Contacts of the helix formed by residues 20 - 33 (chain D) in PDB entry 1E3S
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 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLY 3.3 12.0 + - - +
18D GLY 3.3 1.6 + - - -
19D ALA* 1.4 82.8 - - - +
21D GLY* 1.3 70.2 + - - +
22D LEU 3.4 2.1 + - - -
23D GLY 3.4 0.9 + - - -
24D LEU* 3.2 19.6 + - - -
204D PRO* 3.6 15.2 - - - +
301D NAD 2.7 47.4 + - - +
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Residues in contact with GLY 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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20D SER* 1.3 78.0 + - - +
22D LEU* 1.3 63.4 + - - -
24D LEU* 3.4 5.9 + - - +
25D SER* 3.2 23.7 + - - -
203D THR* 4.1 14.1 - - - -
204D PRO* 4.2 7.6 - - - +
230D PRO* 4.3 5.6 - - - +
301D NAD 3.4 13.7 - - - -
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Residues in contact with LEU 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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21D GLY* 1.3 71.0 - - - +
23D GLY* 1.3 60.2 + - - +
25D SER* 3.5 4.6 + - - +
26D THR* 2.8 29.7 + - - -
91D CYS* 4.3 3.6 - - - -
153D THR* 4.7 0.7 - - + -
198D PRO* 4.3 10.3 - - + -
201D PHE* 3.9 24.2 - - + -
203D THR* 3.9 19.1 - - + -
230D PRO* 4.1 12.8 - - + -
233D TYR* 4.0 41.2 - - + -
301D NAD 2.9 60.2 + - + +
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Residues in contact with GLY 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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15D ILE* 3.6 23.0 - - - +
17D GLY 3.7 12.3 + - - -
18D GLY* 4.0 6.3 - - - -
20D SER 3.4 3.4 + - - -
21D GLY 3.4 0.6 - - - -
22D LEU* 1.3 77.6 - - - +
24D LEU* 1.3 62.6 + - - +
26D THR* 3.3 4.6 + - - -
27D ALA* 3.1 19.8 + - - +
91D CYS* 3.8 17.6 - - - +
301D NAD 4.6 0.6 + - - -
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Residues in contact with LEU 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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18D GLY 3.4 23.2 + - - +
19D ALA 3.9 11.2 - - - +
20D SER* 3.2 25.1 + - - +
21D GLY 3.8 2.9 - - - +
23D GLY* 1.3 74.4 - - - +
25D SER* 1.3 57.9 + - - +
27D ALA* 3.2 5.4 + - + +
28D LYS* 2.9 54.3 + - + +
39D LEU* 5.0 2.7 - - + -
50D GLU* 3.8 43.1 - - + +
54D LEU* 4.9 9.2 - - + -
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Residues in contact with SER 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 GLY 3.2 14.9 + - - -
22D LEU 4.0 2.5 - - - -
24D LEU* 1.3 78.8 - - - +
26D THR* 1.3 60.6 + - - +
28D LYS* 3.5 12.3 + - - +
29D ARG* 3.1 18.9 + - - +
230D PRO* 3.2 41.0 + - - +
231D ALA* 3.4 11.8 + - - +
234D ALA* 3.6 7.8 - - - +
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Residues in contact with THR 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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15D ILE* 4.1 11.2 - - + -
22D LEU 2.8 21.8 + - - -
23D GLY* 3.5 8.2 - - - -
24D LEU 3.2 0.2 - - - -
25D SER* 1.3 77.9 - - - +
27D ALA* 1.3 61.7 + - - +
29D ARG* 3.5 1.7 + - - +
30D LEU* 3.1 37.9 + - + +
89D VAL* 4.7 8.3 - - + -
233D TYR* 3.4 23.0 - - - -
234D ALA* 3.7 12.7 - - - +
237D VAL* 3.8 30.7 - - + -
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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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15D ILE* 3.7 14.5 - - + +
23D GLY 3.1 11.6 + - - +
24D LEU* 3.5 9.4 - - + +
26D THR* 1.3 74.2 - - - +
28D LYS* 1.3 65.7 + - - +
30D LEU* 4.2 1.1 - - - +
31D VAL* 2.9 29.3 + - - +
37D ALA* 4.4 8.7 - - + -
39D LEU* 3.5 31.9 - - + -
54D LEU* 4.1 12.3 - - + -
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Residues in contact with LYS 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 LEU* 2.9 49.9 + - + +
25D SER* 3.8 10.5 - - - +
27D ALA* 1.3 75.0 - - - +
29D ARG* 1.3 62.6 + - - +
31D VAL* 4.0 1.0 - - - +
32D GLY* 3.0 21.3 + - - -
50D GLU* 4.5 8.0 + - - -
53D LYS* 5.1 8.5 - - - +
54D LEU* 3.9 31.1 - - + +
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Residues in contact with ARG 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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239B MET* 6.2 0.8 - - - +
242B GLU* 5.5 0.6 + - - -
25D SER 3.1 17.1 + - - +
26D THR 4.0 2.2 - - - +
28D LYS* 1.3 74.7 - - - +
30D LEU* 1.3 64.1 + - + +
32D GLY* 3.3 3.2 + - - -
33D GLN* 3.1 39.7 + - + +
231D ALA* 4.9 6.2 + - - +
234D ALA* 3.7 36.1 - - + -
235D HIS* 3.6 38.1 - - - +
238D GLN* 3.2 29.0 + - - +
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Residues in contact with LEU 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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8D VAL* 4.3 14.4 - - + -
13D ALA* 4.4 21.3 - - + -
15D ILE* 4.6 6.1 - - + -
26D THR* 3.1 34.9 + - + +
27D ALA* 4.2 2.5 - - - +
29D ARG* 1.3 78.0 - - + +
31D VAL* 1.3 65.3 + - + +
33D GLN* 3.0 15.4 + - - +
34D GLY 3.4 0.3 + - - -
35D ALA* 3.0 32.6 + - + +
37D ALA* 5.8 2.9 - - + -
89D VAL* 5.4 2.5 - - + -
234D ALA 5.4 1.3 - - - +
237D VAL* 4.7 2.2 - - + -
238D GLN* 4.3 24.5 - - + +
241D ILE* 4.1 29.8 - - + -
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Residues in contact with VAL 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 2.9 23.3 + - - +
28D LYS 4.1 1.6 - - - +
30D LEU* 1.3 74.2 - - - +
32D GLY* 1.3 62.0 + - - +
34D GLY* 3.1 14.4 + - - -
35D ALA 3.7 18.0 + - - +
37D ALA* 3.8 26.9 - - + -
54D LEU* 3.9 33.4 - - + +
57D ASN* 4.1 23.5 + - + +
58D CYS* 4.4 7.2 - - + -
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Residues in contact with GLY 32 (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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28D LYS 3.0 15.2 + - - -
29D ARG* 3.7 5.6 - - - -
30D LEU 3.3 0.2 - - - -
31D VAL* 1.3 75.0 - - - +
33D GLN* 1.3 64.7 + - - +
34D GLY 3.4 1.4 + - - -
54D LEU* 5.8 0.2 - - - +
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Residues in contact with GLN 33 (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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8D VAL* 3.5 20.0 + - + +
9D LYS* 3.8 21.1 + - - +
29D ARG* 3.1 27.3 + - + +
30D LEU 3.0 6.2 + - - +
32D GLY* 1.3 79.3 + - - +
34D GLY* 1.3 57.9 + - - +
35D ALA 3.6 0.2 - - - -
238D GLN* 3.6 31.3 + - - +
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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