Contacts of the helix formed by residues 20 - 33 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B GLY 3.3 10.6 + - - +
18B GLY 3.3 1.2 - - - -
19B ALA* 1.3 79.4 - - - +
21B GLY* 1.3 67.6 + - - +
22B LEU 3.4 0.3 + - - -
23B GLY 3.4 1.7 + - - -
24B LEU* 3.0 22.6 + - - -
204B PRO* 3.7 14.6 - - - +
301B NAD 2.8 47.5 + - - +
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B SER* 1.3 75.3 + - - +
22B LEU* 1.3 64.9 + - - -
24B LEU* 3.3 5.2 + - - +
25B SER* 3.1 24.8 + - - -
203B THR* 4.2 15.0 - - - -
204B PRO* 4.3 5.1 - - - +
230B PRO* 4.2 6.6 - - - +
301B NAD 3.4 13.9 - - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY* 1.3 68.6 - - - -
23B GLY* 1.3 64.5 + - - +
25B SER* 3.5 5.2 + - - -
26B THR* 2.8 29.6 + - - -
91B CYS* 4.3 4.0 - - - -
153B THR* 4.7 0.2 - - + -
198B PRO* 4.3 11.2 - - + -
201B PHE* 4.0 23.6 - - + -
203B THR* 3.9 18.8 - - + -
230B PRO* 4.0 13.5 - - + -
233B TYR* 4.0 41.6 - - + -
301B NAD 3.0 58.6 + - + +
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.6 26.2 - - - +
17B GLY 3.9 10.9 + - - -
18B GLY* 4.0 6.2 - - - -
20B SER 3.4 3.0 + - - -
21B GLY 3.4 0.6 - - - -
22B LEU* 1.3 79.6 - - - +
24B LEU* 1.3 62.5 + - - +
26B THR* 3.3 3.9 + - - -
27B ALA* 3.0 19.9 + - - +
91B CYS* 3.8 17.2 - - - +
301B NAD 4.8 1.0 + - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY* 3.4 20.6 + - - +
19B ALA 4.0 11.4 - - - +
20B SER* 3.0 26.7 + - - +
21B GLY 3.8 2.7 - - - +
23B GLY* 1.3 77.1 - - - +
25B SER* 1.3 58.2 - - - +
27B ALA* 3.2 4.4 + - + +
28B LYS* 3.0 53.3 + - + +
39B LEU* 4.9 4.3 - - + -
50B GLU* 3.9 41.1 - - + +
54B LEU* 4.9 7.6 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.1 17.3 + - - -
22B LEU 4.0 2.2 - - - -
23B GLY 3.3 0.2 - - - -
24B LEU* 1.3 76.6 - - - +
26B THR* 1.3 61.0 + - - +
28B LYS* 3.5 12.6 + - - +
29B ARG* 3.2 18.7 + - - +
230B PRO* 3.4 24.4 + - - +
231B ALA* 3.3 28.6 + - - +
234B ALA* 3.6 6.1 - - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 4.1 10.5 - - + -
22B LEU 2.8 22.3 + - - -
23B GLY* 3.5 8.1 - - - -
25B SER* 1.3 74.3 - - - +
27B ALA* 1.3 63.8 + - - +
29B ARG* 3.5 1.9 + - - +
30B LEU* 3.1 42.9 + - + +
89B VAL* 4.7 9.0 - - + -
233B TYR* 3.4 23.0 - - - -
234B ALA* 3.7 12.9 - - - +
237B VAL* 3.8 30.1 - - + -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.7 14.3 - - + +
23B GLY 3.0 11.2 + - - +
24B LEU* 3.2 9.4 + - + +
26B THR* 1.3 75.0 - - - +
28B LYS* 1.3 66.6 + - - +
30B LEU* 4.9 0.9 - - - -
31B VAL* 2.9 28.4 + - - +
37B ALA* 4.4 8.3 - - + -
39B LEU* 3.6 32.3 - - + -
54B LEU* 4.4 11.9 - - + -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 3.0 47.1 + - + +
25B SER* 3.7 13.2 - - - +
27B ALA* 1.3 74.9 - - - +
29B ARG* 1.3 63.1 + - - +
31B VAL* 4.0 1.0 - - - +
32B GLY* 3.0 21.0 + - - -
50B GLU* 4.5 8.1 + - - -
53B LYS* 5.3 8.3 - - - +
54B LEU* 4.2 29.4 - - + +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER 3.2 14.3 + - - +
26B THR 3.9 1.8 - - - +
27B ALA 3.3 0.2 - - - -
28B LYS* 1.3 78.0 - - - +
30B LEU* 1.3 63.6 + - + +
32B GLY* 3.2 3.9 + - - -
33B GLN* 3.1 36.3 + - + +
231B ALA* 5.0 5.4 + - - +
234B ALA* 3.6 37.7 - - + -
235B HIS* 3.7 36.9 - - - +
238B GLN* 3.2 29.0 + - - +
242D GLU* 5.6 0.4 + - - -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 4.4 16.2 - - + -
13B ALA* 4.5 20.9 - - + -
15B ILE* 4.6 6.7 - - + -
26B THR* 3.1 35.1 + - + +
27B ALA* 4.2 2.7 - - - +
29B ARG* 1.3 73.0 - - + +
31B VAL* 1.3 66.4 + - + +
33B GLN* 3.0 12.9 + - - +
34B GLY 3.3 0.3 + - - -
35B ALA* 3.0 34.4 + - + +
36B THR 5.9 0.2 - - - +
37B ALA* 5.8 2.9 - - + -
89B VAL* 5.3 2.7 - - + -
234B ALA 5.4 1.3 - - - +
237B VAL* 4.6 1.6 - - + -
238B GLN* 4.3 24.7 - - + +
241B ILE* 4.1 29.8 - - + -
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 2.9 22.0 + - - +
28B LYS 4.2 2.0 - - - +
30B LEU* 1.3 74.2 - - - +
32B GLY* 1.3 57.3 + - - +
34B GLY* 3.0 19.4 + - - -
35B ALA 3.6 18.0 - - - +
36B THR 4.8 0.2 - - - -
37B ALA* 3.7 26.5 - - + -
54B LEU* 4.1 34.8 - - + +
57B ASN* 4.0 22.3 + - + +
58B CYS* 4.4 8.5 - - + -
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Residues in contact with GLY 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS 3.0 15.4 + - - -
29B ARG* 3.2 5.8 + - - -
31B VAL* 1.3 75.5 - - - +
33B GLN* 1.3 64.7 + - - +
34B GLY 3.4 1.0 + - - -
54B LEU* 5.7 0.4 - - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.6 19.9 + - + +
9B LYS* 3.9 20.4 + - - +
29B ARG* 3.4 26.9 + - + +
30B LEU 3.0 6.3 + - - +
32B GLY* 1.3 80.6 + - - +
34B GLY* 1.3 60.3 + - - +
35B ALA 3.6 0.4 - - - -
238B GLN* 3.6 31.4 + - - +
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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