Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 1KYZ
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 SER 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A HIS* 3.5 21.6 + - - -
14A ILE* 1.3 77.7 - - - +
16A ASP* 1.3 65.3 + - - +
17A GLU* 3.5 19.7 - - - +
18A GLU* 3.2 27.3 + - - +
19A ALA* 3.0 22.1 + - - +
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Residues in contact with ASP 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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14A ILE 3.9 1.9 + - - +
15A SER* 1.3 72.7 - - - +
17A GLU* 1.3 74.5 + - - +
19A ALA* 3.3 3.1 + - - -
20A ASN* 2.8 24.9 + - - +
113E LYS* 2.6 35.6 + - - +
114E TYR* 3.5 21.8 + - - +
190E LYS* 4.8 5.2 + - - +
354E PHE* 3.9 10.3 - - + -
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Residues in contact with GLU 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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15A SER* 3.5 19.5 - - - +
16A ASP* 1.3 90.6 + - - +
18A GLU* 1.3 55.6 + - - +
20A ASN* 3.3 1.6 + - - +
21A LEU* 2.9 41.8 + - + +
190E LYS* 3.4 22.2 + - - -
354E PHE* 3.8 16.6 + - + -
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Residues in contact with GLU 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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13A HIS 4.5 2.4 - - - +
14A ILE* 3.5 33.3 - - + +
15A SER* 3.2 19.2 + - - +
17A GLU* 1.3 78.6 - - - +
19A ALA* 1.3 66.9 + - - +
21A LEU* 3.2 9.1 + - - +
22A PHE* 2.9 22.1 + - + +
5E GLY* 5.0 5.6 - - - -
6E GLU* 3.5 14.7 + - - +
7E THR* 3.3 36.0 + - - -
111E VAL* 4.7 4.7 - - + -
308E LEU* 4.1 11.6 - - + +
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Residues in contact with ALA 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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14A ILE* 4.5 4.7 - - + +
15A SER 3.0 16.1 + - - +
16A ASP* 3.7 4.9 - - - +
18A GLU* 1.3 76.1 - - - +
20A ASN* 1.3 58.2 + - - +
22A PHE* 3.3 3.3 + - - +
23A ALA* 2.9 28.1 + - - +
110E THR 4.7 0.2 - - - +
111E VAL* 3.7 36.2 - - - +
113E LYS* 4.2 13.5 - - + -
114E TYR* 3.9 16.8 - - + +
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Residues in contact with ASN 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 ASP 2.8 17.7 + - - +
17A GLU 3.5 4.0 - - - +
19A ALA* 1.3 75.8 - - - +
21A LEU* 1.3 63.2 + - - +
23A ALA* 3.2 3.6 + - - +
24A MET* 2.9 42.3 + - - +
114E TYR* 3.6 29.5 - - + -
124E ILE* 4.2 8.1 - - - +
183E HIS* 5.9 1.8 + - - -
186E ILE* 4.1 5.2 - - - +
354E PHE* 3.6 54.1 + - + +
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Residues in contact with LEU 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 GLU* 2.9 27.1 + - + +
18A GLU* 3.8 5.6 - - - +
20A ASN* 1.3 83.1 - - - +
22A PHE* 1.3 57.1 + - - +
24A MET* 3.3 10.1 + - + +
25A GLN* 3.1 26.9 + - - +
5E GLY* 5.4 3.1 - - - +
308E LEU* 3.7 28.6 - - + +
309E ALA* 3.8 30.5 - - + +
312E GLY* 5.6 1.4 - - - -
354E PHE* 4.9 1.8 - - - -
355E ASN* 3.7 40.4 - - + +
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Residues in contact with PHE 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 GLU 2.9 17.7 + - - +
19A ALA 3.5 4.7 - - - +
20A ASN 3.2 0.2 - - - -
21A LEU* 1.3 75.8 - - - +
23A ALA* 1.3 64.5 + - - +
25A GLN* 3.3 10.9 + - - +
26A LEU* 3.1 51.7 + - + +
7E THR* 3.6 35.9 - - + +
8E GLN 4.2 15.3 - - - -
9E ILE* 4.2 7.4 - - + -
