Contacts of the helix formed by residues 72 - 90 (chain C) in PDB entry 1SCF
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 ASN 72 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.5 25.2 - - + +
21C ASN* 3.0 47.5 + - - +
22C LEU* 3.9 5.3 - - - +
63C PHE* 3.5 28.5 - - + -
71C SER* 1.3 72.5 - - - +
73C TYR* 1.3 60.2 + - - +
75C ILE* 3.9 3.9 - - - +
76C ILE* 2.8 39.2 + - + +
21D ASN* 3.1 29.2 + - - +
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LEU* 3.2 45.7 - - + +
61C ASP* 5.9 0.4 - - - -
63C PHE* 3.6 25.2 - - + +
64C SER* 3.8 6.0 + - - +
65C ASN* 3.6 59.2 - - + +
71C SER* 3.8 2.9 - - - +
72C ASN* 1.3 76.9 - - - +
74C SER* 1.3 57.8 + - - +
76C ILE* 4.8 0.2 - - - -
77C ASP* 2.8 53.3 + - - +
21D ASN* 4.9 0.4 + - - -
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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
----------------------------------------------------------
65C ASN* 4.5 6.7 - - - -
70C LEU* 3.5 12.9 - - - +
71C SER* 3.2 25.3 + - - -
73C TYR* 1.3 84.9 - - - +
75C ILE* 1.3 60.5 + - - +
77C ASP* 3.4 7.4 + - - +
78C LYS* 3.3 42.1 + - - -
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP* 3.6 41.3 - - + +
17C LYS* 4.4 6.5 - - + -
18C LEU* 4.1 34.3 - - + +
21C ASN* 5.7 1.3 - - - +
70C LEU* 3.9 33.9 - - + +
71C SER 3.0 22.7 + - - +
72C ASN* 4.0 7.9 - - - +
74C SER* 1.3 73.4 - - - +
76C ILE* 1.3 64.7 + - - +
78C LYS* 3.4 10.9 + - + +
79C LEU* 3.2 29.8 + - + +
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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
----------------------------------------------------------
18C LEU* 3.8 28.0 - - + -
56C LEU* 3.6 44.2 - - + +
59C LEU* 3.9 16.6 - - + +
60C LEU* 3.7 14.6 - - + -
63C PHE* 3.6 35.4 - - + -
72C ASN 2.8 29.0 + - - +
73C TYR* 4.6 0.4 - - - +
75C ILE* 1.3 76.1 - - - +
77C ASP* 1.3 62.4 + - - +
79C LEU* 3.1 7.2 + - - +
80C VAL* 3.0 22.5 + - - +
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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
----------------------------------------------------------
60C LEU* 3.6 17.0 - - + +
73C TYR* 2.8 35.3 + - + +
74C SER* 3.4 10.0 - - - +
76C ILE* 1.3 75.5 - - - +
78C LYS* 1.3 63.1 + - + +
80C VAL* 3.5 7.1 + - - +
81C ASN* 2.7 40.8 + - - -
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Residues in contact with LYS 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP* 5.7 1.2 + - - -
70C LEU* 4.4 10.3 - - - +
74C SER* 3.3 36.6 + - - +
75C ILE* 3.4 11.0 + - - +
77C ASP* 1.3 80.3 - - + +
79C LEU* 1.3 67.2 + - + +
81C ASN* 3.1 8.0 + - - +
82C ILE* 2.9 38.1 + - + +
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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
----------------------------------------------------------
11C ASN* 4.7 17.9 - - + +
15C VAL* 4.0 22.2 - - + -
18C LEU* 4.2 13.2 - - + -
56C LEU* 3.9 15.9 - - + -
75C ILE* 3.2 20.4 + - + +
76C ILE* 3.1 8.8 + - - +
78C LYS* 1.3 83.4 - - + +
80C VAL* 1.3 57.7 + - - +
82C ILE* 3.2 11.0 + - + +
83C VAL* 2.9 34.8 + - - +
116C PHE* 3.8 29.2 - - + -
119C PHE* 3.9 20.0 - - + -
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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
----------------------------------------------------------
53C SER* 5.1 2.5 - - - +
56C LEU* 3.8 32.8 - - + +
57C THR* 3.3 27.6 - - + +
60C LEU* 5.0 8.1 - - + -
76C ILE* 3.0 17.3 + - + +
77C ASP* 3.6 10.8 - - - +
79C LEU* 1.3 73.9 - - - +
81C ASN* 1.3 60.8 + - - +
83C VAL* 3.3 6.2 + - - +
84C ASP* 2.9 44.5 + - - +
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ASP* 2.7 38.2 + - - -
78C LYS* 3.1 10.8 + - - +
80C VAL* 1.3 82.4 - - - +
