Contacts of the helix formed by residues 30 - 40 (chain C) in PDB entry 1SDS
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 GLY 30 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C LYS* 1.3 73.5 - - - +
31C ALA* 1.3 59.6 + - - -
33C GLU 3.3 0.2 + - - -
34C VAL* 2.9 30.0 + - - +
91C ALA* 4.8 0.2 - - - +
93C SER* 3.0 19.0 + - - -
209F G 3.6 15.8 + - - -
210F U 3.3 11.4 - - - -
211F G 3.0 15.2 - - - +
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Residues in contact with ALA 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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30C GLY* 1.3 70.8 - - - -
32C ASN* 1.3 56.0 + - - +
34C VAL* 4.0 1.6 - - - +
35C THR* 2.6 39.1 + - - +
57C VAL* 3.9 28.0 - - + +
58C VAL* 4.8 1.8 - - + -
60C HIS* 5.2 2.5 - - + -
61C LEU* 5.4 1.5 - - + +
92C SER* 3.9 8.3 - - - +
93C SER* 3.6 10.6 + - - +
209F G 4.3 0.2 + - - -
210F U 2.8 23.5 + - - +
211F G 3.6 1.6 + - - +
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Residues in contact with ASN 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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31C ALA* 1.3 78.9 - - - +
33C GLU* 1.3 58.5 + - - +
35C THR* 3.7 4.3 - - - -
36C LYS* 2.9 61.3 + - - +
211F G 3.1 25.5 + - + +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS* 3.8 38.1 + - + +
29C LYS* 3.3 17.7 + - - +
32C ASN* 1.3 69.5 - - + +
34C VAL* 1.3 65.1 + - - +
36C LYS* 3.5 23.0 + - - +
37C ALA* 3.0 24.8 + - - +
209F G 4.3 1.9 - - - +
211F G 2.8 53.1 + - + +
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Residues in contact with VAL 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LYS 3.7 7.4 - - - +
30C GLY 2.9 20.6 + - - +
31C ALA 4.0 2.2 - - - +
33C GLU* 1.3 76.7 - - - +
35C THR* 1.3 64.0 + - - +
37C ALA* 3.3 3.3 + - - +
38C VAL* 3.1 23.3 + - + +
46C VAL* 3.9 30.5 - - + -
61C LEU* 4.1 18.8 - - + -
93C SER* 3.5 27.8 - - - +
94C VAL* 3.6 15.3 - - - -
95C ALA* 3.6 18.8 - - + +
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Residues in contact with THR 35 (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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31C ALA 2.6 23.5 + - - -
32C ASN* 3.7 6.3 - - - -
34C VAL* 1.3 78.3 - - - +
36C LYS* 1.3 64.2 + - + +
38C VAL* 3.3 4.5 + - - +
39C GLU* 3.0 37.1 + - + +
60C HIS* 2.8 34.3 + - + +
61C LEU* 3.9 7.8 - - - +
64C LEU* 4.0 14.1 - - + -
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Residues in contact with LYS 36 (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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32C ASN* 2.9 47.5 + - - +
33C GLU* 3.8 24.5 - - - +
34C VAL 3.3 0.2 - - - -
35C THR* 1.3 77.2 - - + +
37C ALA* 1.3 58.1 + - - +
39C GLU* 3.4 7.4 + - - +
40C ARG* 3.0 65.8 + - - +
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Residues in contact with ALA 37 (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* 4.0 9.6 - - + -
33C GLU 3.0 18.8 + - - +
34C VAL* 3.5 6.1 - - - +
35C THR 3.2 0.2 - - - -
36C LYS* 1.3 74.7 - - - +
38C VAL* 1.3 60.3 + - - +
40C ARG* 3.2 2.6 + - - +
41C GLY 2.9 22.0 + - - -
42C ILE* 3.1 36.8 + - + +
43C ALA* 4.3 7.9 - - + -
95C ALA* 4.5 1.8 - - + -
97C ILE* 4.0 16.8 - - + -
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Residues in contact with VAL 38 (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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34C VAL* 3.1 20.8 + - + +
35C THR* 3.8 4.9 - - - +
37C ALA* 1.3 74.4 - - - +
39C GLU* 1.3 64.1 + - - +
41C GLY* 2.9 14.6 + - - -
43C ALA* 4.1 8.1 - - + -
46C VAL* 3.8 28.7 - - + -
61C LEU* 5.0 2.0 - - + -
64C LEU* 3.5 37.0 - - + +
65C CYS* 4.3 8.1 - - - +
68C LYS* 3.8 19.9 - - + +
70C ILE* 3.8 22.2 - - + +
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Residues in contact with GLU 39 (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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35C THR* 3.0 35.7 + - + +
36C LYS* 3.6 7.9 - - - +
37C ALA 3.3 0.2 - - - -
38C VAL* 1.3 77.0 - - - +
40C ARG* 1.3 61.4 + - + +
41C GLY* 3.4 0.9 + - - -
64C LEU* 3.2 33.4 - - - +
68C LYS* 3.8 22.9 + - - +
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Residues in contact with ARG 40 (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* 5.7 5.7 - - - +
36C LYS* 3.0 55.7 + - - +
37C ALA* 3.8 4.9 - - - +
38C VAL 3.2 0.2 - - - -
39C GLU* 1.3 77.9 - - + +
41C GLY* 1.3 61.4 + - - +
42C ILE* 3.6 27.8 + - + +
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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