Contacts of the helix formed by residues 72 - 92 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN* 2.8 49.7 + - - +
17B LYS 4.6 0.3 - - - +
18B LEU* 3.4 31.5 - - + +
21B ASN* 3.4 34.1 + - - +
22B LEU* 4.4 1.7 - - - +
63B PHE* 3.4 25.2 - - + -
71B SER* 1.3 70.4 - - - +
73B TYR* 1.3 52.7 + - - +
75B ILE* 3.8 3.4 - - - +
76B ILE* 2.8 43.0 + - + +
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 4.6 0.8 + - - -
60B LEU* 3.4 39.6 - - + +
63B PHE* 3.4 39.9 - - + +
64B SER* 3.6 21.3 - - - +
65B ASN* 3.7 33.0 - - + +
71B SER* 3.1 2.8 + - - +
72B ASN* 1.3 77.5 - - - +
74B SER* 1.3 67.1 + - - +
77B ASP* 3.0 40.8 + - + +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASN* 3.2 13.3 + - - -
66B ILE 4.8 1.4 + - - -
69B GLY 4.9 2.2 + - - -
70B LEU* 4.7 12.8 - - - -
71B SER* 3.1 27.0 + - - -
73B TYR* 1.3 79.1 - - - +
75B ILE* 1.3 62.4 + - - +
77B ASP* 3.7 7.2 - - - +
78B LYS* 3.2 24.1 + - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASP* 3.6 42.0 - - + +
17B LYS* 4.1 14.1 - - + +
18B LEU* 3.8 32.1 - - + +
70B LEU* 3.9 34.1 - - + -
71B SER 2.9 24.3 + - - +
72B ASN* 3.8 7.0 - - - +
74B SER* 1.3 78.6 - - - +
76B ILE* 1.3 63.7 + - - +
78B LYS* 3.3 8.4 + - + +
79B LEU* 3.0 27.8 + - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 24.2 - - + -
56B LEU* 3.3 41.7 - - + +
59B LEU* 3.6 20.0 - - + +
60B LEU* 3.9 14.4 - - + +
63B PHE* 3.4 37.5 - - + -
72B ASN 2.8 26.2 + - - +
75B ILE* 1.3 73.2 - - - +
77B ASP* 1.3 55.3 + - - +
79B LEU* 2.8 29.2 + - - +
80B VAL* 2.8 14.1 + - + +
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Residues in contact with ASP 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.4 29.2 - - + +
73B TYR* 3.0 32.3 + - + +
74B SER* 3.7 7.7 - - - +
76B ILE* 1.3 74.3 - - - +
78B LYS* 1.3 60.8 + - - +
80B VAL* 3.2 8.1 + - - +
81B ASN* 3.0 40.5 + - - +
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Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 4.1 22.6 - - - +
14B ASP* 3.5 26.1 + - + +
70B LEU* 6.0 2.7 - - + +
74B SER 3.2 11.2 + - - +
75B ILE* 3.4 11.0 - - + +
77B ASP* 1.3 79.0 + - - +
79B LEU* 1.3 65.1 + - + +
81B ASN* 3.4 10.7 + - - +
82B ILE* 3.2 35.2 + - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 5.3 6.7 - - + +
14B ASP* 5.7 1.8 - - + -
15B VAL* 4.0 22.9 - - + +
18B LEU* 3.8 17.5 - - + -
56B LEU* 3.9 18.6 - - + +
75B ILE* 3.0 22.8 + - + +
76B ILE* 2.8 12.7 + - - +
78B LYS* 1.3 73.6 - - + +
80B VAL* 1.3 65.3 + - - +
82B ILE* 3.4 16.2 + - + +
83B VAL* 3.1 26.5 + - - +
116B PHE* 3.5 34.1 - - + -
119B PHE* 4.1 18.3 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 5.2 1.6 - - - +
56B LEU* 3.9 34.1 - - + +
57B THR* 3.6 17.9 - - + +
60B LEU* 4.2 12.3 - - + -
76B ILE* 2.8 21.2 + - + +
77B ASP* 3.2 14.1 - - - +
79B LEU* 1.3 75.5 - - - +
81B ASN* 1.3 63.6 + - - +
83B VAL* 3.3 8.3 + - - +
84B ASP* 2.9 46.8 + - - +
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 3.0 37.3 + - - +
78B LYS* 3.4 7.7 + - - +
79B LEU 3.3 0.4 - - - -
80B VAL* 1.3 82.6 - - - +
82B ILE* 1.3 59.7 + - - +
84B ASP* 3.9 5.6 - - - +
85B ASP* 3.1 32.8 + - - +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 4.5 19.3 - - + +
