Contacts of the helix formed by residues 14 - 32 (chain A) in PDB entry 1Q24
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 1.3 66.4 + - - +
16A LYS* 3.3 14.6 - - - -
17A GLU* 3.6 24.7 + - - +
18A PHE* 3.2 21.7 + - - +
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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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14A SER* 1.3 73.2 - - - +
16A LYS* 1.3 76.7 + - + +
18A PHE* 3.4 7.0 + - + +
19A LEU* 3.1 35.1 + - + +
155A GLU* 3.6 29.6 - - - +
292A LYS* 4.5 13.0 - - - +
303A ILE* 5.9 8.5 - - + -
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Residues in contact with LYS 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 SER* 3.3 8.5 - - - -
15A VAL* 1.3 85.6 - - + +
17A GLU* 1.4 60.3 + - - +
19A LEU* 3.5 29.1 - - - +
20A ALA* 3.4 21.3 + - - +
155A GLU* 3.6 17.8 + - - +
288A VAL* 5.5 1.6 - - - +
289A ASN* 6.0 2.0 - - - +
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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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14A SER* 3.4 26.7 + - - +
15A VAL 3.3 0.6 - - - -
16A LYS* 1.4 75.6 - - - +
18A PHE* 1.3 69.7 + - - +
20A ALA* 3.4 7.3 + - - +
21A LYS* 3.3 30.4 + - - +
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Residues in contact with PHE 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 SER 3.2 13.7 + - - +
15A VAL* 3.4 11.2 + - + +
17A GLU* 1.3 84.4 + - - +
19A LEU* 1.4 74.8 + - + +
21A LYS* 3.5 11.6 + - + +
22A ALA* 3.0 37.9 + - + +
99A ASN 5.6 3.1 - - - -
100A PHE* 4.0 25.8 - + - -
156A TYR* 5.0 1.3 - + - -
306A TYR* 3.0 36.1 - + - -
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Residues in contact with LEU 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* 3.1 29.6 + - + +
16A LYS* 3.5 37.2 - - - +
18A PHE* 1.4 93.6 - - + +
20A ALA* 1.3 61.3 + - - +
22A ALA* 3.7 4.9 - - - +
23A LYS* 3.0 29.9 + - - +
100A PHE* 5.9 0.7 - - + -
155A GLU* 4.3 14.4 - - + +
156A TYR* 4.9 15.5 - - + -
159A SER* 3.7 34.3 + - - +
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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 LYS 3.4 12.0 + - - +
17A GLU* 3.4 11.8 + - - +
18A PHE 3.3 0.4 - - - -
19A LEU* 1.3 76.0 - - - +
21A LYS* 1.3 64.9 + - - +
23A LYS* 3.3 15.1 + - - +
24A GLU* 3.4 19.3 + - - +
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Residues in contact with LYS 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* 3.3 21.8 + - - +
18A PHE* 3.7 14.8 - - + +
20A ALA* 1.3 77.5 - - - +
22A ALA* 1.3 62.7 + - - +
24A GLU* 3.3 14.5 + - - +
25A ASP* 3.2 20.9 + - + +
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Residues in contact with ALA 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 PHE* 3.0 30.5 + - + +
19A LEU* 3.7 9.4 - - - +
21A LYS* 1.3 75.3 - - - +
23A LYS* 1.3 59.7 + - - +
25A ASP* 3.6 8.3 + - - +
26A PHE* 3.1 26.5 + - - +
99A ASN 5.8 0.7 - - - +
156A TYR* 4.0 28.2 + - + -
160A LEU* 4.5 3.3 - - + +
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Residues in contact with LYS 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 LEU 3.0 17.5 + - - +
20A ALA* 3.7 8.5 - - - +
21A LYS 3.3 0.4 - - - -
22A ALA* 1.3 73.5 - - - +
24A GLU* 1.3 62.6 + - + +
26A PHE* 3.2 4.5 + - + +
27A LEU* 2.9 48.8 + - + +
159A SER* 3.0 25.3 + - - +
160A LEU* 4.0 20.8 - - + +
161A ASP* 2.9 30.7 + - - -
190A ARG* 4.5 5.8 - - - +
192A LYS* 5.4 2.4 - - - +
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Residues in contact with GLU 24 (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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20A ALA 3.6 13.1 - - - +
