Contacts of the helix formed by residues 26 - 37 (chain C) in PDB entry 3J9X
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 ASN 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B THR* 4.9 3.2 - - - +
32B THR* 4.0 19.4 + - + +
22C ASN 4.6 1.8 - - - +
23C ALA 3.1 15.8 + - - +
24C PHE 3.0 1.4 + - - +
25C SER* 1.3 78.5 + - - +
27C PRO* 1.4 67.6 - - - +
28C THR* 2.7 32.8 + - - +
29C VAL* 2.7 34.7 + - + -
30C ALA* 2.9 12.1 + - - +
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Residues in contact with PRO 27 (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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25C SER 3.2 6.6 - - - +
26C ASN* 1.4 93.0 - - - +
28C THR* 1.3 62.8 + - + +
30C ALA* 4.1 1.2 - - + +
31C SER* 2.8 30.7 + - - -
27D PRO* 3.5 33.2 - - + +
28D THR* 5.7 0.2 - - - -
31D SER* 3.5 19.5 - - - +
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Residues in contact with THR 28 (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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28B THR* 3.1 29.2 - - + +
29B VAL* 4.8 0.9 - - - -
26C ASN* 2.7 21.0 + - - +
27C PRO* 1.3 80.4 - - + +
29C VAL* 1.3 57.9 + - - +
31C SER* 3.2 5.5 + - - -
32C THR* 2.4 40.4 + - - -
27D PRO* 5.5 1.8 - - + -
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Residues in contact with VAL 29 (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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28B THR 4.5 0.2 - - - +
29B VAL* 3.9 27.8 - - + -
32B THR* 3.7 24.7 - - - +
33B ILE* 4.9 7.4 - - + -
23C ALA 3.5 20.2 - - - +
24C PHE* 4.0 8.5 - - - -
26C ASN* 2.7 31.5 + - + +
28C THR* 1.3 75.3 - - - +
30C ALA* 1.3 65.2 + - - +
32C THR* 3.4 0.7 + - - -
33C ILE* 3.0 43.6 + - + +
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Residues in contact with ALA 30 (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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24C PHE* 3.3 39.8 + - + +
25C SER 5.0 0.7 - - - -
26C ASN 2.9 10.7 + - - +
27C PRO* 4.1 2.5 - - + +
29C VAL* 1.3 78.8 - - - +
31C SER* 1.3 57.1 + - - +
33C ILE* 3.9 0.5 - - - +
34C LEU* 2.9 37.6 + - + +
30D ALA* 3.6 27.4 - - + -
34D LEU* 4.5 3.1 - - + -
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Residues in contact with SER 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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27C PRO 2.8 21.1 + - - -
28C THR* 3.2 9.7 + - - -
30C ALA* 1.3 76.4 - - - +
32C THR* 1.3 60.2 + - - +
34C LEU 4.5 0.2 - - - +
35C SER* 2.6 39.8 + - - -
25D SER 3.4 23.8 - - - -
27D PRO* 3.5 24.9 - - - +
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Residues in contact with THR 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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23B ALA* 3.6 35.0 - - + +
26B ASN* 4.0 19.0 + - + +
29B VAL* 3.8 13.5 - - + +
28C THR* 2.4 27.1 + - - -
29C VAL 3.7 3.4 - - - -
30C ALA 3.3 0.2 - - - -
31C SER* 1.3 78.1 + - - +
33C ILE* 1.3 62.8 + - - +
35C SER* 3.2 3.6 + - - -
36C ASN* 3.0 35.6 + - - +
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Residues in contact with ILE 33 (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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3297 A 3.6 42.8 - - - +
3307 T 4.7 8.7 - - - +
118 A 5.4 2.0 - - - +
20B LYS* 3.9 16.8 - - + -
23B ALA* 3.8 22.4 - - + -
29B VAL* 4.9 8.1 - - + -
33B ILE* 5.3 6.1 - - + -
24C PHE* 4.3 14.1 - - + -
29C VAL* 3.0 34.4 + - + +
30C ALA 3.9 2.2 - - - +
32C THR* 1.3 78.4 - - - +
34C LEU* 1.3 59.7 + - + +
36C ASN* 3.1 2.9 + - - +
37C VAL* 3.0 29.4 + - + +
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Residues in contact with LEU 34 (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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3287 T 4.6 6.5 - - + -
3297 A 4.2 23.6 - - - +
24C PHE* 4.0 14.4 - - + -
30C ALA* 2.9 29.9 + - + +
31C SER 4.3 0.4 - - - +
33C ILE* 1.3 77.2 - - - +
35C SER* 1.3 52.6 + - - +
37C VAL* 3.4 7.0 + - + +
38C SER* 2.6 37.3 + - - -
21D PHE* 3.9 24.5 - - + -
24D PHE* 3.5 39.0 - - + +
25D SER* 3.8 25.1 - - - -
30D ALA* 4.6 0.2 - - + -
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Residues in contact with SER 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 SER* 2.6 25.3 + - - -
32C THR* 3.2 6.4 + - - -
34C LEU* 1.3 78.2 - - - +
36C ASN* 1.3 69.6 + - - +
38C SER* 3.3 20.5 + - - -
39C PRO* 4.0 4.2 - - - +
25D SER* 4.5 8.9 - - - -
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Residues in contact with ASN 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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19B ALA* 3.4 30.3 + - + +
22B ASN* 4.0 10.1 - - - +
23B ALA* 3.5 31.3 - - - +
32C THR* 3.0 27.0 + - - +
33C ILE* 3.1 4.9 + - - +
35C SER* 1.3 90.7 + - - +
37C VAL* 1.3 57.9 + - - +
38C SER 3.3 1.0 + - - -
39C PRO* 3.6 11.6 - - - +
40C VAL* 4.3 1.9 - - - +
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3287 T 3.9 22.2 - - - +
3297 A 3.9 5.2 - - - +
16B LYS* 4.7 10.5 - - + -
19B ALA* 3.7 18.6 - - + -
20B LYS* 3.6 30.3 - - + -
33C ILE 3.0 20.3 + - - +
34C LEU* 3.5 15.3 - - + +
36C ASN* 1.3 76.2 - - - +
38C SER* 1.3 69.3 + - - +
39C PRO* 3.5 1.6 - - - -
40C VAL* 3.3 9.2 + - + +
41C ALA* 2.9 20.0 + - + +
21D PHE* 4.5 9.2 - - + -
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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