Contacts of the helix formed by residues 79 - 93 (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 ASP 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C SER* 4.7 1.7 + - - +
75C LYS* 3.8 31.4 + - + +
77C THR* 3.4 6.3 + - + -
78C LEU* 1.3 73.7 - - - +
80C VAL* 1.3 63.6 + - - +
81C ALA* 3.6 8.7 + - - +
82C ASP* 3.0 38.1 + - + +
83C ILE* 3.0 18.9 + - - +
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Residues in contact with VAL 80 (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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78C LEU* 3.9 16.4 + - + -
79C ASP* 1.3 70.8 + - - +
81C ALA* 1.3 57.0 + - - +
83C ILE* 3.3 8.9 + - + +
84C CYS* 2.9 27.8 + - - -
115C THR* 4.0 24.2 - - + +
152C ALA* 3.8 33.2 - - + +
156C ILE* 3.8 27.8 - - + -
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Residues in contact with ALA 81 (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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79C ASP* 3.3 8.4 + - - +
80C VAL* 1.3 77.4 - - - +
82C ASP* 1.3 57.2 + - - +
84C CYS* 3.3 6.0 - - - +
85C GLU* 3.0 23.2 + - - +
109C TYR* 3.6 13.9 + - + +
115C THR* 4.1 22.4 - - + +
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Residues in contact with ASP 82 (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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71C SER* 2.6 31.5 + - - +
74C ALA* 5.0 2.4 - - - +
75C LYS* 3.5 26.7 + - - +
79C ASP* 3.0 30.1 + - + +
81C ALA* 1.3 78.0 - - - +
83C ILE* 1.3 58.8 + - - +
85C GLU* 3.2 11.4 + - - +
86C GLU* 3.0 37.5 + - - +
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Residues in contact with ILE 83 (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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68C LEU* 3.5 33.7 - - + +
71C SER* 3.5 22.4 - - - +
72C LEU* 4.8 4.5 - - + +
78C LEU* 3.7 28.3 - - + -
79C ASP 3.0 15.4 + - - +
80C VAL* 3.6 11.4 - - - +
82C ASP* 1.3 71.9 - - - +
84C CYS* 1.3 61.4 + - - +
86C GLU* 3.2 3.4 + - - +
87C PHE* 2.9 50.6 + - + -
153C GLN* 4.4 7.0 - - + -
156C ILE* 3.4 20.4 - - + -
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Residues in contact with CYS 84 (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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80C VAL 2.9 22.0 + - - -
81C ALA 3.3 10.1 - - - +
83C ILE* 1.3 76.2 - - - +
85C GLU* 1.3 56.3 - - - +
87C PHE* 3.3 8.7 + - - +
88C ALA* 2.8 28.8 + - - +
106C ILE* 4.9 0.5 - - - +
109C TYR* 3.5 33.3 - - + -
115C THR* 3.8 30.1 - - - -
156C ILE* 3.7 31.0 - - - -
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Residues in contact with GLU 85 (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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81C ALA 3.0 11.8 + - - +
82C ASP* 3.2 17.2 + - - +
84C CYS* 1.3 75.2 - - - +
86C GLU* 1.3 53.9 + - + +
88C ALA* 3.1 9.0 + - - +
89C LEU* 2.8 59.9 + - + +
92C LYS* 5.3 4.3 + - - -
109C TYR* 3.1 35.2 + - - +
110C MET* 5.9 0.2 - - - +
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Residues in contact with GLU 86 (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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67C ALA* 3.6 30.3 - - + +
70C ARG* 3.3 38.4 + - - +
71C SER* 4.0 13.6 - - - +
82C ASP* 3.0 27.2 + - - +
83C ILE* 3.2 7.6 + - - +
85C GLU* 1.3 76.5 - - - +
87C PHE* 1.3 58.7 + - - +
89C LEU* 3.8 22.5 - - - +
90C TRP* 2.9 30.5 + - - +
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Residues in contact with PHE 87 (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* 3.7 39.5 - - + -
67C ALA* 3.9 10.1 - - + -
68C LEU* 4.0 10.8 - - + -
83C ILE* 2.9 39.3 + - + -
84C CYS* 3.5 8.3 - - - +
86C GLU* 1.3 76.4 - - - +
88C ALA* 1.3 56.9 + - - +
90C TRP* 3.5 10.6 + + - +
91C LEU* 2.9 28.4 + - - +
106C ILE* 3.8 22.0 - - + +
131C ARG* 3.5 41.1 - - - -
153C GLN* 4.3 5.2 - - - -
156C ILE* 3.8 28.5 - - + -
157C THR* 4.8 0.9 - - + -
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Residues in contact with ALA 88 (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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84C CYS 2.8 14.3 + - - +
85C GLU* 3.4 17.3 - - - +
87C PHE* 1.3 74.3 - - - +
89C LEU* 1.3 59.1 + - - +
91C LEU* 3.2 2.3 + - - +
92C LYS* 2.9 42.5 + - - +
106C ILE* 3.6 12.9 - - + +
109C TYR* 4.2 7.4 - - + -
110C MET* 3.8 27.3 - - + +
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Residues in contact with LEU 89 (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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85C GLU* 2.8 40.8 + - + +
86C GLU* 3.8 28.5 - - - +
88C ALA* 1.3 71.7 - - - +
90C TRP* 1.3 62.0 + - - +
92C LYS* 3.5 22.5 + - + +
93C SER* 3.2 20.8 + - - -
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Residues in contact with TRP 90 (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* 3.6 27.1 - - + -
63C GLU* 2.9 44.7 + - + +
64C MET* 3.6 40.4 - - + -
67C ALA* 4.7 8.3 - - + -
70C ARG* 6.2 0.9 - - - +
86C GLU 2.9 18.3 + - - +
87C PHE* 3.5 11.2 - + - +
89C LEU* 1.3 74.5 - - - +
91C LEU* 1.3 76.6 + - + +
93C SER* 2.6 31.4 + - - -
95C PRO* 3.4 28.4 - - + +
97C ASN 3.8 0.4 - - - -
98C VAL* 3.7 32.1 - - + -
99C GLY 5.5 0.2 - - - -
106C ILE* 4.0 8.3 - - + -
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Residues in contact with LEU 91 (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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87C PHE 2.9 19.4 + - - +
88C ALA 3.2 4.5 + - - +
90C TRP* 1.3 78.4 - - + +
92C LYS* 1.3 59.8 + - + +
94C ARG* 3.0 20.1 + - - +
95C PRO* 3.4 8.1 - - + +
98C VAL* 3.5 43.1 - - + -
103C ARG* 4.1 21.8 - - + +
106C ILE* 3.6 31.2 - - + -
107C ARG* 4.1 22.0 - - + -
110C MET* 4.7 8.3 - - - -
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Residues in contact with LYS 92 (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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85C GLU* 5.3 4.0 + - - -
88C ALA* 2.9 28.1 + - - +
89C LEU* 3.8 22.9 - - - +
90C TRP 3.2 0.2 - - - -
91C LEU* 1.3 76.9 - - + +
93C SER* 1.3 56.7 + - - +
94C ARG* 3.1 20.7 + - - +
110C MET* 3.6 34.0 - - + +
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Residues in contact with SER 93 (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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104A ARG* 2.9 36.3 + - - +
89C LEU 3.2 11.8 + - - -
90C TRP* 2.6 30.8 + - - -
92C LYS* 1.3 74.4 - - - +
94C ARG* 1.3 63.8 + - - +
95C PRO* 4.2 5.5 - - - +
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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