Contacts of the helix formed by residues 67 - 92 (chain C) in PDB entry 3P42
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 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR* 1.3 82.5 + - - +
68C SER* 1.3 66.4 + - - +
69C ALA* 3.5 10.1 + - - +
70C ALA* 3.1 24.5 + - - +
71C LYS* 3.0 22.2 + - - +
116C LEU* 3.9 14.2 - - - +
136C VAL 5.4 1.2 - - - +
138C ASP 3.4 23.2 - - - +
139C TYR* 3.7 20.0 + - + +
140C THR* 4.8 2.2 - - - +
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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
----------------------------------------------------------
67C ASP* 1.3 75.2 - - - +
69C ALA* 1.3 58.1 + - - +
71C LYS* 3.4 12.4 + - - +
72C ALA* 2.9 30.2 + - - +
138C ASP 5.0 0.8 + - - -
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ASP* 3.3 11.1 + - - +
68C SER* 1.3 77.6 - - - +
70C ALA* 1.3 63.0 + - - +
72C ALA* 3.3 6.5 + - - +
73C LYS* 3.0 24.8 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR* 3.6 14.8 - - - +
67C ASP* 3.1 18.8 + - - +
69C ALA* 1.3 77.6 - - - +
71C LYS* 1.3 57.6 + - - +
73C LYS* 3.5 6.6 + - - +
74C ALA* 3.0 29.8 + - - +
114C GLY* 3.7 3.5 - - - -
115C ARG 4.3 12.8 - - - +
116C LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C THR* 5.5 2.0 - - + -
67C ASP 3.0 16.2 + - - +
68C SER* 3.8 10.3 - - - +
70C ALA* 1.3 75.7 - - - +
72C ALA* 1.3 60.5 + - - +
74C ALA* 3.3 1.4 + - - +
75C LEU* 2.9 33.1 + - + +
112C ILE* 3.7 24.0 - - + +
113C THR* 3.3 28.6 + - + +
114C GLY* 4.0 0.4 - - - -
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Residues in contact with ALA 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C SER 2.9 17.9 + - - +
69C ALA* 3.7 7.0 - - - +
71C LYS* 1.3 78.1 - - - +
73C LYS* 1.3 62.5 + - - +
75C LEU* 3.8 6.8 - - - +
76C LYS* 3.1 31.3 + - + +
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Residues in contact with LYS 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 5.0 15.5 + - - +
38A SER* 5.7 5.2 - - - -
69C ALA 3.0 17.2 + - - +
70C ALA* 3.7 6.1 - - - +
72C ALA* 1.3 75.3 - - - +
74C ALA* 1.3 59.0 + - - +
76C LYS* 3.3 9.8 + - - +
77C ASP* 2.9 55.1 + - - +
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.0 19.0 + - - +
71C LYS 3.7 0.9 - - - +
73C LYS* 1.3 78.2 - - - +
75C LEU* 1.3 57.2 + - - +
77C ASP* 3.4 10.0 + - - +
78C TYR* 2.8 29.6 + - - +
112C ILE* 3.6 15.1 - - + +
114C GLY* 3.5 22.9 - - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LYS* 2.9 21.0 + - + +
72C ALA* 3.8 7.0 - - - +
73C LYS 3.2 0.2 - - - -
74C ALA* 1.3 73.2 - - - +
76C LYS* 1.3 61.9 + - + +
78C TYR* 3.3 14.7 + - + +
79C GLN* 2.9 60.8 + - + +
112C ILE* 3.7 17.9 - - + +
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ALA* 3.1 20.4 + - + +
73C LYS* 3.6 9.6 - - - +
75C LEU* 1.3 78.9 - - + +
77C ASP* 1.3 64.2 + - - +
79C GLN* 3.5 6.1 + - - +
80C HIS* 3.1 24.1 + - - +
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Residues in contact with ASP 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LYS* 2.9 47.6 + - - +
74C ALA* 3.6 8.9 - - - +
76C LYS* 1.3 77.5 - - - +
78C TYR* 1.3 62.1 + - - +
80C HIS* 3.4 8.2 + - - +
81C VAL* 3.1 27.6 + - + +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA 2.8 18.3 + - - +
75C LEU* 3.6 9.9 - - + +
76C LYS 3.2 0.2 - - - -
77C ASP* 1.3 78.2 - - - +
79C GLN* 1.3 71.8 + - + +
81C VAL* 3.2 11.2 + - + +
82C MSE 3.0 53.6 + - + +
107C LEU* 2.6 30.9 + - + -
108C LEU* 3.2 19.8 + - - +
110C LEU* 4.0 26.1 + - + -
112C ILE* 3.7 33.0 - - + -
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Residues in contact with GLN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 2.9 41.8 + - + +
76C LYS* 4.0 5.4 - - - +
78C TYR* 1.3 89.1 - - + +
80C HIS* 1.3 58.3 + - - +
82C MSE 3.4 7.3 + - + +
83C ALA* 2.9 30.1 + - - +
