Contacts of the helix formed by residues 23 - 34 (chain D) in PDB entry 1S9C
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 THR 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D TYR* 1.3 85.0 - - - +
24D GLU* 1.3 73.3 + - - +
25D LEU* 3.0 15.4 + - - +
26D GLU* 2.6 33.1 + - - +
27D ALA* 3.3 8.1 + - - +
102D ARG 3.8 5.4 - - - -
103D ALA* 3.7 9.9 - - + -
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C TRP* 6.0 1.1 - - + -
23D THR* 1.3 80.5 - - - +
25D LEU* 1.3 53.0 + - - +
27D ALA* 3.1 7.7 + - - +
28D ILE* 2.7 42.6 + - + +
49D GLU* 3.9 21.5 - - + -
54D PHE* 3.6 20.9 - - + -
102D ARG* 2.7 56.6 + - - +
103D ALA* 4.1 6.0 - - - +
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C MET* 4.8 6.3 - - + -
190C LEU* 3.6 35.9 - - + +
194C TRP* 3.6 37.9 - - + -
23D THR* 3.0 14.1 + - - +
24D GLU* 1.3 79.1 - - - +
26D GLU* 1.3 74.4 + - - +
28D ILE* 3.0 3.3 + - - +
29D MET* 2.8 45.6 + - + +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 4.6 9.6 - - - +
21D ALA 5.1 1.8 - - - +
22D TYR* 3.9 24.2 - - + -
23D THR* 2.6 43.1 + - - +
25D LEU* 1.3 94.1 - - - +
27D ALA* 1.3 62.1 + - - +
29D MET* 3.7 17.9 - - + +
30D TYR* 3.1 22.5 + - - +
60D PHE* 3.8 11.6 - - + -
191D SER* 4.6 2.1 + - - -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 4.9 4.9 - - + -
23D THR 3.3 9.4 + - - +
24D GLU* 3.1 13.0 + - - +
25D LEU 3.0 0.8 - - - -
26D GLU* 1.3 76.6 - - - +
28D ILE* 1.3 66.7 + - - +
30D TYR* 2.9 16.6 + - - +
31D ALA* 2.9 13.1 + - - +
46D PHE 5.0 0.9 - - - -
54D PHE* 4.4 12.8 - - + -
56D CYS* 4.1 27.1 - - + -
57D LEU 5.8 1.0 + - - +
60D PHE* 4.3 11.6 - - - -
102D ARG 5.1 1.3 - - - +
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ALA 5.0 0.9 - - - +
189C ARG* 4.5 0.7 - - - +
190C LEU* 3.8 18.2 - - + -
194C TRP* 4.2 12.1 - - + -
24D GLU 2.7 28.4 + - - +
25D LEU 3.6 2.9 - - - +
27D ALA* 1.3 71.6 - - - +
29D MET* 1.3 63.1 + - - +
31D ALA* 3.1 2.1 + - - +
32D LEU* 2.9 30.3 + - + +
46D PHE 3.7 9.9 - - - +
47D ILE* 3.2 45.5 - - + +
49D GLU* 3.5 28.7 - - + +
54D PHE* 3.7 18.4 - - + -
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Residues in contact with MET 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU* 4.8 5.4 - - + -
29C MET* 3.3 34.5 - - + +
190C LEU* 3.9 22.1 - - + +
25D LEU* 2.8 31.6 + - + +
26D GLU* 3.7 28.5 - - + +
28D ILE* 1.3 76.7 - - - +
30D TYR* 1.3 63.3 + - - +
32D LEU* 3.9 3.5 - - - +
33D GLY* 3.0 19.8 + - - -
187D LEU* 4.8 13.0 - - + +
188D TYR* 5.9 0.3 - - - -
190D LEU* 4.1 34.1 - - + +
191D SER* 4.3 8.6 + - - +
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Residues in contact with TYR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU 3.1 13.4 + - - +
27D ALA 2.9 10.6 + - - +
29D MET* 1.3 77.0 - - - +
31D ALA* 1.3 60.9 + - - +
33D GLY* 3.1 4.0 + - - -
34D VAL* 2.8 57.1 + - + +
57D LEU* 4.4 11.4 - - + -
59D THR* 2.8 42.0 + - - -
60D PHE* 3.7 31.9 - + + -
62D VAL* 5.3 2.1 - - + +
63D ILE* 3.1 30.7 - - + -
188D TYR* 3.4 33.2 + + - -
191D SER* 3.6 9.4 + - - +
217D LEU 4.4 4.9 + - - -
220D PHE* 5.1 1.0 - - - -
221D GLY* 3.9 4.5 - - - -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA 2.9 10.0 + - - +
28D ILE 3.5 7.0 - - - +
30D TYR* 1.3 77.5 - - - +
32D LEU* 1.3 62.2 + - - +
34D VAL* 3.1 9.5 + - - +
35D GLY 3.2 0.7 + - - -
36D ALA* 3.0 28.9 + - + -
46D PHE* 3.6 30.5 - - + +
47D ILE* 5.1 1.6 - - + -
57D LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ASN* 4.4 13.7 - - + +
186C ALA* 3.7 26.7 - - + +
187C LEU* 4.0 26.7 - - + +
190C LEU* 4.0 11.9 - - + -
28D ILE* 2.9 23.7 + - + +
29D MET* 3.9 3.8 - - - +
31D ALA* 1.3 75.4 - - - +
33D GLY* 1.3 60.8 + - - +
34D VAL 2.9 5.2 + - - -
35D GLY* 3.0 14.0 + - - -
36D ALA 3.6 19.9 - - - +
47D ILE* 4.2 22.0 - - + -
184D GLN* 3.9 5.4 + - - -
187D LEU* 3.8 15.6 - - + +
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Residues in contact with GLY 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET 3.0 12.8 + - - -
30D TYR* 3.5 4.7 - - - -
32D LEU* 1.3 76.9 - - - +
34D VAL* 1.3 56.9 + - - +
35D GLY 3.5 0.4 - - - -
184D GLN* 3.0 18.0 + - - -
187D LEU* 3.5 23.9 - - - +
188D TYR* 3.6 19.6 - - - +
218D CYS* 3.3 17.2 - - - -
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Residues in contact with VAL 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TYR* 2.8 32.8 + - + +
31D ALA 3.1 11.4 + - - +
32D LEU 2.9 1.0 - - - -
33D GLY* 1.3 78.2 - - - +
35D GLY* 1.3 49.1 + - - +
57D LEU* 3.7 24.9 - - + -
59D THR* 5.5 0.2 - - - +
188D TYR* 4.2 11.2 - - + -
218D CYS* 3.7 10.3 - - - +
221D GLY* 3.3 35.4 - - - +
222D PHE* 3.3 19.1 - - - -
225D ARG* 2.4 34.6 + - - +
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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