Contacts of the helix formed by residues 53 - 69 (chain Z) in PDB entry 5V04
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 53 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Z THR* 1.3 78.4 + - - +
54Z ARG* 1.3 66.2 + - - +
55Z TYR* 3.2 12.3 - - - -
56Z VAL* 3.3 27.8 + - + +
57Z GLY 3.8 2.8 + - - -
132Z LYS* 3.7 20.0 - - - +
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Residues in contact with ARG 54 (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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12A A 4.9 8.9 + - - +
13A T 3.9 21.8 + - - -
38Z GLY 4.6 1.8 - - - +
41Z ALA* 4.1 31.6 + - + +
42Z CYS* 3.8 18.8 - - - -
52Z THR* 3.7 6.4 + - - +
53Z ASP* 1.3 75.6 + - - +
55Z TYR* 1.3 60.8 + - - +
57Z GLY* 3.3 3.7 + - - +
58Z PHE* 2.9 28.2 + - + +
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Residues in contact with TYR 55 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Z LEU* 3.6 28.0 - - + +
38Z GLY* 3.8 26.0 + - - -
39Z ALA* 4.1 3.4 - - - +
42Z CYS* 4.4 11.4 - - - -
46Z LEU* 4.5 10.5 - - + +
52Z THR 3.7 21.0 + - - -
53Z ASP* 3.9 2.7 - - - -
54Z ARG* 1.3 82.9 - - - +
56Z VAL* 1.3 87.1 + - + +
58Z PHE* 3.5 5.5 - - - +
59Z CYS* 2.9 36.6 + - - -
129Z MET* 3.3 57.7 - - + +
132Z LYS* 3.3 25.8 + - - +
133Z VAL* 3.9 1.6 - - + -
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Residues in contact with VAL 56 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Z ASP* 3.4 24.0 - - + +
54Z ARG 3.2 0.8 - - - -
55Z TYR* 1.3 104.0 - - + +
57Z GLY* 1.3 57.9 + - - +
59Z CYS* 3.3 2.9 + - - +
60Z MET* 2.9 35.6 + - + +
132Z LYS* 4.2 20.6 - - + +
133Z VAL* 4.2 12.2 - - + +
136Z ALA* 3.6 28.9 - - + -
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Residues in contact with GLY 57 (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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53Z ASP 3.8 3.6 + - - -
54Z ARG* 3.3 6.2 + - - -
56Z VAL* 1.3 81.4 - - - +
58Z PHE* 1.3 56.0 + - - +
60Z MET* 3.1 8.3 + - - +
61Z LYS* 2.9 32.3 + - - +
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Residues in contact with PHE 58 (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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11A C 3.7 28.7 - - - -
12A A 3.7 20.0 - - - -
34Z TRP* 3.4 31.4 - - - -
37Z LYS* 3.8 22.7 - - + -
38Z GLY* 3.5 19.7 - - - -
54Z ARG* 2.9 16.0 + - + +
55Z TYR 3.5 7.9 - - - +
56Z VAL 3.2 0.2 - - - -
57Z GLY* 1.3 77.4 - - - +
59Z CYS* 1.3 61.1 + - - +
61Z LYS* 3.1 42.3 - - - +
62Z PHE* 3.2 39.4 - + - -
188Z GLN* 5.6 1.6 - - - -
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Residues in contact with CYS 59 (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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31Z THR* 4.7 3.6 - - + -
34Z TRP* 3.8 48.4 - - + -
35Z LEU* 3.8 18.6 - - - -
55Z TYR 2.9 26.1 + - - +
56Z VAL 3.7 3.6 - - - +
58Z PHE* 1.3 78.2 - - - +
60Z MET* 1.3 58.6 + - + +
62Z PHE* 3.2 6.9 + - - +
63Z VAL* 3.0 32.5 + - + +
133Z VAL* 4.2 22.7 - - + -
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Residues in contact with MET 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Z VAL* 2.9 22.3 + - + +
57Z GLY* 3.1 9.8 + - - +
59Z CYS* 1.3 77.5 - - + +
61Z LYS* 1.3 60.4 + - - +
63Z VAL* 3.7 23.2 - - + +
64Z ASN* 2.9 52.3 + - - +
75Z LEU* 6.2 0.2 - - - -
133Z VAL* 5.1 3.6 - - + +
136Z ALA* 3.6 35.0 - - + +
137Z ALA* 4.3 6.7 - - - -
140Z GLN* 3.6 32.1 - - + +
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Residues in contact with LYS 61 (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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12A A 3.6 19.8 + - - -
57Z GLY 2.9 13.8 + - - +
58Z PHE* 3.1 42.7 - - - +
60Z MET* 1.3 73.9 - - - +
62Z PHE* 1.3 68.9 + - + +
64Z ASN* 3.8 7.3 - - - +
65Z MET* 2.9 29.1 + - - +
188Z GLN* 3.0 46.3 + - + +
