Contacts of the helix formed by residues 60 - 78 (chain C) in PDB entry 2WW9
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 60 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 5.6 0.7 - - - +
22A LEU* 4.7 3.0 + - - -
23A PRO* 5.0 3.8 - - - -
24A PHE* 3.4 45.9 - - - +
25A GLU* 5.8 0.9 - - - +
166A LEU* 5.6 1.7 - - - +
59C VAL* 1.4 79.9 - - - +
61C SER* 1.4 69.8 + - - +
62C LEU* 3.3 29.8 + - - +
63C VAL* 3.6 31.0 + - + +
64C VAL* 3.7 13.0 + - - +
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PRO* 3.5 18.3 - - - +
24A PHE* 4.0 2.6 - - - +
25A GLU* 3.4 22.1 + - - -
170A VAL* 3.9 6.1 - - - +
175A PHE* 3.5 39.6 - - - -
60C ASP* 1.4 75.4 + - - +
62C LEU* 1.4 62.7 + - - +
63C VAL 3.4 0.2 - - - -
64C VAL* 3.2 23.3 - - - +
65C LEU* 3.5 12.0 + - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 6.2 2.7 - - + -
60C ASP* 3.2 21.7 + - - +
61C SER* 1.4 78.3 - - - +
63C VAL* 1.4 58.9 + - + +
65C LEU* 3.3 19.3 + - + +
66C PHE* 3.0 53.4 + - + -
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Residues in contact with VAL 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 3.8 23.3 - - + +
60C ASP* 3.6 26.3 + - + +
61C SER 3.4 0.4 - - - -
62C LEU* 1.4 75.5 - - + +
64C VAL* 1.4 59.3 + - - +
66C PHE* 3.5 10.1 + - + +
67C LEU* 3.0 30.8 + - + +
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Residues in contact with VAL 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.6 28.3 - - + +
166A LEU* 3.7 46.9 - - + -
167A LEU* 5.2 5.6 - - + -
170A VAL* 4.9 9.0 - - + -
175A PHE* 6.4 0.2 - - + -
59C VAL* 5.5 0.8 - - + +
60C ASP 3.7 5.6 + - - +
61C SER* 3.2 32.8 - - - +
63C VAL* 1.4 78.3 - - - +
65C LEU* 1.4 59.4 + - - +
67C LEU* 3.5 7.4 + - + +
68C SER* 3.2 23.6 + - - -
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Residues in contact with LEU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 3.6 36.8 - - + -
42A ILE* 3.8 18.2 - - + -
163A PHE* 5.5 0.2 - - - -
175A PHE* 6.5 1.8 - - + -
61C SER 3.5 10.8 - - - +
62C LEU* 3.3 26.0 + - + +
63C VAL 3.3 0.4 - - - -
64C VAL* 1.4 80.9 - - + +
66C PHE* 1.4 69.8 + - + +
68C SER* 3.6 3.8 + - - -
69C VAL* 3.4 30.4 + - + +
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.0 49.2 + - + +
63C VAL* 3.8 9.4 - - + +
65C LEU* 1.4 81.7 - - + +
67C LEU* 1.4 64.3 + - - +
69C VAL* 3.4 12.2 - - + +
70C GLY* 3.3 19.2 + - - -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A GLY 5.0 11.7 - - - +
163A PHE* 5.0 10.8 - - + -
63C VAL* 3.0 22.0 + - + +
64C VAL* 3.7 9.6 - - + +
66C PHE* 1.4 76.3 - - - +
68C SER* 1.4 63.6 + - - +
70C GLY* 3.6 1.4 + - - -
71C PHE* 3.1 38.1 + - + +
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Residues in contact with SER 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.3 14.3 - - - +
163A PHE* 3.2 53.0 - - - -
64C VAL 3.2 7.6 + - - -
65C LEU 4.0 3.8 - - - -
66C PHE 3.3 0.2 - - - -
67C LEU* 1.4 81.5 - - - +
69C VAL* 1.4 60.1 + - - +
71C PHE* 3.2 8.7 + - - +
72C ILE* 3.0 32.6 + - - +
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PHE* 5.5 3.8 - - + -
42A ILE* 5.2 9.6 - - + -
45A PHE* 6.3 2.9 - - + -
65C LEU* 3.4 27.5 + - + +
66C PHE* 3.4 22.2 - - + +
68C SER* 1.4 76.6 - - - +
70C GLY* 1.4 60.6 + - - +
72C ILE* 3.4 13.9 + - + +
73C PHE* 3.0 45.3 + - + -
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Residues in contact with GLY 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE 3.3 8.8 + - - -