21A LYS* 3.3 13.9 + - - +
23A LYS* 1.3 74.5 - - + +
25A ASP* 1.3 64.9 + - - +
27A LEU* 3.3 11.2 + - + +
28A LYS* 3.2 41.1 + - - +
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Residues in contact with ASP 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 LYS* 3.2 11.0 + - + +
22A ALA* 3.8 11.2 - - - +
23A LYS 3.3 0.2 - - - -
24A GLU* 1.3 79.2 - - - +
26A PHE* 1.3 61.5 + - - +
28A LYS* 3.6 5.9 + - - +
29A LYS* 3.3 51.0 + - - +
97A ALA 4.8 2.3 - - - +
99A ASN* 4.1 20.4 - - - +
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Residues in contact with PHE 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 ALA 3.1 19.2 + - - +
23A LYS* 3.2 6.0 + - + +
25A ASP* 1.3 75.0 + - - +
27A LEU* 1.3 64.2 + - + +
29A LYS 3.5 0.9 + - - -
30A TRP* 2.7 62.6 + + + +
94A ILE* 4.4 3.6 - - - -
97A ALA* 3.4 46.5 - - + +
98A VAL* 4.2 5.6 - - + -
156A TYR* 4.9 2.0 - - - +
160A LEU* 3.7 37.0 - - + -
162A LEU* 4.0 24.2 - - + -
190A ARG* 3.7 30.5 - - - -
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Residues in contact with LEU 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 LYS* 2.9 41.8 + - + +
24A GLU* 3.3 11.4 + - + +
26A PHE* 1.3 84.8 - - + +
28A LYS* 1.3 63.5 + - + +
30A TRP* 3.4 8.2 - - + +
31A GLU* 2.9 44.0 + - + +
190A ARG* 3.6 36.6 - - - +
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Residues in contact with LYS 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 GLU* 3.2 28.5 + - - +
25A ASP* 4.0 6.7 - - - +
26A PHE 3.4 0.2 - - - -
27A LEU* 1.3 80.3 - - - +
29A LYS* 1.3 62.2 + - + +
31A GLU* 5.1 1.8 - - + -
32A ASN* 2.9 35.7 + - - +
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Residues in contact with LYS 29 (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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25A ASP* 3.3 40.1 + - - +
26A PHE 3.9 3.4 - - - +
27A LEU 3.2 0.4 - - - -
28A LYS* 1.3 78.7 - - + +
30A TRP* 1.3 64.0 + - - +
32A ASN 4.3 5.6 - - - +
33A PRO* 3.3 14.6 - - - +
96A GLN* 3.0 43.8 + - - +
97A ALA* 3.7 23.3 - - - +
98A VAL 5.5 1.9 + - - +
99A ASN* 5.3 9.6 - - - +
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Residues in contact with TRP 30 (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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26A PHE* 2.7 46.2 + + + +
27A LEU* 3.1 9.8 + - + +
29A LYS* 1.3 75.8 - - - +
31A GLU* 1.3 83.3 + - - +
33A PRO* 3.7 4.3 - - - +
90A ASN* 5.4 8.3 - - - -
93A ARG* 3.0 87.8 + - + +
94A ILE* 3.9 22.7 - - + -
96A GLN* 4.5 1.1 - - - +
97A ALA* 4.0 3.8 - - - +
190A ARG* 3.1 50.8 - - + +
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Residues in contact with GLU 31 (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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27A LEU* 2.9 32.9 + - + +
28A LYS* 5.1 2.2 - - + -
30A TRP* 1.3 94.6 + - - +
32A ASN* 1.3 77.3 + - - +
33A PRO* 3.4 8.1 - - - +
93A ARG* 4.3 8.1 + - - +
190A ARG* 5.0 1.2 + - - -
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Residues in contact with ASN 32 (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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28A LYS* 2.9 30.3 + - - +
29A LYS* 3.4 9.2 - - - +
31A GLU* 1.3 92.6 + - - +
33A PRO* 1.3 65.3 - - - +
34A ALA* 3.9 0.9 + - - -
96A GLN* 4.8 0.2 - - - +
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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
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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