Contacts of the helix formed by residues 30 - 40 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LYS* 1.3 73.4 - - - +
31A ALA* 1.3 59.5 + - - -
34A VAL* 2.9 28.8 + - - +
91A ALA* 4.8 0.2 - - - +
93A SER* 3.0 19.9 + - - -
209D G 3.7 15.9 + - - -
210D U 3.4 11.0 - - - -
211D G 3.0 15.4 - - - +
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Residues in contact with ALA 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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30A GLY* 1.3 70.8 - - - -
32A ASN* 1.3 56.0 + - - +
34A VAL* 4.1 1.5 - - - +
35A THR* 2.6 38.4 + - - +
57A VAL* 4.0 29.8 - - + +
58A VAL* 4.8 1.8 - - + -
60A HIS* 5.2 2.5 - - + -
61A LEU* 5.6 1.3 - - + -
92A SER* 3.8 7.4 - - - +
93A SER* 3.7 11.5 + - - +
209D G 4.3 0.2 + - - -
210D U 2.8 24.0 + - - +
211D G 3.6 1.6 + - - +
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Residues in contact with ASN 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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31A ALA* 1.3 79.7 - - - +
33A GLU* 1.3 59.7 + - - +
35A THR* 3.8 4.1 - - - -
36A LYS* 2.9 61.3 + - - +
211D G 3.1 28.4 + - + +
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Residues in contact with GLU 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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28A LYS* 3.8 38.3 + - + +
29A LYS* 3.4 16.7 + - - +
32A ASN* 1.3 70.9 - - + +
34A VAL* 1.3 61.0 + - - +
36A LYS* 3.8 23.6 - - - +
37A ALA* 2.9 29.8 + - - +
209D G 4.4 2.1 - - - +
211D G 2.8 51.4 + - + +
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Residues in contact with VAL 34 (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* 3.7 7.0 - - - +
30A GLY 2.9 21.7 + - - +
31A ALA* 4.1 2.2 - - - +
33A GLU* 1.3 75.2 - - - +
35A THR* 1.3 64.2 + - - +
37A ALA* 3.2 2.8 + - - +
38A VAL* 3.0 23.5 + - + +
46A VAL* 3.9 30.5 - - + -
61A LEU* 4.1 17.9 - - + -
93A SER* 3.6 28.7 - - - +
94A VAL* 3.7 15.0 - - - -
95A ALA* 3.7 18.6 - - + +
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Residues in contact with THR 35 (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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31A ALA 2.6 22.9 + - - -
32A ASN* 3.8 5.6 - - - -
34A VAL* 1.3 79.0 - - - +
36A LYS* 1.3 62.8 + - + +
38A VAL* 3.3 4.1 + - - +
39A GLU* 2.9 51.2 + - + +
60A HIS* 2.9 37.7 + - + +
61A LEU* 3.9 8.3 - - - +
64A LEU* 4.2 6.1 - - + -
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Residues in contact with LYS 36 (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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32A ASN* 2.9 46.2 + - - +
33A GLU* 3.8 24.3 - - - +
34A VAL 3.3 0.2 - - - -
35A THR* 1.3 76.9 - - - +
37A ALA* 1.3 57.4 + - - +
39A GLU* 3.3 14.1 + - - +
40A ARG* 2.9 39.7 + - + +
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Residues in contact with ALA 37 (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* 4.0 10.8 - - + +
33A GLU 2.9 18.5 + - - +
34A VAL 3.2 5.4 + - - +
36A LYS* 1.3 77.0 - - - +
38A VAL* 1.3 59.0 + - - +
40A ARG* 3.2 1.4 + - - -
41A GLY 3.0 22.3 + - - -
42A ILE* 3.0 36.5 + - + +
43A ALA* 3.7 7.1 + - + -
95A ALA* 4.4 2.7 - - + -
97A ILE* 3.9 17.3 - - + -
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Residues in contact with VAL 38 (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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34A VAL* 3.0 25.3 + - + +
35A THR* 3.3 5.1 + - - +
37A ALA* 1.3 75.7 - - - +
39A GLU* 1.3 61.6 + - - +
41A GLY* 3.1 14.4 + - - -
43A ALA* 4.1 11.4 - - + -
46A VAL* 3.7 29.6 - - + -
61A LEU* 4.9 2.0 - - + -
64A LEU* 3.7 34.1 - - + +
65A CYS* 4.3 12.6 - - - -
68A LYS* 3.8 28.7 - - + +
70A ILE* 4.8 6.1 - - + +
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Residues in contact with GLU 39 (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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35A THR* 2.9 44.3 + - + +
36A LYS* 3.8 15.0 - - - +
38A VAL* 1.3 75.9 - - - +
40A ARG* 1.3 61.4 + - + +
41A GLY 3.1 1.0 + - - -
64A LEU* 4.2 16.6 - - + +
68A LYS* 4.2 19.7 + - - +
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Residues in contact with ARG 40 (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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36A LYS* 2.9 29.2 + - + +
37A ALA* 3.7 5.8 - - - +
38A VAL 3.2 0.2 - - - -
39A GLU* 1.3 77.9 - - + +
41A GLY* 1.3 61.9 + - - +
42A ILE* 3.4 22.9 + - + +
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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