Contacts of the helix formed by residues 20 - 33 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY 3.3 11.1 + - - +
18C GLY 3.3 1.4 + - - -
19C ALA* 1.3 81.2 - - - +
21C GLY* 1.3 74.8 + - - +
22C LEU 3.4 2.4 + - - -
23C GLY 3.4 0.3 + - - -
24C LEU* 3.1 21.0 + - - -
204C PRO* 3.6 15.2 - - - +
301C NAD 2.9 42.5 + - - +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 1.3 76.5 + - - +
22C LEU* 1.4 63.3 + - - -
24C LEU* 3.8 5.2 - - - +
25C SER* 3.1 25.3 + - - -
203C THR* 4.1 14.6 - - - -
204C PRO* 4.3 5.3 - - - +
230C PRO* 4.2 5.9 - - - +
301C NAD 3.5 14.1 - - - -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 1.4 68.7 - - - -
23C GLY* 1.3 64.7 + - - +
25C SER* 3.6 4.7 + - - -
26C THR* 2.8 30.7 + - - -
91C CYS* 4.3 3.4 - - - -
198C PRO* 4.3 10.3 - - + -
201C PHE* 3.9 24.7 - - + -
203C THR* 3.9 17.7 - - + -
230C PRO* 4.0 13.5 - - + -
233C TYR* 3.9 41.6 - - + -
301C NAD 2.9 58.7 + - + +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.6 25.9 - - - +
17C GLY 3.8 11.0 + - - -
18C GLY* 3.9 6.7 - - - -
20C SER 3.4 3.6 + - - -
22C LEU* 1.3 77.9 - - - +
24C LEU* 1.4 62.2 + - - +
26C THR* 3.3 5.3 + - - -
27C ALA* 3.1 19.1 + - - +
91C CYS* 3.8 17.0 - - - +
301C NAD 4.6 1.0 + - - -
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Residues in contact with LEU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLY 3.4 21.7 + - - +
19C ALA 4.0 11.0 - - - +
20C SER* 3.1 27.4 + - - +
21C GLY 3.8 2.5 - - - +
23C GLY* 1.4 76.5 - - - +
25C SER* 1.3 62.9 + - - +
27C ALA* 3.1 6.5 + - + +
28C LYS* 2.9 49.6 + - + +
39C LEU* 5.0 1.6 - - + -
50C GLU* 3.8 43.1 - - + +
54C LEU* 4.9 9.4 - - + -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY 3.1 15.0 + - - -
22C LEU 4.0 2.7 - - - -
24C LEU* 1.3 79.0 - - - +
26C THR* 1.3 61.4 + - - +
28C LYS* 3.4 13.8 + - - +
29C ARG* 3.1 19.9 + - - +
230C PRO* 3.3 40.4 + - - +
231C ALA* 3.3 12.5 + - - +
234C ALA* 3.6 7.7 - - - +
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 4.0 16.2 - - + -
22C LEU 2.8 22.0 + - - -
23C GLY* 3.5 7.4 - - - -
25C SER* 1.3 75.4 - - - +
27C ALA* 1.3 63.5 + - - +
29C ARG* 3.4 1.4 + - - +
30C LEU* 3.1 32.9 + - + +
89C VAL* 4.7 8.5 - - + -
233C TYR* 3.4 22.5 - - - -
234C ALA* 3.7 12.6 - - + +
237C VAL* 3.8 30.5 - - + -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.7 13.8 - - + +
23C GLY 3.1 11.5 + - - +
24C LEU* 3.1 8.5 + - + +
26C THR* 1.3 74.3 - - - +
28C LYS* 1.3 64.4 + - - +
30C LEU* 4.8 1.1 - - - -
31C VAL* 2.9 30.0 + - - +
37C ALA* 4.4 9.6 - - + -
39C LEU* 3.6 31.6 - - + -
54C LEU* 4.4 12.6 - - + -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 2.9 47.0 + - + +
25C SER* 3.6 13.9 - - - +
26C THR 3.4 0.2 - - - -
27C ALA* 1.3 76.6 - - - +
29C ARG* 1.3 61.3 + - - +
31C VAL* 4.0 0.9 - - - +
32C GLY* 3.1 20.4 + - - -
50C GLU* 4.5 7.2 + - - -
53C LYS* 5.2 8.1 - - - +
54C LEU* 4.2 30.6 - - + +
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLU* 5.6 0.4 + - - -
25C SER 3.1 16.2 + - - +
26C THR 3.9 3.4 - - - +
28C LYS* 1.3 75.4 - - - +
30C LEU* 1.3 64.8 + - + +
32C GLY* 3.3 2.9 + - - -
33C GLN* 3.1 42.2 + - + +
231C ALA* 4.9 5.4 + - - +
234C ALA* 3.6 35.4 - - + -
235C HIS* 3.6 37.3 - - - +
238C GLN* 3.2 30.1 + - - +
239C MET* 5.5 1.2 - - - -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 4.4 15.5 - - + -
13C ALA* 4.4 22.0 - - + -
15C ILE* 4.6 5.8 - - + -
26C THR* 3.1 33.8 + - + +
27C ALA* 4.1 2.9 - - - +
29C ARG* 1.3 77.8 - - + +
31C VAL* 1.3 64.6 + - + +
33C GLN* 3.0 15.2 + - - +
34C GLY 3.3 0.5 + - - -
35C ALA* 3.1 30.7 + - + +
37C ALA* 5.7 3.1 - - + -
89C VAL* 5.3 2.7 - - + -
234C ALA 5.3 1.6 - - - +
237C VAL* 4.6 2.0 - - + -
238C GLN* 4.3 24.5 - - + +
241C ILE* 4.1 29.8 - - + -
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA 2.9 20.7 + - - +
28C LYS 4.2 1.8 - - - +
30C LEU* 1.3 75.1 - - + +
32C GLY* 1.3 57.2 + - - +
34C GLY* 3.0 19.4 + - - -
35C ALA 3.6 19.1 + - - +
36C THR 4.6 0.2 - - - -
37C ALA* 3.8 26.0 - - + -
54C LEU* 4.1 32.8 - - + +
57C ASN* 4.0 23.0 + - + +
58C CYS* 4.4 7.4 - - + -
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Residues in contact with GLY 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS 3.1 15.7 + - - -
29C ARG* 3.6 6.1 - - - -
30C LEU 3.3 0.4 - - - -
31C VAL* 1.3 74.6 - - - +
33C GLN* 1.3 64.7 + - - +
34C GLY 3.3 0.9 + - - -
54C LEU* 5.8 0.2 - - - +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.6 20.8 + - + +
9C LYS* 3.8 20.8 + - - +
29C ARG* 3.1 28.7 + - + +
30C LEU 3.0 5.7 + - - +
32C GLY* 1.3 79.7 + - - +
34C GLY* 1.3 58.9 + - - +
35C ALA 3.6 0.2 - - - -
238C GLN* 3.6 30.2 + - - +
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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