Contacts of the helix formed by residues 72 - 88 (chain C) in PDB entry 2WWB
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 PRO 72 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C LEU* 4.9 22.2 - - + +
67C LYS* 5.6 8.7 - - + +
69C GLY* 4.3 7.6 - - - +
71C VAL* 1.3 89.9 - - + +
73C VAL* 1.4 61.3 + - - +
74C LEU 3.3 2.7 - - - -
75C VAL* 3.2 25.9 + - + +
76C MET* 3.6 25.6 + - + +
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Residues in contact with VAL 73 (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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37A ILE* 5.2 4.5 - - + -
161A ILE* 3.8 27.9 - - + +
164A LEU* 4.5 18.6 - - + -
165A LEU* 3.9 33.7 - - + -
168A LEU* 5.8 4.0 - - + -
67C LYS 6.1 0.7 - - - +
70C PRO 3.5 21.1 - - - +
71C VAL 3.0 11.0 + - - +
72C PRO* 1.4 72.6 - - - +
74C LEU* 1.4 76.9 + - + +
76C MET* 3.7 12.3 + - - +
77C SER* 3.5 14.7 + - - -
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Residues in contact with LEU 74 (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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37A ILE* 4.6 17.7 - - + -
41A ILE* 6.1 3.4 - - + -
70C PRO* 5.9 2.0 - - + -
71C VAL* 3.7 28.2 - - + +
72C PRO 3.3 0.6 - - - -
73C VAL* 1.4 84.7 - - + +
75C VAL* 1.4 59.2 + - + +
77C SER* 3.3 9.4 + - - +
78C LEU* 2.9 34.3 + - + +
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Residues in contact with VAL 75 (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 VAL* 4.9 11.2 - - + -
72C PRO* 3.2 20.3 + - + +
74C LEU* 1.4 75.0 - - + +
76C MET* 1.4 72.4 + - + +
78C LEU* 3.5 11.0 + - + +
79C LEU* 3.3 39.9 + - + +
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Residues in contact with MET 76 (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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157A VAL* 4.7 5.2 - - + +
160A LEU* 6.3 3.4 - - + -
161A ILE* 3.6 23.1 - - + -
164A LEU* 5.1 9.6 - - + -
72C PRO* 3.7 29.4 - - + +
73C VAL* 4.0 4.3 - - - +
74C LEU 3.3 0.4 - - - -
75C VAL* 1.4 89.2 - - + +
77C SER* 1.4 58.1 + - - +
79C LEU* 4.0 7.9 + - - +
80C PHE* 3.5 19.9 + - - +
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Residues in contact with SER 77 (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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41A ILE* 4.5 10.1 - - - +
157A VAL* 5.7 0.4 - - - -
161A ILE* 3.4 36.0 - - - +
73C VAL 3.5 5.2 + - - -
74C LEU* 3.3 12.1 + - - +
76C MET* 1.4 77.3 - - - +
78C LEU* 1.4 58.5 + - - +
80C PHE* 3.2 9.6 + - - +
81C ILE* 3.1 35.0 + - - +
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Residues in contact with LEU 78 (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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74C LEU* 2.9 21.8 + - + +
75C VAL* 3.8 11.2 - - + +
76C MET 3.5 0.4 - - - -
77C SER* 1.4 71.9 - - - +
79C LEU* 1.4 68.8 + - + +
81C ILE* 3.3 35.4 - - + +
82C ALA* 3.5 10.5 + - + +
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Residues in contact with LEU 79 (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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75C VAL* 3.3 31.7 + - + +
76C MET* 4.3 8.5 - - - +
78C LEU* 1.4 80.3 - - + +
80C PHE* 1.4 61.3 + - - +
82C ALA* 3.5 6.4 + - + +
83C SER* 3.1 31.3 + - - +
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Residues in contact with PHE 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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48A ILE* 4.7 11.0 - - + -
49A PRO 5.0 4.3 - - - -
77A MET* 4.1 21.1 - - + -
153A ILE 4.4 1.6 - - - -
154A GLN* 3.5 64.8 - - + -
157A VAL* 3.7 29.2 - - + -