87E TYR* 3.6 22.7 - - + -
88E ILE 4.4 0.2 - - - -
89E ILE* 4.1 11.9 - - + -
111E VAL* 3.7 44.9 - - + -
112E ALA* 5.4 0.7 - - - -
115E LEU* 5.4 2.0 - - + -
308E LEU* 3.8 5.1 - - + +
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Residues in contact with ALA 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 ALA 2.9 17.2 + - - +
20A ASN 3.6 4.7 - - - +
22A PHE* 1.3 77.8 - - + +
24A MET* 1.3 57.3 + - - +
26A LEU* 3.4 5.7 + - - +
27A ALA* 2.8 28.1 + - - +
111E VAL 5.8 0.9 - - - +
114E TYR* 3.7 24.7 - - + +
115E LEU* 4.0 24.0 - - + +
124E ILE* 3.7 17.8 - - + +
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Residues in contact with MET 24 (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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20A ASN* 2.9 34.1 + - - +
21A LEU* 3.7 13.2 - - + +
22A PHE 3.2 0.4 - - - -
23A ALA* 1.3 76.9 - - - +
25A GLN* 1.3 62.8 + - - +
27A ALA* 3.4 11.4 + - + +
28A SER* 3.5 15.8 + - - -
124E ILE* 3.7 20.2 - - + -
127E LEU* 3.5 28.5 - - + -
183E HIS* 3.6 30.7 - - + +
312E GLY* 5.5 12.2 - - - +
315E HIS* 4.5 0.9 + - - +
316E ILE* 5.1 15.5 - - + -
354E PHE 5.9 1.1 - - - +
355E ASN* 6.4 0.9 - - + -
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Residues in contact with GLN 25 (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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21A LEU 3.1 14.5 + - - +
22A PHE* 3.3 10.0 + - - +
24A MET* 1.3 76.5 - - - +
26A LEU* 1.3 58.7 + - - +
28A SER 3.4 3.1 + - - -
29A ALA* 2.9 29.6 + - - +
87A TYR* 2.9 37.1 + - - +
8E GLN* 3.6 3.5 - - - +
9E ILE* 3.1 50.6 + - + +
308E LEU* 3.5 22.2 - - + +
311E LYS* 3.8 20.4 - - + +
312E GLY* 6.0 4.0 - - - +
315E HIS* 3.7 10.1 - - + -
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Residues in contact with LEU 26 (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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22A PHE* 3.1 54.1 + - + +
23A ALA* 3.7 5.8 - - - +
25A GLN* 1.3 76.4 - - - +
27A ALA* 1.3 64.5 + - - +
28A SER 3.2 0.9 + - - -
29A ALA* 3.4 14.8 + - + +
9E ILE* 3.7 10.8 - - + -
32E LEU* 3.6 36.6 - - + -
33E PRO* 4.6 1.3 - - + +
36E LEU* 3.8 16.0 - - + +
89E ILE* 3.9 23.3 - - + -
115E LEU* 4.0 18.2 - - + -
128E ASN* 3.2 16.9 + - - -
132E GLN* 4.3 0.2 + - - -
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Residues in contact with ALA 27 (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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23A ALA 2.8 17.6 + - - +
24A MET* 3.6 10.8 - - + +
25A GLN 3.2 0.6 - - - -
26A LEU* 1.3 77.6 - - - +
28A SER* 1.3 58.6 + - - +
115E LEU* 6.1 0.2 - - - +
124E ILE* 4.1 9.2 - - + +
127E LEU* 3.6 32.8 - - + -
128E ASN* 3.4 15.3 - - + +
131E ASN* 3.4 12.3 - - - +
132E GLN* 2.8 22.0 + - - -
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Residues in contact with SER 28 (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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24A MET 3.5 7.7 + - - -
25A GLN 3.4 3.8 + - - -
26A LEU 3.2 0.2 - - - -
27A ALA* 1.3 80.1 - - - +
29A ALA* 1.3 58.4 + - - +
30A SER* 3.1 8.0 + - - -
31A VAL* 3.1 18.7 + - - +
131E ASN* 3.8 11.9 - - - -
132E GLN* 3.7 5.6 - - - -
315E HIS* 2.7 38.1 + - - +
316E ILE* 5.0 4.2 - - - +
319E ILE* 3.7 27.1 - - - +
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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