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Residues in contact with PHE 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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34Z TRP* 3.6 43.3 - + + -
37Z LYS* 4.3 12.6 - - - -
58Z PHE* 3.2 50.0 - + - -
59Z CYS 3.2 8.2 + - - +
61Z LYS* 1.3 83.1 - - + +
63Z VAL* 1.3 64.9 + - - +
65Z MET* 3.1 8.6 + - + +
66Z LEU* 3.0 29.0 + - - +
186Z MET* 3.4 20.0 - - + -
187Z ASP* 3.3 28.0 - - - -
188Z GLN* 3.6 27.4 - - + +
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Residues in contact with VAL 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Z TRP* 4.1 16.6 - - + -
59Z CYS* 3.0 23.2 + - + +
60Z MET* 3.7 30.1 - - + +
62Z PHE* 1.3 76.3 - - - +
64Z ASN* 1.3 57.4 + - - +
66Z LEU* 3.3 9.0 + - - +
67Z LEU* 2.9 36.2 + - + +
73Z PRO* 4.7 6.2 - - + +
75Z LEU* 4.2 23.3 - - + -
133Z VAL* 6.4 0.2 - - + -
137Z ALA* 5.6 1.1 - - + -
142Z VAL* 3.9 29.6 - - + -
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Residues in contact with ASN 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 MET* 2.9 45.3 + - - +
61Z LYS* 3.9 7.3 - - - +
62Z PHE 3.3 0.2 - - - -
63Z VAL* 1.3 72.7 - - - +
65Z MET* 1.3 59.7 + - - +
67Z LEU* 3.8 12.1 - - - +
68Z SER* 2.9 28.9 + - - -
140Z GLN* 3.7 20.8 - - - +
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Residues in contact with MET 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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19Z VAL* 4.0 9.4 - - - -
61Z LYS 2.9 18.8 + - - +
62Z PHE* 3.1 9.2 + - + +
64Z ASN* 1.3 74.5 - - - +
66Z LEU* 1.3 85.6 + - + +
68Z SER* 2.4 26.4 + - - +
69Z HIS* 2.9 32.3 + - + -
186Z MET* 3.9 17.5 - - + -
187Z ASP 3.9 6.5 - - - +
188Z GLN 3.5 20.2 - - - +
189Z PHE* 3.8 14.1 - - - +
190Z GLY* 3.9 23.6 - - - +
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Residues in contact with LEU 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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19Z VAL* 4.1 15.0 - - + -
27Z VAL* 5.5 1.8 - - + -
29Z VAL* 4.2 2.7 - - + -
34Z TRP* 3.6 29.4 - - + -
62Z PHE 3.0 15.4 + - - +
63Z VAL* 3.6 7.2 - - - +
65Z MET* 1.3 97.3 - - + +
67Z LEU* 1.3 59.6 + - - +
69Z HIS* 3.4 6.1 + - - -
71Z ILE* 3.0 51.2 + - + +
73Z PRO* 4.1 26.5 - - + -
168Z ILE* 3.8 26.2 - - + -
186Z MET* 4.3 1.1 - - + -
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Residues in contact with LEU 67 (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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63Z VAL* 2.9 26.8 + - + +
64Z ASN* 3.9 15.5 - - - +
66Z LEU* 1.3 74.5 - - - +
68Z SER* 1.3 64.3 + - - +
70Z GLY* 3.1 12.8 + - - -
71Z ILE 3.4 18.4 - - - +
72Z LYS* 5.0 0.7 - - - -
73Z PRO* 3.6 17.5 - - + -
140Z GLN* 4.5 15.9 - - + +
142Z VAL* 3.8 25.1 - - + -
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Residues in contact with SER 68 (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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23Z LYS* 5.1 3.3 + - - -
64Z ASN 2.9 15.9 + - - -
65Z MET* 2.4 29.8 + - - +
67Z LEU* 1.3 78.1 - - - +
69Z HIS* 1.3 70.3 + - - +
70Z GLY* 3.3 3.1 + - - -
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Residues in contact with HIS 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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18Z HIS* 3.3 20.4 + + - -
19Z VAL* 3.9 15.5 - - + -
20Z ARG* 3.4 38.2 + - + +
23Z LYS* 3.3 29.4 - - - +
65Z MET* 2.9 48.4 + - + +
66Z LEU 3.4 4.2 + - - +
67Z LEU 3.2 0.4 - - - -
68Z SER* 1.3 88.2 + - - +
70Z GLY* 1.3 61.5 + - - +
71Z ILE* 3.4 8.2 + - + +
189Z PHE 3.9 6.3 + - - -
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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) + - + + + + + -
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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