Contacts of the helix formed by residues 59 - 68 (chain C) in PDB entry 2WOE
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 59 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C ASP* 2.6 27.3 + - - +
25C ALA* 3.8 13.5 - - + -
28C GLU* 6.2 0.2 - - - +
51C LEU* 4.3 13.2 - - + -
53C LEU* 3.8 32.8 - - + -
58C ILE* 1.3 79.3 - - - +
60C ASP* 1.3 66.6 + - - -
61C ASP* 3.0 12.6 + - - -
62C THR* 3.5 1.7 + - - -
63C GLU* 3.1 34.8 + - - +
96C VAL* 4.3 12.8 - - + -
97C ASN* 5.0 2.4 + - - -
245C ASP* 3.8 6.2 + - - +
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Residues in contact with ASP 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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59C THR* 1.3 78.4 + - - +
61C ASP* 1.3 67.2 + - - +
63C GLU* 4.2 2.2 + - - -
64C MET* 2.8 27.7 + - - +
90C TRP* 3.6 24.1 - - + -
96C VAL* 5.1 0.6 - - - +
97C ASN* 3.3 35.0 + - - +
99C GLY 3.7 10.7 + - - -
130C MET* 3.7 11.1 - - + +
245C ASP* 4.1 0.3 - - - +
401C AR6 3.0 45.5 + - - -
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Residues in contact with ASP 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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17C LEU* 4.6 2.0 - - + -
21C ASP* 3.1 11.9 - - + +
59C THR* 3.0 12.8 + - - -
60C ASP* 1.3 76.5 + - - +
62C THR* 1.3 60.6 + - - +
64C MET* 4.3 1.0 - - - +
65C SER* 2.9 26.4 + - - -
130C MET* 3.5 29.0 - - + +
131C ARG* 4.6 0.5 - - - +
245C ASP* 2.8 26.7 - - - +
246C THR* 2.8 37.8 + - - +
249C ALA* 3.9 17.2 - - + +
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Residues in contact with THR 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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14C PHE* 4.8 2.0 - - + -
17C LEU* 4.0 14.9 + - + +
18C ALA* 3.4 29.2 + - + -
21C ASP* 2.8 33.3 + - - +
58C ILE* 3.4 27.7 - - + +
61C ASP* 1.3 74.5 - - - +
63C GLU* 1.3 61.5 + - - +
65C SER* 3.3 2.4 + - - -
66C LEU* 2.9 39.2 + - + +
280C ILE* 4.3 9.4 - - + -
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Residues in contact with GLU 63 (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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57C GLN* 5.9 0.5 + - - -
58C ILE* 4.1 23.0 - - + +
59C THR* 3.1 28.2 + - - +
60C ASP* 4.1 1.7 - - - +
62C THR* 1.3 76.8 - - - +
64C MET* 1.3 56.7 + - - +
66C LEU* 3.3 9.8 + - + +
67C ALA* 3.0 26.5 + - - +
70C ARG* 5.4 0.5 + - - -
90C TRP* 2.9 39.2 + - + +
95C PRO* 3.6 16.1 - - - +
96C VAL* 4.8 6.8 + - - +
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Residues in contact with MET 64 (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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60C ASP* 2.8 23.1 + - - +
63C GLU* 1.3 68.4 - - - +
65C SER* 1.3 64.8 + - - +
67C ALA* 3.3 8.4 + - - +
68C LEU* 3.0 23.7 + - - +
87C PHE* 3.7 33.5 - - + -
90C TRP* 3.6 38.8 - - + -
102C CYS* 3.9 15.0 - - + -
106C ILE* 4.2 9.4 - - + -
130C MET* 3.4 22.7 - - + -
131C ARG* 3.7 39.8 - - + +
157C THR* 5.3 0.2 - - + -
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Residues in contact with SER 65 (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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14C PHE* 4.0 11.0 - - - -
17C LEU* 3.5 19.1 - - - +
61C ASP 2.9 22.5 + - - -
62C THR 3.5 4.5 - - - -
64C MET* 1.3 78.7 - - - +
66C LEU* 1.3 57.2 + - - +
68C LEU* 3.3 1.8 + - - -
69C GLY* 2.9 25.8 + - - -
130C MET 3.5 4.5 + - - -
131C ARG* 3.3 24.7 - - - +
133C LEU* 5.2 0.9 + - - +
134C PRO* 3.3 23.9 - - - +
283C GLN* 4.1 0.3 - - - +
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Residues in contact with LEU 66 (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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14C PHE* 3.7 15.9 - - + -
58C ILE* 4.5 11.0 - - + -
62C THR* 2.9 34.6 + - + +
63C GLU* 3.3 7.8 + - + +
65C SER* 1.3 75.8 - - - +
67C ALA* 1.3 57.6 + - - +
70C ARG* 2.9 40.0 + - - +
276C VAL* 4.7 8.5 - - + -
279C GLU* 3.9 20.2 - - + -
280C ILE* 3.9 21.3 - - + -
283C GLN* 2.9 35.9 + - - +
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Residues in contact with ALA 67 (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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63C GLU 3.0 14.2 + - - +
64C MET* 3.6 9.4 - - - +
65C SER 3.2 0.4 - - - -
66C LEU* 1.3 75.4 - - - +
68C LEU* 1.3 62.8 + - - +
70C ARG* 3.4 20.9 + - - +
71C SER* 3.3 16.3 + - - -
86C GLU* 3.6 31.4 - - + +
87C PHE* 3.9 19.5 - - + -
90C TRP* 4.7 9.2 - - + -
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Residues in contact with LEU 68 (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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64C MET 3.0 16.4 + - - +
65C SER 3.7 3.6 - - - +
67C ALA* 1.3 77.6 - - - +
69C GLY* 1.3 56.8 + - - +
71C SER* 3.3 3.5 + - - -
72C LEU* 3.1 40.2 + - + +
78C LEU* 5.6 0.4 - - + -
83C ILE* 3.5 41.3 - - + -
87C PHE* 4.0 11.8 - - + -
131C ARG* 3.2 24.7 - - + +
134C PRO* 4.1 11.2 - - + -
135C ALA* 4.3 9.9 - - + +
153C GLN* 3.7 32.5 - - + +
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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