Contacts of the helix formed by residues 82 - 95 (chain C) in PDB entry 2WLM
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 SER 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.2 7.1 - - - +
78C ALA* 6.0 0.2 - - - +
79C ARG* 3.2 40.6 + - - +
80C PRO 3.1 3.2 + - - -
81C GLY* 1.3 76.7 - - - +
83C PHE* 1.3 64.2 + - - +
84C THR* 4.0 1.1 + - - -
85C ASP* 2.9 34.1 + - - +
86C ALA* 3.2 17.5 + - - +
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Residues in contact with PHE 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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62C ALA* 3.7 28.0 - - + -
65C ALA* 3.5 17.7 - - + -
66C LEU* 3.2 35.7 - - + -
69C LEU* 3.9 18.0 - - + +
81C GLY 4.1 1.8 + - - -
82C SER* 1.3 69.1 - - - +
84C THR* 1.3 60.0 + - - +
86C ALA* 3.1 2.8 + - - +
87C PHE* 2.6 52.3 + + + +
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Residues in contact with THR 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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107B PRO* 5.7 10.3 - - + -
79C ARG* 4.1 13.6 + - - +
82C SER* 3.3 1.1 + - - -
83C PHE* 1.3 81.6 - - - +
85C ASP* 1.3 72.9 + - - +
87C PHE* 2.9 8.6 + - + +
88C PHE* 2.8 56.7 + - + -
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Residues in contact with ASP 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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77C ASN 4.4 2.8 - - - +
78C ALA* 3.6 22.3 - - + -
79C ARG* 2.7 53.4 + - - +
82C SER* 2.9 24.1 + - - +
84C THR* 1.3 75.8 - - - +
86C ALA* 1.3 57.8 + - - +
88C PHE* 3.5 4.3 + - - -
89C PHE* 2.8 31.1 + - - +
102C LEU* 3.9 12.6 - - + +
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Residues in contact with ALA 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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65C ALA* 3.8 22.1 - - + +
68C TYR* 4.7 7.5 - - + -
69C LEU* 3.9 24.5 - - + -
75C ILE* 4.6 9.2 - - + -
78C ALA* 5.4 0.6 - - - +
82C SER 3.2 9.7 + - - +
83C PHE 3.1 8.3 + - - +
85C ASP* 1.3 77.5 - - - +
87C PHE* 1.3 58.3 - - - +
89C PHE* 3.3 9.6 + - - +
90C SER* 2.8 30.1 + - - -
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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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114B THR* 4.7 5.6 - - + -
58C LEU* 3.7 35.0 - - + -
61C ASN* 3.6 20.4 - - + -
62C ALA* 3.7 22.9 - - + -
65C ALA* 3.5 8.8 - - - +
83C PHE* 2.6 39.0 + + + +
84C THR* 2.9 6.0 + - - +
86C ALA* 1.3 72.7 - - - +
88C PHE* 1.3 84.6 + + - +
90C SER* 2.9 20.6 + - - -
91C VAL* 3.0 32.8 + - + +
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Residues in contact with PHE 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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107B PRO* 4.0 10.1 - - + -
110B ASN* 3.1 41.5 - - + +
111B THR* 3.4 19.1 - - - -
113B VAL* 5.9 0.2 - - + -
114B THR* 3.2 33.4 - - + -
84C THR* 2.8 53.3 + - + +
85C ASP* 4.0 4.3 - - - +
87C PHE* 1.3 88.2 - + - +
89C PHE* 1.3 55.1 + - - +
91C VAL* 3.1 5.7 - - + +
92C GLN* 2.6 46.5 + - - +
102C LEU* 5.1 3.4 - - + -
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Residues in contact with PHE 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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68C TYR* 3.6 31.9 - + - -
75C ILE* 2.9 37.5 - - + -
85C ASP 2.8 19.5 + - - +
