Contacts of the helix formed by residues 72 - 89 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.5 25.8 - - + +
21A ASN* 3.3 38.5 + - - +
22A LEU* 4.0 5.5 - - - +
63A PHE* 3.5 28.1 - - + -
70A LEU* 5.1 1.0 - - - +
71A SER* 1.3 69.1 - - - +
73A TYR* 1.3 65.5 + - - +
75A ILE* 3.8 6.4 - - - +
76A ILE* 3.0 32.3 + - + +
21B ASN* 2.9 38.5 + - - +
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.3 62.2 - - + +
63A PHE* 3.6 23.8 - - + +
64A SER 3.5 21.9 + - - +
65A ASN* 3.5 39.4 + - + -
71A SER* 3.3 4.4 + - - +
72A ASN* 1.3 79.2 - - - +
74A SER* 1.4 64.2 + - - +
76A ILE* 4.7 0.7 - - - -
77A ASP* 3.0 35.3 + - + +
21B ASN* 4.7 0.2 + - - -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 4.9 2.1 + - - -
71A SER* 3.0 29.3 + - - -
73A TYR* 1.4 79.6 - - - +
75A ILE* 1.3 61.7 + - - +
77A ASP* 3.4 10.4 + - - +
78A LYS* 3.0 35.6 + - - +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 3.6 53.2 - - + +
17A LYS* 4.3 9.9 - - + -
18A LEU* 3.9 25.6 - - + +
70A LEU* 3.5 31.2 - - + -
71A SER 3.1 15.8 + - - +
72A ASN* 3.9 9.0 - - - +
74A SER* 1.3 75.7 - - - +
76A ILE* 1.3 64.0 + - - +
78A LYS* 3.0 21.8 + - - +
79A LEU* 3.0 20.2 + - + +
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 3.8 23.6 - - + -
22A LEU* 5.6 0.9 - - + -
56A LEU* 3.4 40.8 - - + +
59A LEU* 4.1 16.6 - - + +
60A LEU* 3.8 12.1 - - + +
63A PHE* 3.5 37.0 - - + -
72A ASN* 3.0 25.6 + - + +
73A TYR* 3.9 4.3 - - - +
75A ILE* 1.3 73.9 - - - +
77A ASP* 1.3 50.6 + - - +
79A LEU* 3.0 11.7 + - - +
80A VAL* 2.6 40.0 + - + +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.0 17.8 - - + +
73A TYR* 3.0 29.3 + - + +
74A SER* 3.4 11.7 - - - +
76A ILE* 1.3 74.9 - - - +
78A LYS* 1.3 68.4 + - - +
80A VAL* 3.4 9.5 + - - +
81A ASN* 3.1 39.2 + - - +
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ASP* 2.8 29.0 + - - -
74A SER* 3.0 25.3 + - - +
75A ILE* 3.0 11.1 + - - +
77A ASP* 1.3 81.6 - - - +
79A LEU* 1.4 59.1 + - + +
81A ASN* 3.3 12.7 + - - +
82A ILE* 3.1 32.8 + - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 4.9 7.0 - - + +
14A ASP* 5.4 3.1 - - + -
15A VAL* 4.0 22.0 - - + +
18A LEU* 4.0 17.7 - - + -
56A LEU* 3.9 16.8 - - + -
75A ILE* 3.0 23.4 + - + +
76A ILE* 3.0 8.3 + - - +
78A LYS* 1.4 74.7 - - + +
80A VAL* 1.3 65.8 + - - +
82A ILE* 3.4 15.5 + - + +
83A VAL* 3.0 30.3 + - - +
116A PHE* 3.6 32.3 - - + -
119A PHE* 3.9 17.9 - - + -
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 4.9 1.8 - - - +
56A LEU* 3.7 28.3 - - + +
57A THR* 3.5 31.9 - - + +
60A LEU* 4.5 7.6 - - + -
76A ILE* 2.6 26.6 + - + +
77A ASP* 3.6 12.6 - - - +
79A LEU* 1.3 72.8 - - - +
81A ASN* 1.3 59.6 + - - +
83A VAL* 3.5 5.9 + - - -
84A ASP* 3.0 53.2 + - - +
