.1 - - + +
93W PHE* 5.8 2.5 - - + -
71Z SER* 3.2 23.3 + - - +
72Z LYS* 3.2 26.8 + - + +
74Z CYS* 1.3 73.8 - - - +
76Z TYR* 1.3 65.8 + - - +
78Z THR* 2.9 12.2 + - - -
79Z TYR* 2.8 23.9 + - - +
93Z PHE* 4.3 5.6 - - + -
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Residues in contact with TYR 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F VAL* 5.1 0.6 - - + +
150F GLY 2.9 25.7 + - - -
151F THR* 3.2 5.7 + - - -
152F LEU* 3.0 59.2 + - + -
155F LEU* 4.1 10.3 - - + -
38Z THR* 4.1 10.5 - - + -
72Z LYS 3.0 7.2 + - - +
73Z VAL 3.0 12.8 + - - +
75Z MET* 1.3 76.5 - - - +
77Z PHE* 1.3 68.8 + + - +
79Z TYR* 3.6 14.7 - + - +
80Z LYS* 2.9 53.7 + - + +
93Z PHE* 3.7 25.4 - + + -
111Z ASP* 4.7 6.0 + - - -
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Residues in contact with PHE 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21Z LEU* 4.3 19.1 - - + -
31Z VAL* 4.4 11.2 - - + -
35Z HIS* 3.6 20.6 - - + +
36Z ALA* 3.9 22.9 - - - -
38Z THR* 3.8 31.2 - - + -
39Z SER* 4.1 23.8 - - - -
42Z ILE* 4.3 6.5 - - + -
70Z LEU* 6.2 0.2 - - + -
73Z VAL* 3.1 34.9 + - + -
74Z CYS* 3.4 19.3 - - - +
75Z MET 3.1 0.8 - - - -
76Z TYR* 1.3 82.7 - + - +
78Z THR* 1.3 63.1 + - + +
80Z LYS* 3.1 4.6 + - - +
81Z VAL* 3.1 29.3 + - - +
110Z LEU* 5.1 0.2 - - + -
111Z ASP* 5.3 3.6 - - - -
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Residues in contact with THR 78 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W PHE* 4.9 14.4 - - + +
15W PHE* 4.4 29.2 - - + +
16W THR 6.5 0.4 - - - -
69W PRO* 3.7 24.8 + - - +
72W PRO* 5.4 1.6 - - - +
31Z VAL* 5.8 2.7 - - + -
32Z LYS 6.3 0.2 - - - +
35Z HIS* 3.5 31.5 - - + +
74Z CYS 3.4 9.2 + - - +
75Z MET* 2.9 17.7 + - - -
77Z PHE* 1.3 76.9 - - + +
79Z TYR* 1.3 59.7 + - - +
81Z VAL* 3.7 1.8 + - - +
82Z ARG* 3.5 18.7 + - - +
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Residues in contact with TYR 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F VAL* 3.7 24.5 - - + +
155F LEU* 4.5 9.7 - - + +
69W PRO* 3.6 12.8 - - + -
70W GLN* 3.6 26.0 - - + -
75Z MET 2.8 17.4 + - - +
76Z TYR* 3.6 16.4 - + - +
78Z THR* 1.3 77.6 + - - +
80Z LYS* 1.3 66.5 + - - +
82Z ARG 3.7 0.2 + - - -
83Z TYR* 3.5 39.9 + + + +
90Z ILE* 3.8 14.2 - - + +
91Z PRO 2.4 31.0 + - - -
92Z GLU* 4.5 0.3 - - - -
93Z PHE* 3.8 42.5 + + + +
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Residues in contact with LYS 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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148C ARG* 5.5 5.7 - - - +
149F VAL* 4.3 30.1 + - + +
150F GLY 6.0 0.2 - - - -
151F THR* 6.2 1.1 - - - +
38Z THR* 3.9 28.7 - - + +
76Z TYR* 2.9 42.9 + - + +
77Z PHE* 3.9 4.3 - - - +
79Z TYR* 1.3 81.7 - - + +
81Z VAL* 1.3 63.3 + - + +
83Z TYR 4.2 0.2 - - - -
84Z THR* 3.1 35.1 + - - +
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Residues in contact with VAL 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z GLU* 5.2 4.3 - - + +
35Z HIS* 3.5 51.4 - - + +
38Z THR* 4.7 7.6 - - - +
77Z PHE 3.1 17.3 + - - +
78Z THR 4.2 4.0 - - - +
79Z TYR 3.3 0.6 - - - -
80Z LYS* 1.3 79.5 - - + +
82Z ARG* 1.3 63.3 + - - +
84Z THR* 3.5 15.2 - - - +
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Residues in contact with ARG 82 (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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2W ASP* 4.6 17.9 + - - +
4W PHE* 3.5 42.2 - - + -
64W SER* 4.8 9.3 + - - -
68W ARG* 6.2 0.8 - - - +
69W PRO* 4.7 1.5 - - + +
78Z THR 3.5 14.3 + - - +
79Z TYR 3.7 0.2 + - - -
81Z VAL* 1.3 82.0 - - - +
83Z TYR* 1.3 105.6 + - + +
84Z THR* 3.1 7.4 + - - +
85Z ASN 4.4 3.6 + - - -
86Z SER* 4.5 8.6 + - - -
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Residues in contact with TYR 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F VAL* 3.3 22.2 - - + +
68W ARG* 5.5 3.6 - - - +
69W PRO* 4.0 26.2 - - + +
70W GLN* 4.1 9.1 + - - -
79Z TYR* 3.5 28.9 + + + +
80Z LYS 4.2 2.7 - - - -
82Z ARG* 1.3 117.8 + - + +
84Z THR* 1.3 56.8 + - - +
85Z ASN 3.9 0.4 - - - -
86Z SER* 4.6 13.8 - - - +
88Z THR* 4.8 10.8 - - - -
89Z GLU 4.5 7.6 - - - -
90Z ILE* 4.3 24.9 - - + +
91Z PRO* 3.4 41.8 - - + +
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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
------------------------------------------------------------
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