Contacts of the helix formed by residues 12 - 21 (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 VAL 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ASN* 1.4 68.7 - - - +
13A LYS* 1.3 61.4 + - - +
14A ASP 3.3 0.7 - - - -
15A VAL* 3.8 13.2 - - + -
16A THR* 3.3 28.9 + - + +
120A ASN* 3.9 22.2 - - - +
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Residues in contact with LYS 13 (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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11A ASN* 3.2 3.8 + - + +
12A VAL* 1.3 76.1 - - - +
14A ASP* 1.3 64.9 - - + +
16A THR* 3.0 19.8 + - - -
17A LYS* 3.2 32.3 + - - +
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Residues in contact with ASP 14 (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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11A ASN* 3.7 9.5 + - + +
13A LYS* 1.3 83.4 - - + +
15A VAL* 1.3 57.7 + - - +
17A LYS* 3.3 18.9 + - - +
18A LEU* 2.9 30.0 + - - +
70A LEU* 5.9 0.2 - - - +
75A ILE* 3.6 30.1 - - + +
78A LYS* 2.8 33.6 + - - -
79A LEU* 5.4 4.9 - - + -
68B GLU* 5.7 0.3 - - - +
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Residues in contact with VAL 15 (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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11A ASN 3.9 14.1 + - - +
12A VAL* 3.7 11.1 + - + +
13A LYS 3.4 0.2 - - - -
14A ASP* 1.3 76.8 - - - +
16A THR* 1.3 59.4 + - + +
18A LEU* 3.3 5.8 + - - +
19A VAL* 3.0 29.5 + - + +
75A ILE* 5.2 0.7 - - - -
79A LEU* 4.0 26.0 - - + -
116A PHE* 3.6 28.9 - - + -
119A PHE* 4.1 11.2 - - + -
120A ASN* 3.5 33.7 - - - +
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Residues in contact with THR 16 (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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12A VAL* 3.3 19.0 + - + +
13A LYS* 3.0 14.9 + - - -
15A VAL* 1.3 77.5 - - + +
17A LYS* 1.4 52.6 + - - +
19A VAL* 3.5 6.4 + - - +
20A ALA* 2.8 35.6 + - - +
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Residues in contact with LYS 17 (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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13A LYS* 3.2 26.9 + - - +
14A ASP* 3.3 21.9 + - - +
16A THR* 1.4 76.2 + - - +
18A LEU* 1.3 57.2 + - - +
20A ALA* 4.4 1.3 - - - -
21A ASN* 2.9 24.7 + - - +
70A LEU* 4.7 1.1 - - + -
75A ILE* 4.3 9.4 - - + -
66B ILE* 3.2 30.6 - - + +
67B SER 5.7 1.8 - - - -
68B GLU* 3.1 45.3 - - - +
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Residues in contact with LEU 18 (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 2.9 16.6 + - - +
15A VAL* 3.6 4.5 - - - +
16A THR 3.2 0.2 - - - -
17A LYS* 1.3 72.4 - - - +
19A VAL* 1.3 57.5 + - - +
21A ASN* 2.6 26.2 + - - -
22A LEU* 2.9 33.5 + - + +
59A LEU* 6.2 0.2 - - + -
72A ASN* 3.5 39.0 - - + +
75A ILE* 3.9 14.8 - - + +
76A ILE* 3.8 26.0 - - + -
79A LEU* 4.0 13.7 - - + -
116A PHE* 3.5 31.2 - - + -
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Residues in contact with VAL 19 (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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15A VAL* 3.0 17.2 + - + +
16A THR* 3.7 6.1 - - - +
18A LEU* 1.3 74.6 - - - +
20A ALA* 1.3 61.1 + - - +
21A ASN 3.4 0.2 + - - -
22A LEU* 3.4 21.7 - - - +
24A LYS* 6.1 0.7 - - - +
112A PRO* 4.0 8.7 - - + +
113A GLU* 4.0 29.2 - - + +
116A PHE* 3.4 41.3 - - + -
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Residues in contact with ALA 20 (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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16A THR 2.8 21.8 + - - +
17A LYS* 3.6 0.7 - - - +
18A LEU 3.2 0.2 - - - -
19A VAL* 1.3 73.2 - - - +
21A ASN* 1.3 60.7 + - - +
22A LEU 3.4 0.2 - - - -
63B PHE* 3.6 10.0 - - - +
64B SER* 3.5 45.4 + - - +
65B ASN 4.7 3.1 - - - +
66B ILE* 3.6 26.2 - - + -
73B TYR 5.8 0.2 + - - -
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Residues in contact with ASN 21 (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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17A LYS 2.9 15.7 + - - +
18A LEU 2.6 13.9 + - - +
20A ALA* 1.3 73.9 - - - +
22A LEU* 1.3 56.8 + - - +
23A PRO* 4.7 0.3 - - - +
70A LEU* 4.0 17.9 - - + +
72A ASN* 3.3 35.7 + - - +
21B ASN* 4.1 8.6 - - - +
63B PHE* 3.4 5.2 - - - -
66B ILE* 3.7 15.6 - - + +
71B SER* 3.8 1.2 - - - +
72B ASN* 2.8 68.2 + - - +
73B TYR 4.6 0.5 + - - -
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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