158A ALA* 5.1 6.1 - - + -
76C MET 3.5 13.2 + - - +
77C SER* 3.2 13.2 + - - +
79C LEU* 1.4 78.7 - - - +
81C ILE* 1.4 68.2 + - + +
82C ALA 3.5 0.3 + - - -
83C SER* 3.6 5.4 + - - -
84C VAL* 3.5 23.3 + - + +
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Residues in contact with ILE 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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44A VAL* 4.6 16.6 - - + -
48A ILE* 3.6 29.9 - - + +
77C SER* 3.1 16.5 + - - +
78C LEU* 3.3 33.0 - - + +
80C PHE* 1.4 79.9 - - + +
82C ALA* 1.4 61.3 + - + +
84C VAL* 3.5 10.4 - - - +
85C PHE* 3.4 25.6 - - + -
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Residues in contact with ALA 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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78C LEU* 3.5 10.1 + - + +
79C LEU* 3.5 10.9 + - + +
80C PHE 3.3 0.2 - - - -
81C ILE* 1.4 81.6 - - + +
83C SER* 1.4 63.4 + - - +
84C VAL 3.5 0.5 + - - -
85C PHE* 3.6 22.4 + - - +
86C MET* 4.0 5.0 + - - +
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Residues in contact with SER 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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79C LEU* 3.1 18.3 + - - +
80C PHE* 3.6 6.7 + - - -
81C ILE 3.5 0.2 - - - -
82C ALA* 1.4 78.8 - - - +
84C VAL* 1.4 62.4 + - - +
86C MET* 3.2 7.9 + - - +
87C LEU* 3.2 37.9 + - - +
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Residues in contact with VAL 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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48A ILE* 3.8 24.5 - - + -
49A PRO* 3.6 28.4 - - + +
50A LEU* 3.7 11.0 - - - -
51A PHE* 3.8 8.1 - - + +
154A GLN* 3.5 26.9 - - - +
80C PHE* 3.5 14.1 + - + +
81C ILE 3.5 16.4 - - - +
83C SER* 1.4 78.4 - - - +
85C PHE* 1.4 60.1 + - + +
87C LEU* 3.9 7.6 - - - -
88C HIS* 3.0 27.2 + - + +
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Residues in contact with PHE 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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48A ILE* 3.5 28.9 - - + -
49A PRO* 3.9 15.0 - - + -
81C ILE* 3.4 22.4 - - + -
82C ALA* 3.8 11.9 - - - +
83C SER 3.2 1.0 - - - -
84C VAL* 1.4 75.9 - - - +
86C MET* 1.4 63.4 + - - +
88C HIS 2.9 19.1 + - - +
90C TRP* 3.7 34.1 - + + -
93C TYR* 3.6 46.2 - + + +
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Residues in contact with MET 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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82C ALA 4.0 4.6 + - - +
83C SER* 3.2 11.9 + - - +
85C PHE* 1.4 76.8 - - - +
87C LEU* 1.4 72.3 + - + +
94C THR* 3.2 29.0 - - + +
96C SER* 3.4 32.0 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.5 41.7 - - + -
150A LEU* 5.7 6.7 - - + +
153A ILE* 5.5 5.8 - - + -
154A GLN* 4.2 13.9 - - - +
83C SER* 3.2 28.7 + - - +
84C VAL* 3.8 11.2 - - - +
86C MET* 1.4 95.6 - - + +
88C HIS* 1.4 57.6 + - - +
95C ARG* 3.5 6.7 - - - +
96C SER* 3.0 31.7 + - - +
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Residues in contact with HIS 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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49A PRO* 4.5 9.0 - - + +
50A LEU 3.4 22.2 + - - +
51A PHE* 4.1 15.8 - - + +
52A GLY 3.5 24.8 + - - -
55A SER 4.6 8.3 + - - -
84C VAL* 3.0 16.9 + - + +
85C PHE* 2.9 22.1 - - - +
86C MET 3.4 1.4 - - - -
87C LEU* 1.4 78.9 - - - +
89C ILE* 1.4 99.9 + - + +
90C TRP* 4.7 0.7 - - - +
93C TYR* 3.8 2.3 - - - -
94C THR 4.3 4.0 - - - -
95C ARG* 3.4 27.3 + - - +
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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