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Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 3.1 31.5 + - - +
78A LYS* 3.4 15.5 - - - +
79A LEU 3.2 0.2 - - - -
80A VAL* 1.3 79.2 - - - +
82A ILE* 1.3 63.0 + - + +
84A ASP* 4.1 6.3 - - - +
85A ASP* 3.2 29.5 + - - +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 4.4 29.2 - - + +
78A LYS* 3.1 18.1 + - + +
79A LEU* 3.4 20.8 + - + +
81A ASN* 1.3 73.4 - - + +
83A VAL* 1.3 63.3 + - - +
85A ASP* 3.4 24.8 - - - +
86A LEU* 3.7 10.2 + - + +
119A PHE* 4.5 6.5 - - + -
123A ILE* 3.9 28.0 - - + -
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.4 45.3 - - + +
52A LEU* 4.3 6.5 - - + -
53A SER* 4.3 9.9 - - - +
56A LEU* 4.0 11.2 - - + -
79A LEU 3.0 18.3 + - - +
80A VAL* 4.2 4.5 - - - +
82A ILE* 1.3 79.8 - - - +
84A ASP* 1.3 61.1 + - - +
86A LEU* 3.1 8.8 + - - +
87A VAL* 3.0 24.5 + - - +
119A PHE* 3.3 24.2 - - + -
123A ILE* 4.7 7.2 - - + -
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Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER* 2.6 30.8 + - - -
57A THR* 5.0 0.2 + - - -
80A VAL* 3.0 38.9 + - - +
81A ASN* 4.1 7.3 - - - +
82A ILE 3.4 0.2 - - - -
83A VAL* 1.3 72.6 - - - +
85A ASP* 1.3 62.7 + - - +
87A VAL* 3.3 16.7 + - - +
88A GLU* 3.3 21.1 + - + +
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASN* 3.2 24.0 + - - +
82A ILE* 3.4 15.6 - - - +
84A ASP* 1.3 73.7 - - - +
86A LEU* 1.3 61.9 + - + +
88A GLU* 3.5 6.7 + - - +
89A CYS* 3.0 27.8 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A VAL* 4.2 10.8 - - + -
82A ILE* 3.7 14.4 - - + +
83A VAL* 3.1 8.4 + - - +
85A ASP* 1.3 80.6 - - + +
87A VAL* 1.3 60.1 + - - +
88A GLU 3.2 0.4 - - - -
89A CYS* 4.2 9.4 - - + -
90A VAL* 3.0 34.1 + - - +
123A ILE* 3.4 35.4 - - + +
126A PHE* 3.6 51.6 - - + -
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.5 39.7 - - + +
50A VAL* 4.0 20.9 - - + +
53A SER* 4.4 6.7 - - - -
83A VAL 3.0 16.7 + - - +
84A ASP* 3.3 14.1 + - + +
86A LEU* 1.3 75.9 - - - +
88A GLU* 1.3 66.3 + - - +
90A VAL* 3.7 7.2 - - - +
91A LYS* 3.3 20.6 + - - +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASP* 3.3 13.6 + - + +
85A ASP* 3.8 8.1 - - - +
86A LEU 3.2 0.2 - - - -
87A VAL* 1.3 84.6 - - - +
89A CYS* 1.3 65.9 + - - +
90A VAL 3.3 0.9 - - - -
91A LYS* 2.9 27.4 + - - +
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Residues in contact with CYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP 3.0 22.0 + - - +
86A LEU* 3.9 16.8 - - + +
88A GLU* 1.3 71.2 - - - +
90A VAL* 1.4 57.9 + - - +
91A LYS 3.0 10.9 + - - -
126A PHE* 5.3 7.9 - - + -
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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
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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