67C LEU 3.9 3.1 - - - -
68C SER 3.3 0.4 - - - -
69C VAL* 1.4 80.7 - - - +
71C PHE* 1.4 57.9 + - - +
73C PHE* 3.6 10.5 + - - +
74C SER* 3.2 26.3 + - - -
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Residues in contact with PHE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.3 14.6 - - + -
155A PHE* 5.8 6.1 - + - -
156A GLN* 3.5 35.7 - - + -
159A GLY* 5.0 9.2 - - - -
160A ALA* 3.8 28.5 - - + -
67C LEU* 3.1 27.4 + - + +
68C SER* 3.2 12.8 + - - +
70C GLY* 1.4 73.9 - - - +
72C ILE* 1.4 65.6 - - + +
74C SER* 3.3 8.1 + - - -
75C VAL* 3.1 49.2 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 3.9 28.0 - - + +
45A PHE* 4.2 24.9 - - + +
48A PHE* 3.5 37.5 - - + +
79A LEU* 5.1 17.5 - - + -
68C SER* 3.0 21.5 + - - +
69C VAL* 3.6 15.3 - - + +
71C PHE* 1.4 79.1 - - + +
73C PHE* 1.4 67.5 + - + +
75C VAL* 3.6 3.7 + - - +
76C ILE* 3.4 24.3 + - + +
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Residues in contact with PHE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 6.4 1.8 - + - -
69C VAL* 3.0 37.7 + - + +
70C GLY* 3.9 9.0 - - - +
71C PHE 3.4 0.2 - - - -
72C ILE* 1.4 80.0 - - + +
74C SER* 1.4 60.6 + - - +
76C ILE* 3.3 20.7 - - + +
77C ALA* 4.6 4.2 + - - +
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Residues in contact with SER 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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70C GLY 3.2 18.0 + - - -
71C PHE* 3.5 11.7 - - - -
72C ILE 3.3 0.4 - - - -
73C PHE* 1.4 78.3 - - - +
75C VAL* 1.4 64.4 + - - +
76C ILE 3.6 0.2 + - - -
77C ALA* 4.2 5.5 + - - +
78C LEU* 4.2 15.4 + - - +
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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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48A PHE* 5.8 1.1 - - + -
49A PRO 3.3 23.2 - - - +
50A LEU* 4.0 0.7 - - - -
51A VAL* 3.6 29.9 - - + +
79A LEU* 3.5 22.0 - - + -
156A GLN* 5.0 7.2 - - + +
71C PHE* 3.1 48.9 + - + +
72C ILE 4.2 2.5 - - - +
74C SER* 1.4 76.6 - - - +
76C ILE* 1.4 65.9 + - - +
78C LEU 3.3 20.4 + - - +
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Residues in contact with ILE 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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48A PHE* 3.5 40.6 - - + -
49A PRO* 4.6 21.2 - - + +
75B ILE* 5.5 7.6 - - + -
79B ILE* 5.8 6.0 - - + +
72C ILE* 3.4 13.5 + - + +
73C PHE* 3.3 28.0 - - + +
75C VAL* 1.4 79.8 - - - +
77C ALA* 1.4 69.9 + - + +
78C LEU 4.3 2.1 - - - +
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Residues in contact with ALA 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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79B ILE* 5.8 4.0 - - - +
73C PHE 5.1 2.5 - - - +
74C SER 4.2 7.0 + - - +
75C VAL 3.4 0.4 - - - -
76C ILE* 1.4 89.3 - - + +
78C LEU* 1.4 63.2 + - + +
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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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50A LEU 4.7 1.2 - - - +
51A VAL* 3.6 54.0 - - + -
52A GLY 4.4 2.3 + - - -
53A LEU* 5.8 13.7 - - + -
149A GLN* 5.8 1.8 - - - +
156A GLN* 5.8 0.7 - - - +
74C SER* 4.2 11.6 + - - +
75C VAL 3.3 14.0 + - - +
76C ILE 4.3 2.1 - - - +
77C ALA* 1.4 82.3 - - + +
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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