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Residues in contact with HIS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LYS 3.1 17.3 + - - +
77C ASP* 3.5 9.2 - - - +
78C TYR 3.2 0.2 - - - -
79C GLN* 1.3 77.0 - - - +
81C VAL* 1.3 64.0 + - + +
83C ALA* 3.3 7.0 + - - +
84C GLN* 3.0 62.3 + - + +
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 3.1 17.8 + - + +
78C TYR* 3.2 13.7 + - + +
80C HIS* 1.3 80.6 - - + +
82C MSE 1.3 68.9 + - - +
84C GLN* 3.2 7.8 + - - +
85C LEU* 3.0 42.9 + - + +
107C LEU* 4.7 9.0 - - + -
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Residues in contact with MSE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 3.0 47.9 + - + +
79C GLN* 3.8 6.1 - - - +
81C VAL* 1.3 78.5 - - - +
83C ALA* 1.3 57.8 + - - +
85C LEU* 3.8 15.0 - - - +
86C ALA* 3.1 27.5 + - - +
104C ARG* 3.5 41.3 - - + +
107C LEU* 3.8 23.3 - - - -
108C LEU* 3.5 34.1 - - + -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLN 2.9 17.6 + - - +
80C HIS* 3.8 8.3 - - - +
81C VAL 3.2 0.2 - - - -
82C MSE 1.3 75.4 - - - +
84C GLN* 1.3 62.3 + - + +
86C ALA* 3.3 5.7 + - - +
87C SER* 2.9 34.3 + - - +
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Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 3.0 57.8 + - + +
81C VAL* 3.2 6.9 + - - +
83C ALA* 1.3 75.1 - - - +
85C LEU* 1.3 60.7 + - + +
87C SER* 3.2 9.2 + - - -
88C TRP* 2.8 34.2 + - - +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C VAL* 3.0 37.2 + - + +
82C MSE 3.8 11.2 - - - +
84C GLN* 1.3 76.8 - - + +
86C ALA* 1.3 58.6 + - - +
88C TRP* 4.6 16.2 - - + -
89C GLU* 3.0 23.9 + - - +
100C ILE* 3.3 32.0 - - + +
103C VAL* 4.6 15.0 - - + -
104C ARG* 4.3 24.5 - - + +
107C LEU* 4.1 19.5 - - + -
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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
----------------------------------------------------------
82C MSE 3.1 18.1 + - - +
83C ALA* 3.8 6.1 - - - +
84C GLN 3.2 0.4 - - - -
85C LEU* 1.3 74.8 - - - +
87C SER* 1.3 65.0 + - - +
89C GLU* 3.4 6.4 + - - +
90C ALA* 3.2 21.8 + - - +
104C ARG* 4.2 17.0 - - - +
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA* 2.9 21.8 + - - +
84C GLN* 3.7 10.0 + - - -
86C ALA* 1.3 73.7 - - - +
88C TRP* 1.3 66.6 + - - +
90C ALA* 3.2 8.0 + - - +
91C GLU* 3.1 37.7 + - - +
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Residues in contact with TRP 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 GLN 2.8 21.0 + - - +
85C LEU* 4.0 15.5 - - + +
87C SER* 1.3 74.1 - - - +
89C GLU* 1.3 62.5 + - - +
91C GLU* 3.0 16.3 + - + +
92C ALA* 2.9 33.7 + - + +
96C VAL* 3.8 18.5 - - + +
100C ILE* 3.2 32.5 - - + +
182C GLY 6.0 1.6 - - - -
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C LEU 3.0 18.6 + - - +
86C ALA* 3.8 5.5 - - - +
87C SER 3.3 0.4 - - - -
88C TRP* 1.3 77.6 - - - +
90C ALA* 1.3 63.0 + - - +
91C GLU 3.3 0.2 + - - -
92C ALA* 3.5 8.2 + - - +
97C ALA* 3.6 28.4 - - + +
100C ILE* 3.7 18.0 - - + +
101C LYS* 3.6 36.7 - - - +
104C ARG* 3.1 34.2 + - - -
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Residues in contact with ALA 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ALA 3.2 9.6 + - - +
87C SER* 3.2 11.7 + - - +
89C GLU* 1.3 81.5 - - - +
91C GLU* 1.3 62.6 + - + +
92C ALA 4.6 1.9 - - - +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 3.1 26.7 + - - +
88C TRP* 3.0 19.9 + - + +
90C ALA* 1.3 80.0 - - + +
92C ALA* 1.3 63.5 + - - +
93C ASP* 4.0 0.3 + - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TRP* 2.9 26.4 + - - +
89C GLU 3.5 4.3 + - - +
90C ALA 4.6 1.7 - - - +
91C GLU* 1.3 82.3 - - - +
93C ASP* 1.3 72.7 + - - +
94C ASP* 3.7 3.6 + - - +
96C VAL* 4.0 6.3 - - + -
97C ALA* 3.8 21.9 - - - +
100C ILE* 3.9 13.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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