Contacts of the helix formed by residues 20 - 33 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLY 3.3 11.2 + - - +
18A GLY 3.3 1.4 + - - -
19A ALA* 1.3 80.8 - - - +
21A GLY* 1.3 73.9 + - - +
22A LEU 3.4 0.2 + - - -
23A GLY 3.4 2.4 + - - -
24A LEU* 3.1 21.4 + - - -
204A PRO* 3.6 15.8 - - - +
301A NAD 2.9 41.7 + - - +
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Residues in contact with GLY 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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20A SER* 1.3 76.9 + - - +
22A LEU* 1.4 62.8 + - - -
24A LEU* 3.3 4.9 + - - +
25A SER* 3.1 24.6 + - - -
203A THR* 4.0 16.4 - - - -
204A PRO* 4.3 4.7 - - - +
230A PRO* 4.3 6.4 - - - +
301A NAD 3.4 13.7 - - - -
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Residues in contact with LEU 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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21A GLY* 1.4 68.4 - - - +
23A GLY* 1.3 65.5 + - - +
25A SER* 4.0 4.1 - - - -
26A THR* 2.9 30.0 + - - -
91A CYS* 4.2 3.8 - - - -
153A THR* 4.7 0.7 - - + -
198A PRO* 4.3 11.0 - - + -
201A PHE* 4.0 26.7 - - + -
203A THR* 4.0 13.2 - - + -
230A PRO* 4.0 15.5 - - + -
233A TYR* 3.9 42.1 - - + -
301A NAD 2.9 57.9 + - + +
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Residues in contact with GLY 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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15A ILE* 3.6 18.3 - - - +
17A GLY 3.8 12.5 + - - -
18A GLY* 3.9 6.5 - - - -
20A SER 3.4 4.0 + - - -
22A LEU* 1.3 79.8 - - - +
24A LEU* 1.3 61.9 + - - +
26A THR* 3.3 4.1 + - - -
27A ALA* 3.1 19.8 + - - +
91A CYS* 3.8 23.2 - - - +
301A NAD 4.6 0.8 + - - -
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Residues in contact with LEU 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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18A GLY 3.3 22.2 + - - +
19A ALA 4.0 11.2 - - - +
20A SER* 3.1 24.8 + - - +
21A GLY 3.8 2.5 - - - +
23A GLY* 1.3 76.5 - - - +
25A SER* 1.3 57.1 + - - +
27A ALA* 3.2 6.6 + - + +
28A LYS* 3.0 52.9 + - + +
39A LEU* 4.9 2.2 - - + -
50A GLU* 3.9 44.2 - - + +
54A LEU* 4.8 9.2 - - + -
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Residues in contact with SER 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 GLY 3.1 14.6 + - - -
22A LEU 4.0 2.9 - - - -
24A LEU* 1.3 78.5 - - - +
26A THR* 1.4 61.4 + - - +
28A LYS* 3.4 12.9 + - - +
29A ARG* 3.2 18.5 + - - +
230A PRO* 3.4 24.6 + - - +
231A ALA* 3.4 28.2 + - - +
234A ALA* 3.6 7.6 - - - +
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Residues in contact with THR 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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15A ILE* 4.0 11.4 - - + -
22A LEU 2.9 22.8 + - - -
23A GLY* 3.6 7.4 - - - -
25A SER* 1.4 74.4 - - - +
27A ALA* 1.3 64.6 + - - +
29A ARG* 3.4 1.7 + - - +
30A LEU* 3.1 38.1 + - + +
89A VAL* 4.7 8.5 - - + -
233A TYR* 3.4 23.0 - - - -
234A ALA* 3.7 12.1 - - + +
237A VAL* 3.8 30.7 - - + -
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Residues in contact with ALA 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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15A ILE* 3.7 14.9 - - + +
23A GLY 3.1 11.4 + - - +
24A LEU* 3.6 9.2 - - + +
26A THR* 1.3 77.3 - - - +
28A LYS* 1.3 61.6 + - - +
30A LEU* 4.9 0.9 - - - -
31A VAL* 3.0 29.5 + - - +
37A ALA* 4.4 8.1 - - + -
39A LEU* 3.6 31.2 - - + -
54A LEU* 4.2 13.0 - - + -
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Residues in contact with LYS 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 LEU* 3.0 45.8 + - + +
25A SER* 3.8 12.1 - - - +
26A THR 3.3 0.2 - - - -
27A ALA* 1.3 75.5 - - - +
29A ARG* 1.3 61.7 + - - +
31A VAL* 4.1 1.0 - - - +
32A GLY* 3.0 21.5 + - - -
50A GLU* 4.5 7.7 + - - -
53A LYS* 5.3 8.4 - - - +
54A LEU* 3.9 34.5 - - + +
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Residues in contact with ARG 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 SER 3.2 16.3 + - - +
26A THR 3.9 2.9 - - - +
27A ALA 3.3 0.2 - - - -
28A LYS* 1.3 77.0 - - - +
30A LEU* 1.3 65.0 + - + +
32A GLY* 3.2 2.8 + - - -
33A GLN* 3.1 40.7 + - + +
231A ALA* 4.9 5.4 + - - +
234A ALA* 3.6 33.9 - - + +
235A HIS* 3.6 37.5 - - - +
238A GLN* 3.3 28.0 + - - +
242C GLU* 5.6 0.6 + - - -
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Residues in contact with LEU 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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8A VAL* 4.3 17.9 - - + -
13A ALA* 4.5 21.8 - - + -
15A ILE* 4.6 4.7 - - + -
26A THR* 3.1 34.3 + - + +
27A ALA* 4.2 2.7 - - - +
29A ARG* 1.3 78.2 - - + +
31A VAL* 1.3 62.1 + - + +
33A GLN* 3.1 12.8 + - - +
34A GLY 3.4 0.5 + - - -
35A ALA* 2.9 37.0 + - + +
37A ALA* 5.8 3.1 - - + -
89A VAL* 5.4 2.5 - - + -
234A ALA 5.4 1.8 - - - +
237A VAL* 4.6 3.1 - - + -
238A GLN* 4.3 23.6 - - + +
241A ILE* 4.1 27.6 - - + -
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Residues in contact with VAL 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 ALA 3.0 21.6 + - - +
28A LYS 4.2 1.6 - - - +
30A LEU* 1.3 72.6 - - - +
32A GLY* 1.3 63.8 + - - +
34A GLY* 2.9 16.5 + - - -
35A ALA 3.6 18.8 - - - +
37A ALA* 3.7 26.5 - - + -
54A LEU* 3.9 32.5 - - + +
57A ASN* 4.0 22.9 + - + +
58A CYS* 4.4 8.3 - - + -
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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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28A LYS 3.0 15.4 + - - -
29A ARG* 3.2 6.0 + - - -
31A VAL* 1.3 76.4 - - - +
33A GLN* 1.3 63.7 + - - +
34A GLY 3.4 0.9 + - - -
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Residues in contact with GLN 33 (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 VAL* 3.6 19.7 + - + +
9A LYS* 3.8 20.3 + - - +
29A ARG* 3.1 28.1 + - + +
30A LEU 3.1 4.2 + - - +
32A GLY* 1.3 79.6 + - - +
34A GLY* 1.3 58.6 + - - +
35A ALA 3.6 0.6 + - - -
238A GLN* 3.6 30.1 + - - +
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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