Contacts of the helix formed by residues 17 - 31 (chain D) in PDB entry 3ERE
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 ASN 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A T 4.4 2.5 - - - -
15D ALA 3.4 4.6 + - - +
16D ALA* 1.3 75.4 - - - +
18D ARG* 1.3 64.0 + - - +
19D ALA* 2.8 19.5 + - - +
20D GLY* 2.6 33.0 + - - +
21D ARG* 2.9 23.4 + - - +
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A T 3.8 31.3 + - - +
2A T 3.6 23.1 + - - +
17D ASN* 1.3 74.5 - - - +
19D ALA* 1.3 66.5 + - - +
21D ARG* 3.1 29.6 + - - +
22D GLN* 2.8 34.7 + - - +
59D ASP* 3.7 9.0 - - - +
62D GLU* 3.2 34.6 + - - -
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Residues in contact with ALA 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASN* 2.8 16.1 + - - +
18D ARG* 1.3 76.2 - - - +
20D GLY* 1.3 60.4 + - - +
22D GLN* 3.8 10.6 - - - +
23D ALA* 3.0 23.3 + - - +
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Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ALA* 4.7 7.6 - - - -
17D ASN* 2.6 24.0 + - - -
19D ALA* 1.3 69.5 - - - +
21D ARG* 1.3 66.9 + - - +
23D ALA* 3.3 9.9 + - - +
24D ARG* 3.3 22.3 + - - +
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Residues in contact with ARG 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A T 3.0 41.0 + - - -
16D ALA* 4.2 9.0 + - + +
17D ASN 2.9 14.5 + - - +
18D ARG* 3.3 16.9 - - - +
20D GLY* 1.3 74.8 - - - +
22D GLN* 1.3 56.4 + - - +
24D ARG* 2.8 25.3 + - - +
25D ILE* 2.9 16.8 + - + +
44D LEU* 4.2 13.5 - - + -
49D ILE* 4.0 27.8 - - + +
51D VAL* 3.6 36.9 - - - +
55D THR* 3.3 14.2 - - - +
59D ASP* 2.7 39.3 + - - -
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ARG* 2.8 30.1 + - - +
19D ALA* 3.8 8.8 - - - +
21D ARG* 1.3 72.9 - - - +
23D ALA* 1.3 62.6 + - - +
25D ILE* 3.2 11.5 + - - +
26D VAL* 3.1 28.2 + - - +
59D ASP* 2.9 35.9 + - + +
62D GLU* 2.9 47.4 + - - +
63D LEU* 3.8 24.9 - - + +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA 3.0 14.1 + - - +
20D GLY* 3.4 13.5 - - - +
22D GLN* 1.3 78.6 - - - +
24D ARG* 1.3 66.4 + - + +
26D VAL* 3.5 6.9 + - - +
27D ALA* 3.2 19.9 + - - +
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Residues in contact with ARG 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLY 3.3 12.5 + - - +
21D ARG 2.8 8.1 + - - +
23D ALA* 1.3 78.2 + - - +
25D ILE* 1.3 65.3 - - - +
27D ALA* 3.2 28.6 + - - +
28D ILE* 2.9 32.8 + - - +
44D LEU* 4.0 12.6 - - + -
47D GLU* 2.7 45.3 + - - +
49D ILE* 3.8 16.2 - - + -
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ARG* 2.9 19.6 + - + +
22D GLN* 3.2 14.5 + - - +
24D ARG* 1.3 75.0 - - - +
26D VAL* 1.3 59.3 + - - +
28D ILE* 2.9 8.8 + - - +
29D LEU* 2.8 45.3 + - + +
40D LEU* 3.9 20.9 - - + -
44D LEU* 4.1 18.6 - - + -
56D LEU* 3.8 17.9 - - + -
59D ASP* 3.6 38.8 - - + +
60D LEU* 4.1 4.0 - - + -
63D LEU* 4.0 12.8 - - + -
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Residues in contact with VAL 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLN 3.1 12.0 + - - +
23D ALA* 3.7 9.4 - - - +
25D ILE* 1.3 76.1 - - - +
27D ALA* 1.3 63.2 + - - +
29D LEU* 3.5 1.4 + - - +
30D SER* 3.1 24.2 + - - -
63D LEU* 4.0 26.5 - - + -
80D VAL* 4.0 26.7 - - + +
82D GLU* 3.7 26.7 - - - +
86D PRO* 6.4 1.1 - - + -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA 3.2 10.1 + - - +
24D ARG* 3.2 36.3 + - - +
25D ILE 3.2 0.6 - - - -
26D VAL* 1.3 80.6 - - - +
28D ILE* 1.3 60.3 + - - +
30D SER* 2.8 23.1 + - - -
31D SER* 4.1 3.6 + - - -
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ARG* 2.9 22.9 + - - +
25D ILE* 2.9 4.7 + - - +
27D ALA* 1.3 76.0 - - - +
29D LEU* 1.3 61.5 + - - +
30D SER 3.2 2.7 + - - -
31D SER* 3.6 2.4 + - - -
32D ALA* 3.0 30.6 + - + +
34D VAL* 4.5 3.6 - - + -
40D LEU* 4.2 10.3 - - + -
43D LEU* 3.7 46.0 - - + +
44D LEU* 3.5 30.5 - - + -
47D GLU* 3.8 27.8 - - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 2.8 35.2 + - + +
26D VAL 4.1 3.4 - - - +
28D ILE* 1.3 71.2 - - - +
30D SER* 1.3 63.0 + - - +
31D SER 3.3 0.4 + - - -
32D ALA 3.6 6.5 - - - +
34D VAL* 3.4 36.6 - - + -
40D LEU* 4.3 14.1 - - + -
60D LEU* 4.0 14.1 - - + -
65D ALA* 4.3 1.8 - - + -
78D TYR* 4.0 33.2 - - + +
79D VAL* 5.3 2.3 - - - +
80D VAL* 3.2 37.5 - - + +
96D ARG* 3.5 15.4 + - - -
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Residues in contact with SER 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D VAL* 3.1 19.6 + - - -
27D ALA* 2.8 19.2 + - - -
28D ILE 3.2 0.2 - - - -
29D LEU* 1.3 77.7 - - - +
31D SER* 1.3 63.1 + - - +
80D VAL* 5.5 4.7 - - - +
82D GLU* 6.3 3.1 - - - -
86D PRO 5.5 6.9 + - - -
96D ARG* 3.2 23.4 + - - +
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Residues in contact with SER 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA 4.1 2.9 + - - -
28D ILE 3.6 3.4 + - - -
30D SER* 1.3 85.7 + - - +
32D ALA* 1.3 60.0 + - - +
96D ARG* 3.4 11.6 - - - +
99D ARG* 3.3 25.6 + - - +
172D SO4 4.3 10.0 + - - -
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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