82C ILE* 1.3 62.5 + - + +
84C ASP* 3.4 4.3 + - - +
85C ASP* 3.2 27.8 + - - +
1023C CA 2.8 27.7 - - - -
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Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 4.7 22.2 - - + -
78C LYS* 2.9 31.6 + - + +
79C LEU* 3.5 11.4 - - + +
81C ASN* 1.3 77.5 - - + +
83C VAL* 1.3 63.3 + - + +
85C ASP* 3.2 23.4 - - - +
86C LEU* 3.4 20.4 - - + +
119C PHE* 5.4 4.0 - - + -
123C ILE* 5.1 15.0 - - + -
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C VAL* 3.2 38.6 - - + +
52C LEU* 4.3 4.7 - - + -
53C SER* 3.7 18.6 - - - +
56C LEU* 3.9 10.3 - - + -
79C LEU 2.9 20.8 + - - +
80C VAL* 3.9 4.7 - - - +
82C ILE* 1.3 72.7 - - + +
84C ASP* 1.3 60.4 + - - +
86C LEU* 3.2 11.3 + - + +
87C VAL* 3.0 31.6 + - - +
119C PHE* 3.6 29.4 - - + -
123C ILE* 4.5 7.4 - - + -
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Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C SER* 2.8 27.0 + - - -
57C THR* 5.2 0.5 + - - -
80C VAL* 2.9 33.7 + - - +
81C ASN* 3.7 6.6 - - - +
82C ILE 3.4 0.2 - - - -
83C VAL* 1.3 74.3 - - - +
85C ASP* 1.3 58.6 + - - +
87C VAL* 3.2 10.2 + - - +
88C GLU* 3.0 35.2 + - + +
1023C CA 4.2 15.3 - - - -
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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
----------------------------------------------------------
81C ASN 3.2 13.2 + - - +
82C ILE* 3.2 15.6 - - - +
84C ASP* 1.3 76.4 - - - +
86C LEU* 1.3 64.9 + - + +
88C GLU* 3.7 8.2 + - - +
89C CYS* 2.9 26.7 + - - +
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Residues in contact with LEU 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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49C VAL* 4.2 11.9 - - + -
82C ILE* 3.4 19.5 - - + +
83C VAL* 3.2 10.6 + - - +
85C ASP* 1.3 78.2 - - + +
87C VAL* 1.3 59.6 + - - +
89C CYS* 3.7 9.3 - - + +
90C VAL* 2.9 33.3 + - - +
123C ILE* 3.5 42.6 - - + -
126C PHE* 4.0 42.7 - - + -
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Residues in contact with VAL 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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104A SER 4.9 14.1 - - - +
49C VAL* 3.4 35.9 - - + +
50C VAL* 3.6 23.8 - - + -
53C SER* 4.2 6.7 - - - +
83C VAL 3.0 17.6 + - - +
84C ASP* 3.2 13.7 + - - +
86C LEU* 1.3 74.8 - - - +
88C GLU* 1.3 68.5 + - - +
90C VAL* 3.4 14.9 + - + +
91C LYS* 3.6 10.6 + - - +
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Residues in contact with GLU 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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104A SER* 5.1 11.1 + - - -
84C ASP* 3.0 22.1 + - + +
85C ASP* 4.1 7.6 - - - +
86C LEU 3.4 0.2 - - - -
87C VAL* 1.3 82.2 - - - +
89C CYS* 1.3 60.0 + - - +
90C VAL 3.3 0.4 + - - -
91C LYS* 3.6 34.5 + - - +
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Residues in contact with CYS 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 ASP 2.9 19.9 + - - +
86C LEU* 3.7 13.9 - - + +
87C VAL 3.3 0.4 - - - -
88C GLU* 1.3 74.1 - - - +
90C VAL* 1.3 64.5 + - - +
91C LYS 3.4 3.9 - - - -
126C PHE* 4.9 14.6 - - + -
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 5.1 4.9 - - + -
46C SER* 4.1 38.6 - - - +
49C VAL* 4.2 13.9 - - + -
50C VAL* 5.9 1.3 - - + -
86C LEU 2.9 18.8 + - - +
87C VAL* 3.6 9.0 - - + +
88C GLU 3.3 0.4 - - - -
89C CYS* 1.3 76.2 - - - +
91C LYS* 1.4 64.5 + - - +
126C PHE* 4.4 17.7 - - + -
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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) + - + + + + + -
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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