Contacts of the helix formed by residues 11 - 23 (chain A) in PDB entry 1SFU
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 ALA 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN* 3.5 6.6 - - + +
10A ASP* 1.3 78.1 - - - +
12A GLU* 1.3 56.6 + - - +
14A PHE* 3.4 10.8 + - - +
15A SER* 2.8 33.5 + - - +
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Residues in contact with GLU 12 (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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8A VAL* 4.3 24.5 - - + +
9A ASN 4.5 4.6 + - - +
10A ASP* 3.2 0.6 - - - +
11A ALA* 1.3 76.9 - - - +
13A ILE* 1.3 66.3 + - + +
15A SER* 3.8 6.9 - - - -
16A LEU* 3.0 66.5 + - + +
41A ILE* 5.2 1.2 - - - +
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Residues in contact with ILE 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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9A ASN 3.8 7.9 - - - +
10A ASP* 3.2 40.8 - - + +
12A GLU* 1.3 83.7 - - - +
14A PHE* 1.3 66.0 + - - +
16A LEU* 3.0 6.6 + - - +
17A VAL* 2.9 34.9 + - + +
41A ILE* 3.7 33.7 - - + -
45A LYS* 4.0 32.8 - - + +
46A ILE* 4.8 0.7 - - + -
49A GLN* 4.1 16.4 - - + +
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Residues in contact with PHE 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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10A ASP 2.8 8.9 + - - +
11A ALA* 3.5 14.8 - - - +
13A ILE* 1.3 76.1 - - - +
15A SER* 1.3 64.5 + - - +
17A VAL* 3.3 1.7 + - - +
18A LYS* 2.9 47.1 + - + +
49A GLN* 3.1 41.1 - - + +
52A LYS* 4.4 7.9 - - + -
53A LEU* 3.7 37.6 - - + +
56A GLU* 3.4 34.5 - - - -
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Residues in contact with SER 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 ALA* 2.8 22.5 + - - +
12A GLU* 3.8 8.4 - - - -
14A PHE* 1.3 85.0 - - - +
16A LEU* 1.3 62.2 + - - +
18A LYS* 3.9 5.4 - - - +
19A LYS* 3.1 26.4 + - - +
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Residues in contact with LEU 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 GLU* 3.0 57.2 + - + +
13A ILE* 3.0 4.2 + - - +
15A SER* 1.3 78.1 - - - +
17A VAL* 1.3 62.9 + - - +
19A LYS* 3.5 9.6 + - + +
20A GLU* 3.1 27.0 + - - +
39A LEU* 3.6 20.0 - - + +
41A ILE* 4.0 22.2 - - + -
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Residues in contact with VAL 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 ILE* 2.9 25.5 + - + +
14A PHE 3.8 3.6 - - - +
16A LEU* 1.3 74.2 - - - +
18A LYS* 1.3 66.0 + - - +
20A GLU* 3.1 4.9 + - - +
21A VAL* 3.0 25.7 + - + +
35A LEU* 4.2 11.0 - - + -
39A LEU* 4.1 8.1 - - + -
46A ILE* 4.0 28.9 - - + +
49A GLN* 4.1 17.9 - - + -
50A LEU* 3.7 34.1 - - + +
53A LEU* 4.5 7.0 - - + -
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PHE* 2.9 29.9 + - + +
15A SER* 3.9 5.8 - - - +
17A VAL* 1.3 76.4 - - - +
19A LYS* 1.3 64.0 + - - +
21A VAL* 3.0 10.9 - - - +
22A LEU* 3.0 48.3 + - + +
53A LEU* 3.9 26.9 - - + +
56A GLU* 4.8 8.5 + - - -
58A THR* 4.2 19.8 + - + -
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Residues in contact with LYS 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 SER 3.1 18.4 + - - +
16A LEU* 3.7 10.5 - - + +
18A LYS* 1.3 76.7 - - - +
20A GLU* 1.3 67.6 + - - +
22A LEU* 3.5 8.3 + - - +
23A SER* 3.3 21.1 + - - -
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Residues in contact with GLU 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 LEU 3.1 15.6 + - - +
17A VAL 3.1 8.4 + - - +
19A LYS* 1.3 81.5 - - - +
21A VAL* 1.3 61.2 + - - +
23A SER* 2.5 27.8 + - - -
24A LEU* 3.7 8.6 + - - +
30A THR* 6.4 0.2 - - - -
35A LEU* 3.9 18.2 - - + +
38A ARG* 4.1 21.9 + - - -
39A LEU* 3.8 26.8 - - + +
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Residues in contact with VAL 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 VAL* 3.0 15.8 + - + +
18A LYS* 3.0 18.6 - - - +
20A GLU* 1.3 76.0 - - - +
22A LEU* 1.3 64.0 + - + +
24A LEU* 3.0 38.2 + - + +
30A THR* 4.9 4.5 - - + -
35A LEU* 4.6 9.4 - - + -
50A LEU* 4.3 24.0 - - + -
53A LEU* 3.6 21.8 - - + -
58A THR* 4.3 13.5 - - + +
59A VAL* 4.5 15.0 - - + -
69A TRP* 5.5 0.4 - - + -
71A LYS* 3.5 13.6 - - - +
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Residues in contact with LEU 22 (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 LYS* 3.0 46.9 + - + +
19A LYS* 3.9 7.0 - - - +
21A VAL* 1.3 78.5 - - - +
23A SER* 1.3 58.9 + - - +
24A LEU 3.2 1.6 + - - -
58A THR* 3.8 22.9 - - + -
71A LYS* 3.6 34.5 + - + +
75A CYS* 4.1 16.6 - - + -
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Residues in contact with SER 23 (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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19A LYS 3.3 11.1 + - - -
20A GLU* 2.5 28.4 + - - -
22A LEU* 1.3 76.1 - - - +
24A LEU* 1.3 64.6 + - - +
25A ASN* 3.9 4.9 + - - +
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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