Contacts of the helix formed by residues 19 - 32 (chain A) in PDB entry 3DAN
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 PHE 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.6 1.8 - - - +
18A PRO* 1.3 77.3 - - + +
20A PHE* 1.3 66.1 + - + +
22A PRO* 3.1 18.5 - - - +
23A ILE* 3.5 37.1 - - + +
60A PRO* 3.4 30.8 - - + +
61A PHE* 3.8 35.4 - + - -
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Residues in contact with PHE 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 ILE* 3.9 37.8 - - + +
19A PHE* 1.3 82.0 - - - +
21A GLN* 1.3 82.6 + - - +
23A ILE* 3.2 9.2 + - + +
24A LYS* 3.1 44.3 + - + +
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Residues in contact with GLN 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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14A SER 5.6 0.7 - - - +
15A TYR 3.3 29.6 - - - +
16A GLY* 4.2 6.5 - - - -
17A ILE 2.9 24.7 + - - +
20A PHE* 1.3 90.0 - - - +
22A PRO* 1.3 58.3 - - - +
24A LYS* 3.1 22.4 + - - +
25A ASP* 2.8 68.9 + - - +
55A ASN* 3.7 0.9 - - - +
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Residues in contact with PRO 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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15A TYR 4.7 1.1 - - - +
17A ILE 3.6 0.4 - - - +
18A PRO 2.7 30.3 - - - +
19A PHE* 3.1 16.2 - - - +
21A GLN* 1.3 92.9 - - + +
23A ILE* 1.3 55.6 + - - +
25A ASP* 3.9 1.4 - - + +
26A ARG* 3.1 28.8 + - - +
55A ASN* 4.1 20.5 - - + +
56A MET 5.5 2.9 - - - +
57A PRO* 6.0 0.2 - - - +
59A GLY* 4.6 3.6 - - - -
60A PRO* 4.0 17.3 - - + -
66A PRO* 3.8 31.4 - - + -
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Residues in contact with ILE 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 PHE* 3.5 41.3 - - + +
20A PHE* 3.2 9.1 + - + +
21A GLN 3.1 0.2 - - - -
22A PRO* 1.3 74.7 - - - +
24A LYS* 1.3 66.5 - - - +
26A ARG* 3.3 27.8 + - - +
27A LEU* 3.1 41.0 + - + +
60A PRO* 3.4 25.4 - - + -
220A GLU* 5.5 0.2 - - - +
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Residues in contact with LYS 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 PHE* 3.1 37.5 + - + +
21A GLN* 3.6 28.0 + - - +
23A ILE* 1.3 78.4 - - - +
25A ASP* 1.3 61.2 + - - +
27A LEU* 3.2 16.9 + - + +
28A GLU* 3.2 19.3 + - + +
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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
----------------------------------------------------------
14A SER 5.7 0.2 - - - +
21A GLN* 2.8 40.0 + - - +
22A PRO 3.9 4.7 - - - +
23A ILE 3.2 0.2 - - - -
24A LYS* 1.3 76.0 - - - +
26A ARG* 1.3 59.9 + - - +
28A GLU* 3.1 11.4 + - - +
29A TYR* 2.9 24.5 + - - +
39A TYR* 3.4 28.9 + - + +
43A ARG* 3.7 15.0 + - - -
55A ASN* 2.9 39.0 + - + +
56A MET 6.5 0.2 - - - -
57A PRO* 6.4 0.2 - - - -
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Residues in contact with ARG 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 PRO 3.1 16.6 + - - +
23A ILE* 3.3 31.1 + - - +
25A ASP* 1.3 76.0 - - - +
27A LEU* 1.3 60.3 + - + +
29A TYR* 3.5 7.8 - - - +
30A PHE* 3.0 40.5 + - + +
56A MET 5.7 0.6 - - - -
57A PRO* 4.3 22.9 - - + -
58A PRO* 2.8 36.1 + - - -
59A GLY 4.2 1.4 - - - -
60A PRO* 4.0 20.8 - - - +
220A GLU* 2.7 33.0 + - - +
224A HIS* 3.1 20.3 + - - +
225A THR* 3.1 29.7 + - - +
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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 ILE* 3.1 27.3 + - + +
24A LYS* 3.4 16.2 - - + +
25A ASP 3.1 0.4 - - - -
26A ARG* 1.3 79.3 - - - +
28A GLU* 1.3 56.9 + - - +
31A TYR* 2.8 48.5 + - + +
32A GLY 3.6 0.7 + - - -
216A TRP* 5.0 11.4 - - + -
220A GLU* 3.7 38.1 - - + +
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Residues in contact with GLU 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 LYS* 3.2 11.2 + - + +
25A ASP* 3.1 13.6 + - - +
27A LEU* 1.3 77.2 - - - +
29A TYR* 1.3 59.3 + - - +
32A GLY* 2.9 35.1 + - - +
35A GLY 4.8 4.2 - - - +
38A GLU* 5.1 0.3 - - - +
39A TYR* 3.7 11.5 - - + +
42A SER* 3.9 9.4 + - - -
43A ARG* 3.0 41.8 + - - -
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Residues in contact with TYR 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 2.9 17.1 + - - +
26A ARG* 3.5 9.0 - - - +
27A LEU 3.3 0.2 - - - -
28A GLU* 1.3 78.9 - - - +
30A PHE* 1.3 88.7 + + - +
35A GLY* 3.8 3.3 - - - -
36A ARG* 3.5 71.8 + - + +
39A TYR* 3.8 34.3 - + + -
40A PHE* 4.2 18.3 - + - -
56A MET* 4.3 8.0 - - + +
57A PRO* 3.6 35.4 - - + -
209A THR* 5.1 2.8 + - - -
375A TYR* 5.8 0.7 - - - -
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Residues in contact with PHE 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 ARG* 3.0 30.3 + - + +
29A TYR* 1.3 104.0 - + - +
31A TYR* 1.3 83.6 + - + +
32A GLY 3.8 1.1 - - - +
35A GLY* 5.7 2.7 - - - -
36A ARG* 4.2 3.6 - - - -
57A PRO* 4.0 20.6 - - + -
58A PRO* 5.7 0.2 - - + -
208A PRO 4.4 1.1 - - - -
209A THR* 3.7 33.2 - - - -
210A LEU 4.1 7.4 - - - -
211A ASP* 3.4 38.3 - - + +
219A GLN* 4.7 0.2 - - - +
220A GLU* 4.1 3.6 - - - -
224A HIS* 3.4 38.8 - + - -
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Residues in contact with TYR 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* 2.8 32.6 + - + +
30A PHE* 1.3 90.9 - - + +
32A GLY* 1.3 67.8 + - - +
33A THR* 3.8 1.6 + - - +
211A ASP* 4.9 1.1 - - - -
214A LEU 3.9 6.5 - - - -
215A PRO* 5.6 0.2 - - + -
216A TRP* 3.5 46.4 - + + -
219A GLN* 3.1 44.0 + - - +
220A GLU* 2.6 35.6 + - - +
224A HIS* 3.8 0.2 + - - -
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Residues in contact with GLY 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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27A LEU 3.6 2.4 + - - -
28A GLU* 2.9 29.8 + - - -
30A PHE 5.2 0.2 - - - -
31A TYR* 1.3 82.3 - - - +
33A THR* 1.3 68.0 + - - -
34A GLY 3.3 0.3 + - - -
35A GLY* 3.1 17.7 + - - -
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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