Contacts of the helix formed by residues 53 - 62 (chain C) in PDB entry 1WZN
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 GLY 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C CYS 2.9 12.3 + - - -
51C GLY 3.0 3.0 + - - -
52C THR* 1.3 78.4 - - - +
54C ILE* 1.3 64.8 + - - +
55C PRO 3.4 2.2 - - - -
56C THR* 3.2 24.5 - - - -
57C LEU* 2.8 34.3 + - - +
79C ALA* 3.9 4.9 - - - +
82C LYS* 4.5 0.4 - - - -
92C PHE* 4.5 2.2 - - - -
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TYR* 4.2 10.1 - - + -
13C ASP* 3.8 10.1 - - - +
16C TYR* 4.8 2.9 - - + +
19C ARG* 3.9 22.7 - - - +
20C ILE* 3.3 46.2 - - + -
23C VAL* 3.6 29.6 - - + +
50C CYS 4.4 0.4 + - - -
52C THR* 3.4 15.5 - - - +
53C GLY* 1.3 78.0 - - - +
55C PRO* 1.3 70.7 - - + +
57C LEU* 3.8 4.4 + - - +
58C GLU* 3.6 10.4 + - - +
82C LYS* 3.9 11.0 - - - +
86C ARG* 5.4 1.6 + - - -
1003C SAH 4.0 9.1 + - - +
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Residues in contact with PRO 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG* 3.8 12.1 - - - +
23C VAL* 3.8 12.1 - - + -
26C GLU* 5.6 0.7 - - - +
27C ILE* 4.1 10.7 - - + +
47C ASP* 4.1 6.5 - - - +
53C GLY 3.8 0.7 - - - -
54C ILE* 1.3 96.0 - - + +
56C THR* 1.3 65.8 + - - +
58C GLU* 3.2 3.4 + - + +
59C LEU* 3.0 29.7 + - - +
112C PHE* 3.4 37.9 - - + -
1003C SAH 3.6 27.1 - - - +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 2.6 27.2 + - + +
50C CYS* 3.5 5.9 + - - +
53C GLY* 3.2 25.4 + - - -
55C PRO* 1.3 80.7 - - - +
57C LEU* 1.3 57.7 + - - +
59C LEU* 3.4 8.8 + - - +
60C ALA* 3.1 27.5 + - - +
66C VAL* 3.6 26.5 - - + +
68C GLY* 4.6 3.1 - - - -
90C ILE* 4.0 7.9 - - + -
92C PHE* 3.8 24.5 - - + -
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Residues in contact with LEU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C THR 4.6 0.4 - - - +
53C GLY* 2.8 30.1 + - - +
54C ILE* 4.1 3.6 - - - +
56C THR* 1.3 75.4 - - - +
58C GLU* 1.3 58.2 + - - +
61C GLU* 3.0 31.0 + - - +
79C ALA 4.4 4.7 - - - +
82C LYS* 3.5 41.5 - - + +
83C ALA* 4.7 4.3 - - + +
86C ARG* 3.1 38.3 + - - +
88C LEU* 3.6 11.2 - - + +
90C ILE* 3.7 25.1 - - + -
92C PHE* 3.8 20.4 - - + -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 3.9 26.3 - - + +
24C LYS* 3.3 33.5 + - - +
27C ILE* 3.2 31.2 - - + -
54C ILE 3.6 3.3 + - - +
55C PRO 3.2 8.4 + - - +
57C LEU* 1.3 76.6 - - - +
59C LEU* 1.3 65.7 + - - +
61C GLU* 3.5 13.9 + - - +
62C ARG* 2.9 58.6 + - - +
86C ARG* 4.4 7.9 + - - +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 3.7 29.8 - - + -
30C VAL* 4.5 5.4 - - + -
31C GLU* 5.6 0.2 - - + -
34C PHE* 4.5 14.6 - - + -
45C VAL* 4.3 24.0 - - + -
47C ASP* 5.3 0.9 - - + -
55C PRO 3.0 20.3 + - - +
56C THR* 3.6 9.9 - - - +
58C GLU* 1.3 72.6 - - - +
60C ALA* 1.3 61.9 + - - +
62C ARG* 2.8 20.9 + - - -
64C TYR* 3.3 40.6 + - + -
66C VAL* 3.9 14.8 - - + -
110C THR* 4.7 3.8 - - + +
112C PHE* 4.2 22.2 - - + -
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Residues in contact with ALA 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C THR 3.1 6.1 + - - +
57C LEU 3.8 3.1 - - - +
59C LEU* 1.3 78.5 - - - +
61C GLU* 1.3 57.7 + - - +
63C GLY* 2.9 21.3 + - - -
64C TYR 3.6 18.7 + - - +
66C VAL* 4.0 4.4 - - + +
88C LEU* 4.3 12.4 - - + +
89C LYS 4.5 4.7 - - - +
90C ILE* 3.6 40.2 - - + -
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 4.0 17.5 + - - -
57C LEU 3.0 17.7 + - - +
58C GLU* 3.6 15.1 - - - +
59C LEU 3.2 0.4 - - - -
60C ALA* 1.3 75.8 - - - +
62C ARG* 1.3 60.0 + - + +
63C GLY 3.3 1.4 + - - -
86C ARG* 2.8 34.6 + - - +
88C LEU* 3.8 19.1 - - + +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 3.2 25.7 + - - +
27C ILE* 3.3 30.3 - - - +
28C ASP* 2.8 34.9 + - - +
31C GLU* 3.0 29.6 + - - +
58C GLU* 2.9 36.1 + - - +
59C LEU 2.8 9.1 + - - +
61C GLU* 1.3 81.6 - - + +
63C GLY* 1.3 56.9 + - - +
64C TYR* 3.5 18.3 + - + -
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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
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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