Contacts of the helix formed by residues 27 - 40 (chain A) in PDB entry 1DS1
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 ASP 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PRO* 5.8 0.9 - - - +
23A THR 4.1 2.2 + - - +
24A PRO 3.3 7.1 + - - +
26A ALA* 1.3 81.0 - - + +
28A LEU* 1.3 63.1 + - - +
29A TYR* 3.6 9.5 + - - +
30A ALA* 3.1 32.6 + - + +
31A PHE* 3.0 19.1 + - - +
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Residues in contact with LEU 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 PRO* 3.2 21.5 + - + +
25A ARG* 4.0 17.2 + - + +
27A ASP* 1.3 75.9 + - - +
29A TYR* 1.3 64.8 + - + +
31A PHE* 3.6 18.3 - - + +
32A LEU* 3.0 32.1 + - + +
119A VAL* 3.7 39.5 - - + +
120A TYR* 4.3 20.2 - - + -
315A GLY* 4.2 13.5 - - - +
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Residues in contact with TYR 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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27A ASP* 3.3 7.1 + - - +
28A LEU* 1.3 80.6 - - + +
30A ALA* 1.3 57.7 + - - +
32A LEU* 3.8 1.6 - - - +
33A ASP* 3.0 29.3 + - - +
313A ARG* 3.5 53.1 + - + +
314A ALA 3.3 25.1 - - - +
315A GLY* 3.7 15.1 + - - -
316A ASP* 2.6 37.2 + - - -
317A VAL 4.9 0.3 + - - -
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Residues in contact with ALA 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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21A PRO* 4.6 6.1 - - + +
27A ASP* 3.1 33.6 + - + +
29A TYR* 1.3 74.7 - - - +
31A PHE* 1.3 67.8 + - - +
33A ASP* 3.4 7.1 + - - +
34A ALA* 3.0 24.3 + - - +
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Residues in contact with PHE 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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20A LEU* 3.8 28.8 - - + +
21A PRO* 3.6 46.0 - - + +
24A PRO* 3.7 30.3 - - + +
27A ASP 3.0 17.1 + - - +
28A LEU* 3.6 8.1 - - + +
30A ALA* 1.3 75.6 - - - +
32A LEU* 1.3 77.3 + - + +
34A ALA* 3.3 4.9 + - - +
35A ALA* 3.0 24.7 + - + +
91A LEU* 3.8 25.8 - - + -
95A GLU 4.4 4.3 - - - -
99A GLY* 4.7 4.0 - - - -
120A TYR* 3.5 28.5 - + - -
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Residues in contact with LEU 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 LEU* 3.0 29.4 + - + +
29A TYR 4.1 1.3 - - - +
31A PHE* 1.3 96.5 - - + +
33A ASP* 1.3 58.4 + - - +
35A ALA* 3.3 2.1 + - - -
36A HIS* 2.9 23.7 + - - +
99A GLY* 4.4 5.6 - - - -
103A ARG* 3.5 14.0 + - + +
108A HIS* 3.7 45.1 - - + +
119A VAL* 4.9 1.6 - - + -
120A TYR* 4.2 6.1 - - + +
314A ALA* 3.6 42.0 - - + +
315A GLY* 3.6 11.2 - - - +
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Residues in contact with ASP 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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29A TYR 3.0 18.0 + - - +
30A ALA* 3.7 7.9 - - - +
32A LEU* 1.3 73.9 - - - +
34A ALA* 1.3 65.3 + - - +
36A HIS* 3.2 13.1 + - - +
37A THR* 3.1 29.1 + - - -
103A ARG* 5.5 2.0 + - - +
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Residues in contact with ALA 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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19A ARG* 4.8 4.8 - - + +
20A LEU* 3.8 10.0 - - + +
21A PRO* 3.8 22.4 - - + -
30A ALA 3.0 13.2 + - - +
31A PHE 3.3 8.5 + - - +
33A ASP* 1.3 76.7 + - - +
35A ALA* 1.3 62.7 + - - +
37A THR* 3.3 7.2 + - - +
38A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 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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20A LEU* 3.7 18.8 - - + +
31A PHE* 3.0 15.6 + - + +
32A LEU* 3.5 12.8 - - + +
33A ASP 3.2 0.2 - - - -
34A ALA* 1.3 76.7 - - - +
36A HIS* 1.3 56.3 + - - +
38A ALA 3.4 0.7 + - - -
39A ALA* 2.9 29.6 + - - +
99A GLY* 3.6 35.4 - - - +
100A LEU* 3.8 7.8 - - - +
103A ARG* 4.2 3.1 - - + -
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Residues in contact with HIS 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 LEU 2.9 13.2 + - - +
33A ASP* 3.2 16.8 + - - +
35A ALA* 1.3 72.7 - - - +
37A THR* 1.3 71.1 + - - +
39A ALA* 3.2 15.6 + - + +
40A ALA* 3.6 5.7 + - - +
103A ARG* 3.5 61.6 + - + +
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Residues in contact with THR 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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19A ARG* 4.8 8.8 + - - +
33A ASP* 3.1 20.4 + - - -
34A ALA* 3.8 8.7 - - - -
36A HIS* 1.3 81.9 + - - +
38A ALA* 1.3 62.1 + - - +
40A ALA* 3.3 18.9 + - - +
41A SER* 4.4 2.1 + - - -
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Residues in contact with ALA 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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16A LEU* 3.9 11.8 - - + +
19A ARG* 4.0 34.1 - - + +
20A LEU* 4.4 7.0 - - + -
34A ALA 3.0 17.7 + - - +
37A THR* 1.3 78.9 - - - +
39A ALA* 1.3 56.0 + - - +
41A SER* 2.9 25.5 + - - -
42A LEU 3.8 2.4 + - - -
100A LEU* 3.5 22.7 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.1 + - - +
36A HIS* 3.2 10.9 + - + +
38A ALA* 1.3 75.1 - - - +
40A ALA* 1.3 61.4 + - - +
41A SER 3.1 0.9 + - - -
42A LEU* 3.2 26.8 + - + +
100A LEU* 3.4 26.2 - - - +
103A ARG 4.6 0.9 - - - -
104A ARG* 3.1 34.3 + - + +
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Residues in contact with ALA 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 HIS 3.6 5.2 + - - +
37A THR* 3.3 15.3 + - - +
38A ALA 3.1 1.0 - - - -
39A ALA* 1.3 77.9 - - - +
41A SER* 1.3 58.4 + - - +
42A LEU 3.4 2.8 + - - +
104A ARG* 3.9 12.9 + - - +
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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