Contacts of the helix formed by residues 68 - 82 (chain H) in PDB entry 5G04
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 68 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H GLU* 3.3 27.3 + - + +
39H GLU* 5.8 1.1 - - - +
42H PHE* 5.3 1.4 - - - +
66H CYS 3.4 0.4 - - - +
67H THR* 1.3 82.1 - - - +
69H PRO* 1.3 75.4 - - + +
70H GLN* 4.2 8.1 - - - +
71H CYS* 3.3 28.8 + - - +
72H LYS* 3.2 22.3 + - - +
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Residues in contact with PRO 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H THR 3.7 3.3 - - - +
68H THR* 1.3 88.8 - - + +
70H GLN* 1.3 65.1 + - + +
72H LYS* 3.2 5.0 + - + -
73H TYR* 3.0 25.9 + - - +
109H GLU 3.7 22.7 - - - +
110H PHE* 3.5 36.3 - - + +
113H SER* 5.1 4.0 - - - +
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Residues in contact with GLN 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F HIS* 5.6 8.6 + - - +
42H PHE* 3.4 48.1 - - + -
68H THR* 3.2 6.7 - - - +
69H PRO* 1.3 84.8 - - + +
71H CYS* 1.3 58.7 + - - +
73H TYR* 3.4 8.9 + - - +
74H LEU* 2.9 29.6 + - - +
113H SER* 6.0 3.1 - - - +
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Residues in contact with CYS 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLU* 4.5 4.5 - - - -
41H LEU* 4.8 3.4 - - - -
42H PHE* 3.4 45.5 - - - -
61H LEU* 4.3 16.2 - - + +
66H CYS* 3.3 34.3 - - + -
68H THR* 3.3 17.4 + - - +
69H PRO 3.3 0.4 - - - -
70H GLN* 1.3 75.7 - - - +
72H LYS* 1.3 61.8 + - - +
74H LEU* 3.3 3.6 + - - +
75H LEU* 2.8 31.7 + - - +
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Residues in contact with LYS 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66H CYS* 3.5 28.3 - - - +
67H THR* 3.4 22.8 + - - +
68H THR 3.2 12.0 + - - +
69H PRO* 3.6 9.2 - - + +
71H CYS* 1.3 74.9 - - - +
73H TYR* 1.3 58.3 + - - +
75H LEU* 3.4 5.2 + - + +
76H ALA* 2.9 29.6 + - - +
91H ILE* 3.8 33.4 - - + +
92H LEU* 4.5 2.0 - - + -
101H LYS* 5.6 1.7 - - - +
109H GLU* 4.6 20.5 + - - +
110H PHE* 4.1 14.1 - - + -
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Residues in contact with TYR 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ASN 4.9 0.4 - - - -
18F HIS* 2.2 70.2 + + + +
19F TYR* 4.5 9.4 - + - -
20F ALA* 5.1 2.8 - - - +
69H PRO 3.0 13.0 + - - +
70H GLN* 3.5 10.8 - - - +
71H CYS 3.3 0.2 - - - -
72H LYS* 1.3 73.1 - - - +
74H LEU* 1.3 65.4 + - + +
76H ALA* 3.0 4.9 + - - +
77H LYS* 2.8 37.7 + - + +
92H LEU* 4.3 7.0 - - + -
110H PHE* 4.2 2.3 - - + -
113H SER* 5.9 1.6 - - - +
116H PHE* 4.1 6.0 + - + +
117H THR* 3.4 42.8 - - + -
120H LEU* 3.5 29.4 - - + +
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Residues in contact with LEU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F TYR* 4.3 21.3 - - + +
42H PHE* 3.7 19.1 - - + +
45H ALA* 4.1 3.8 - - + -
46H THR* 3.4 41.1 - - - +
49H TYR* 4.0 18.2 - - + -
57H ALA* 4.3 4.0 - - + -
61H LEU* 3.8 14.8 - - + -
70H GLN 2.9 18.3 + - - +
71H CYS* 4.0 2.7 - - - +
73H TYR* 1.3 77.8 - - + +
75H LEU* 1.3 63.1 + - - +
77H LYS* 3.2 6.9 + - + +
78H CYS* 2.9 40.7 + - - +
