Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 3Q29
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 GLY 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE* 5.0 1.8 - - - -
16A LYS* 1.3 72.4 - - - +
18A TYR* 1.3 58.3 + - - -
20A GLY* 3.2 3.3 + - - -
21A LEU* 2.9 28.1 + - - +
294A VAL* 3.8 19.4 - - - +
297A ASP* 3.1 23.1 - - - -
298A LYS* 3.6 19.2 + - - +
300A LEU* 6.2 0.2 - - - +
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Residues in contact with TYR 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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12A ILE* 3.6 24.9 - - + -
13A ASN 4.1 1.3 - - - -
14A GLY* 3.5 26.9 - - - -
16A LYS 2.9 19.0 + - - -
17A GLY* 1.3 73.2 - - - +
19A ASN* 1.3 82.3 + - - +
21A LEU* 3.6 8.5 - - - +
22A ALA* 2.9 27.4 + - - +
38A VAL* 3.7 15.2 - - + +
40A HIS* 3.4 49.6 + + + -
297A ASP* 3.5 0.4 + - - -
298A LYS* 6.2 2.2 - - - -
395A SO4 2.9 43.2 + - - -
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Residues in contact with ASN 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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18A TYR* 1.3 90.3 - - - +
20A GLY* 1.3 65.1 + - - +
22A ALA* 3.1 11.1 + - - +
23A GLU* 3.1 28.3 + - - +
297A ASP* 3.1 16.1 + - - +
395A SO4 3.0 40.1 + - - -
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Residues in contact with GLY 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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17A GLY 3.2 3.6 + - - -
19A ASN* 1.3 75.7 - - - +
21A LEU* 1.3 60.6 + - - +
23A GLU* 3.1 23.5 + - - +
24A VAL* 3.3 13.7 + - - +
293A ALA* 3.3 28.3 - - - +
294A VAL* 4.0 4.7 - - - -
297A ASP* 2.9 18.4 + - - -
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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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10A ILE* 3.9 28.7 - - + -
12A ILE* 4.2 17.0 - - + -
17A GLY 2.9 14.6 + - - +
18A TYR* 3.6 9.0 - - - +
20A GLY* 1.3 74.3 - - - +
22A ALA* 1.3 64.7 + - - +
24A VAL* 2.9 18.2 + - + +
25A GLY* 3.1 9.2 + - - -
38A VAL* 4.2 19.1 - - + +
62A PHE* 3.9 13.2 - - + -
280A PHE* 4.0 21.2 - - + -
285A LEU* 3.9 33.0 - - + -
294A VAL* 3.8 10.7 - - + +
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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 TYR 2.9 15.5 + - - +
19A ASN* 3.1 17.2 + - - +
21A LEU* 1.3 76.3 - - - +
23A GLU* 1.3 61.7 + - + +
25A GLY* 3.0 4.7 + - - -
26A LYS* 3.0 19.8 + - - +
36A VAL* 5.6 2.6 - - - +
38A VAL* 3.8 20.4 - - + +
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Residues in contact with GLU 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 ASN* 3.1 16.1 + - - +
20A GLY* 3.1 13.7 + - - +
22A ALA* 1.3 71.7 - - + +
24A VAL* 1.3 66.5 + - - +
26A LYS* 2.9 20.8 + - - +
27A LYS* 3.1 12.1 + - - +
293A ALA* 4.1 19.4 - - + +
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Residues in contact with VAL 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 GLY 3.6 13.2 - - - +
21A LEU* 2.9 14.6 + - + +
23A GLU* 1.3 75.9 - - - +
25A GLY* 1.3 60.6 + - - +
27A LYS* 3.4 8.5 + - + +
28A PHE* 3.2 19.6 + - - +
280A PHE* 3.9 12.8 - - + -
284A TYR* 3.8 31.1 - - + +
285A LEU* 3.8 16.6 - - + +
290A GLY* 3.8 28.3 - - - +
293A ALA* 4.0 8.7 - - + +
294A VAL* 4.4 4.5 - - + -
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Residues in contact with GLY 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 6.8 + - - -
22A ALA 3.0 8.7 + - - -
24A VAL* 1.3 77.1 - - - +
26A LYS* 1.3 57.5 + - - +
28A PHE* 3.2 7.6 + - - +
29A GLU* 2.9 30.1 + - - +
36A VAL* 3.8 34.8 - - - +
280A PHE* 4.0 5.5 - - - -
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Residues in contact with LYS 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 3.0 9.6 + - - +
23A GLU* 2.9 15.1 + - - +
25A GLY* 1.3 74.0 - - - +
27A LYS* 1.3 56.9 + - - +
28A PHE 3.1 4.7 - - - -
29A GLU* 3.5 9.1 + - - +
30A LYS* 3.1 27.7 + - - +
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Residues in contact with LYS 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 GLU 3.1 9.6 + - - +
24A VAL* 3.9 9.6 - - + +
25A GLY 3.4 0.2 - - - -
26A LYS* 1.3 74.1 - - - +
28A PHE* 1.3 58.5 + - - +
30A LYS* 4.0 8.1 - - - -
31A ASP* 3.2 20.5 - - - +
284A TYR* 3.1 21.7 - - + -
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Residues in contact with PHE 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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8A LEU* 4.0 15.3 - - + -
24A VAL 3.2 12.4 + - - +
25A GLY* 3.4 11.9 - - - +
26A LYS 3.1 0.2 - - - -
27A LYS* 1.3 77.2 - - - +
29A GLU* 1.3 58.9 + - - +
30A LYS 3.1 1.6 - - - -
31A ASP* 3.1 1.9 + - - -
32A THR* 3.0 56.3 + - + +
34A ILE* 3.8 16.8 - - + -
36A VAL* 3.6 18.6 - - + -
276A LEU* 3.9 24.2 - - + -
279A GLU* 3.7 15.7 - - - -
280A PHE* 3.8 20.0 - + + -
284A TYR* 3.3 44.4 - + + -
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Residues in contact with GLU 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 GLY 2.9 16.2 + - - +
26A LYS* 3.9 9.0 - - - +
28A PHE* 1.3 76.0 - - - +
30A LYS* 1.3 57.0 + - - +
31A ASP 3.2 0.4 - - - -
33A GLY* 3.2 25.9 + - - +
34A ILE 3.3 21.5 + - - +
35A LYS* 3.6 30.2 - - - +
36A VAL 3.9 6.6 + - - +
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Residues in contact with LYS 30 (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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26A LYS 3.1 17.7 + - - +
27A LYS* 4.4 5.2 - - - -
28A PHE 3.1 1.0 - - - -
29A GLU* 1.3 77.3 - - - +
31A ASP* 1.3 69.4 + - - +
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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