78B LYS* 3.2 30.8 + - + +
79B LEU* 3.4 20.6 + - + +
81B ASN* 1.3 74.5 - - + +
83B VAL* 1.3 62.7 + - - +
85B ASP* 3.2 11.5 + - - +
86B LEU* 3.1 26.6 + - + +
119B PHE* 5.0 2.9 - - + -
123B ILE* 3.7 31.2 - - + -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.9 34.1 - - + +
52B LEU* 4.3 10.8 - - + -
53B SER* 3.7 30.1 - - - +
56B LEU* 4.1 12.1 - - + -
79B LEU 3.1 19.8 + - - +
80B VAL* 3.8 5.8 - - - +
82B ILE* 1.3 77.7 - - - +
84B ASP* 1.3 59.3 + - - +
86B LEU* 3.2 4.6 + - + +
87B VAL* 2.9 31.3 + - - +
119B PHE* 4.3 9.2 - - + -
123B ILE* 4.2 15.5 - - + -
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B SER* 2.7 27.8 + - - -
57B THR* 4.7 1.9 + - - -
80B VAL* 2.9 35.6 + - - +
81B ASN* 4.0 7.0 - - - +
83B VAL* 1.3 76.3 - - - +
85B ASP* 1.3 60.4 + - - +
87B VAL* 3.7 9.7 - - - +
88B GLU* 3.3 31.1 + - - +
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Residues in contact with ASP 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 3.1 24.2 + - - +
82B ILE* 3.2 10.7 + - - +
84B ASP* 1.3 75.2 - - - +
86B LEU* 1.3 59.0 + - + +
88B GLU* 3.5 18.7 + - - +
89B CYS* 3.1 28.8 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.3 8.1 - - + -
82B ILE* 3.1 20.7 + - + +
83B VAL* 3.2 11.2 + - + +
85B ASP* 1.3 76.4 - - + +
87B VAL* 1.3 64.6 + - - +
89B CYS* 3.9 9.1 - - + +
90B VAL* 3.0 31.2 + - - +
123B ILE* 3.4 36.3 - - + +
126B PHE* 3.8 50.5 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 3.9 32.3 - - + +
50B VAL* 4.2 10.8 - - + +
53B SER* 4.1 13.9 - - - -
83B VAL 2.9 20.6 + - - +
84B ASP* 3.7 13.7 - - - +
85B ASP 3.4 0.2 - - - -
86B LEU* 1.3 73.4 - - - +
88B GLU* 1.3 67.9 + - + +
90B VAL* 3.0 13.7 + - - +
91B LYS* 3.0 44.0 + - + +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ASP* 3.3 19.1 + - - +
85B ASP* 3.7 21.6 - - - +
86B LEU 3.4 0.2 - - - -
87B VAL* 1.3 80.7 - - + +
89B CYS* 1.3 60.6 + - - +
91B LYS* 3.2 16.7 + - - +
92B GLU* 3.3 21.5 + - - +
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Residues in contact with CYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP 3.1 19.1 + - - +
86B LEU* 3.9 11.0 - - + +
88B GLU* 1.3 75.1 - - - +
90B VAL* 1.3 70.2 + - - +
92B GLU* 3.4 10.2 + - - +
93B ASN* 3.3 24.0 + - - +
126B PHE* 4.9 9.9 - - - -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 5.0 4.5 - - + -
46B SER* 3.4 41.5 - - - +
49B VAL* 4.7 4.7 - - + -
86B LEU 3.0 20.2 + - - +
87B VAL* 3.0 3.8 + - - +
89B CYS* 1.3 79.9 - - - +
91B LYS* 1.3 62.1 + - + +
92B GLU 3.4 0.4 + - - -
93B ASN* 4.1 8.7 - - + +
98B LEU* 4.0 15.2 - - + +
100B LYS* 3.5 20.6 + - - +
126B PHE* 3.3 34.8 - - + -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B SER* 5.8 1.8 - - - +
50B VAL* 4.5 17.0 - - - +
87B VAL* 3.0 34.5 + - + +
88B GLU* 3.2 9.1 + - - +
90B VAL* 1.3 81.5 - - + +
92B GLU* 1.4 61.7 + - - +
100B LYS* 4.1 13.1 + - + +
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 3.3 18.8 + - - +
89B CYS* 3.7 11.0 - - - +
90B VAL 3.4 0.4 - - - -
91B LYS* 1.4 77.8 - - - +
93B ASN* 1.4 54.5 + - - +
94B SER* 2.8 28.2 + - - -
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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