86C ALA 3.4 3.6 - - - +
88C PHE* 1.3 74.3 - - - +
90C SER* 1.3 60.9 + - - +
92C GLN* 3.1 8.4 + - + +
93C THR* 2.8 31.7 + - - -
102C LEU* 3.3 53.5 - - + +
103C ILE* 4.0 2.5 - - - -
104C PRO* 4.0 16.6 - - + -
113C VAL* 4.4 4.0 - - + -
99D TYR* 3.5 28.7 - + - -
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Residues in contact with SER 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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61C ASN* 2.5 48.3 + - - +
64C PHE* 4.3 0.4 - - - -
65C ALA 4.2 6.5 - - - -
68C TYR* 4.6 3.6 - - - -
86C ALA 2.8 13.6 + - - -
87C PHE* 2.9 12.3 + - - -
89C PHE* 1.3 80.3 - - - +
91C VAL* 1.3 55.0 + - - +
93C THR* 2.8 12.3 - - - +
94C MET 2.8 24.1 + - - -
116C GLU* 2.6 19.5 + - - +
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Residues in contact with VAL 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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113B VAL* 5.4 2.0 - - + -
114B THR* 3.6 33.2 - - + -
117B ALA* 6.1 0.2 - - + -
57C TYR* 4.2 15.3 - - + +
61C ASN* 3.4 25.6 - - - +
87C PHE* 3.0 36.4 + - + +
88C PHE* 3.1 13.6 + - + +
90C SER* 1.3 71.4 - - - +
92C GLN* 1.3 70.0 + - + +
93C THR 3.0 1.9 + - - -
94C MET* 3.0 2.4 + - - +
95C ALA* 2.7 37.1 + - + +
97C ILE* 5.2 6.1 - - + -
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Residues in contact with GLN 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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104B PRO* 4.3 1.4 - - - +
110B ASN* 4.1 16.4 + - - -
113B VAL* 5.1 4.2 - - + +
88C PHE* 2.6 36.1 + - - +
89C PHE* 3.5 8.8 - - + +
91C VAL* 1.3 80.5 - - + +
93C THR* 1.3 59.3 + - - +
96C THR* 3.3 0.7 + - - -
97C ILE* 2.8 39.4 + - + -
98C GLY* 2.9 18.6 + - - +
99C TYR* 3.2 46.7 + - + +
100C GLY 4.9 1.0 + - - -
101C LYS* 5.9 0.5 - - - +
102C LEU* 4.3 21.6 + - - +
99D TYR* 6.3 0.4 - - + -
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Residues in contact with THR 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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68C TYR* 4.3 3.8 - - - +
89C PHE* 2.8 19.1 + - - -
90C SER* 2.8 14.8 - - - +
92C GLN* 1.3 78.0 - - - +
94C MET* 1.3 62.7 + - - +
96C THR* 3.0 24.4 + - - +
113C VAL* 3.6 15.6 + - - +
116C GLU* 2.7 38.6 - - + +
117C ALA* 4.8 3.3 - - - -
97D ILE* 4.5 11.5 - - - +
99D TYR* 2.6 30.1 + - - -
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Residues in contact with MET 94 (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 TYR* 3.3 24.7 - - + -
60C THR* 4.1 15.0 - - - +
61C ASN* 2.7 40.4 - - - +
64C PHE* 5.9 2.7 - - - -
90C SER 2.8 12.7 + - - +
91C VAL* 4.7 2.7 - - - -
93C THR* 1.3 76.2 - - - +
95C ALA* 1.3 58.6 + - - +
96C THR* 3.0 13.9 + - - +
116C GLU* 3.4 26.7 - - + +
117C ALA 4.7 1.3 - - - +
119C CYS* 5.2 3.1 - - - -
120C GLY* 3.4 39.3 - - - +
121C MET 5.0 0.2 + - - -
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Residues in contact with ALA 95 (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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96B THR* 3.8 15.6 + - + +
117B ALA* 4.1 21.3 - - + -
57C TYR* 4.6 9.4 - - + +
91C VAL 2.7 19.8 + - - +
94C MET* 1.3 73.2 - - - +
96C THR* 1.3 76.7 + - - +
97C ILE* 3.2 16.8 + - + -
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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