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Residues in contact with LEU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.9 34.8 - - + +
61H LEU* 3.7 44.7 - - + +
62H LYS* 4.1 11.7 - - + +
66H CYS* 4.1 13.2 - - - -
71H CYS 2.8 21.4 + - - +
72H LYS* 3.7 5.6 - - - +
74H LEU* 1.3 73.3 - - - +
76H ALA* 1.3 61.7 + - - +
78H CYS* 3.3 5.0 + - - +
79H CYS* 3.0 31.0 + - - -
91H ILE* 3.7 23.3 - - + -
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72H LYS 2.9 14.0 + - - +
73H TYR 3.4 4.5 - - - +
75H LEU* 1.3 75.5 - - - +
77H LYS* 1.3 62.8 + - - +
79H CYS* 3.3 1.9 + - - +
80H VAL* 3.1 28.6 + - + +
88H GLY* 3.7 20.6 - - - +
91H ILE* 4.2 4.8 - - + +
92H LEU* 3.4 41.5 - - + -
120H LEU* 4.1 3.6 - - + -
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Residues in contact with LYS 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F HIS 4.3 0.4 - - - +
19F TYR* 3.7 32.1 - - + +
49H TYR* 3.3 30.7 + - + +
73H TYR* 2.8 37.0 + - + +
74H LEU* 3.5 13.7 - - + +
76H ALA* 1.3 72.2 - - - +
78H CYS* 1.4 58.7 + - - +
80H VAL* 3.4 11.0 + - - +
81H ASP* 3.0 38.0 + - - +
120H LEU* 4.0 20.9 - - + +
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Residues in contact with CYS 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H TYR* 3.5 26.9 - - - -
54H ALA 3.5 23.3 - - - +
57H ALA* 3.8 15.5 - - - -
58H TYR* 3.8 20.9 - - + -
61H LEU* 5.4 0.2 - - - -
74H LEU* 2.9 18.1 + - - +
75H LEU* 3.5 10.5 - - - +
77H LYS* 1.4 73.6 - - - +
79H CYS* 1.3 54.7 + - - +
81H ASP* 3.2 9.2 + - - +
82H LEU* 2.8 40.4 + - - +
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Residues in contact with CYS 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.6 17.5 - - - -
75H LEU* 3.0 21.5 + - - +
76H ALA 3.3 0.9 + - - +
78H CYS* 1.3 76.5 - - - +
80H VAL* 1.3 56.2 + - - +
82H LEU* 3.2 7.1 + - - +
83H SER 2.9 7.6 + - - -
84H LYS* 2.8 34.8 + - + +
87H GLU* 3.6 32.3 - - - -
88H GLY* 3.3 33.0 - - - +
91H ILE* 4.3 7.0 - - - -
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76H ALA* 3.1 17.4 + - + +
77H LYS* 3.9 9.4 - - - +
79H CYS* 1.3 73.9 - - - +
81H ASP* 1.3 62.6 + - - +
83H SER* 3.0 19.6 + - - +
85H LEU* 3.9 25.4 - - + +
88H GLY* 4.7 9.2 - - - -
92H LEU* 6.4 0.2 - - + -
120H LEU* 3.8 17.3 - - + -
123H HIS* 4.3 21.1 - - + +
124H VAL* 3.8 26.2 - - + -
127H LYS* 4.9 9.1 + - - +
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Residues in contact with ASP 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49H TYR* 3.8 17.0 + - - +
54H ALA* 3.6 23.8 - - + +
77H LYS* 3.0 24.2 + - - +
78H CYS* 3.4 12.6 - - - +
80H VAL* 1.3 77.6 - - - +
82H LEU* 1.4 57.7 + - - +
83H SER* 3.1 8.4 + - - -
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Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ALA* 3.8 29.6 - - + +
55H TYR* 3.9 19.7 - - + +
58H TYR* 3.4 43.5 - - + -
78H CYS 2.8 25.8 + - - +
79H CYS* 3.6 4.9 - - - +
81H ASP* 1.4 71.6 - - - +
83H SER* 1.3 67.6 + - - +
84H LYS* 3.1 28.0 + - + +
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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