Contacts of the helix formed by residues 26 - 37 (chain y) 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 y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28x THR* 4.9 3.2 - - - +
32x THR* 4.0 19.8 + - + +
22y ASN 3.6 2.2 + - - +
23y ALA 3.1 15.3 + - - +
24y PHE 3.0 1.0 + - - -
25y SER* 1.3 78.5 + - - +
27y PRO* 1.4 67.0 - - - +
28y THR* 2.7 33.9 + - - +
29y VAL* 2.7 34.1 + - + -
30y ALA* 2.9 12.1 + - - -
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Residues in contact with PRO 27 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25y SER 3.2 6.4 - - - +
26y ASN* 1.4 92.7 - - - +
28y THR* 1.3 63.3 + - + +
30y ALA* 4.1 2.3 - - + +
31y SER* 2.8 30.1 + - - -
27z PRO* 3.5 33.3 - - + +
28z THR* 5.7 0.2 - - - -
31z SER* 3.5 19.3 - - - +
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Residues in contact with THR 28 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28x THR* 3.1 29.6 - - + +
29x VAL* 4.8 0.9 - - - -
26y ASN* 2.7 20.0 + - - +
27y PRO* 1.3 80.3 - - + +
29y VAL* 1.3 58.9 + - - +
31y SER* 3.2 5.9 + - - -
32y THR* 2.4 40.1 + - - -
27z PRO* 5.5 1.6 - - + -
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Residues in contact with VAL 29 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28x THR 4.5 0.2 - - - +
29x VAL* 3.9 28.5 - - + -
32x THR* 3.7 24.5 - - - +
33x ILE* 4.9 7.9 - - + -
23y ALA 3.5 18.8 - - - +
24y PHE* 4.0 8.5 - - - -
26y ASN* 2.7 31.6 + - + +
28y THR* 1.3 74.5 - - - +
30y ALA* 1.3 64.8 + - - +
32y THR* 3.7 0.3 - - - -
33y ILE* 3.0 43.6 + - + +
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Residues in contact with ALA 30 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24y PHE* 3.3 39.1 + - + +
25y SER 5.0 0.7 - - - -
26y ASN 2.9 10.6 + - - +
27y PRO 4.1 2.5 - - - +
29y VAL* 1.3 78.6 - - - +
31y SER* 1.3 57.2 + - - +
33y ILE* 3.9 0.5 - - - +
34y LEU* 2.9 37.5 + - + +
30z ALA* 3.6 28.3 - - + -
34z LEU* 4.5 2.9 - - + -
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Residues in contact with SER 31 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27y PRO 2.8 22.8 + - - -
28y THR* 3.2 9.5 + - - -
30y ALA* 1.3 76.8 - - - +
32y THR* 1.3 60.3 + - - +
34y LEU* 4.5 0.4 - - - +
35y SER* 2.6 40.2 + - - -
25z SER 3.4 23.3 - - - -
27z PRO* 3.5 24.6 - - - +
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Residues in contact with THR 32 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23x ALA* 3.6 34.8 - - + +
26x ASN* 4.0 18.4 + - + +
29x VAL* 3.8 12.7 - - + +
28y THR* 2.4 25.9 + - - -
29y VAL 3.7 3.6 - - - -
31y SER* 1.3 77.2 + - - +
33y ILE* 1.3 63.6 + - - +
35y SER* 3.2 3.8 + - - -
36y ASN* 3.0 35.7 + - - +
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Residues in contact with ILE 33 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417 A 3.6 43.1 - - - +
427 T 4.7 8.3 - - - +
2998 A 5.4 2.0 - - - +
20x LYS* 3.9 16.2 - - + -
23x ALA* 3.8 22.0 - - + -
29x VAL* 4.9 7.6 - - + -
33x ILE* 5.3 6.1 - - + -
24y PHE* 4.3 14.8 - - + -
29y VAL* 3.0 33.9 + - + +
30y ALA 3.9 2.0 - - - +
32y THR* 1.3 77.9 - - - +
34y LEU* 1.3 59.5 + - + +
36y ASN* 3.1 2.8 + - - +
37y VAL* 3.0 30.1 + - + +
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Residues in contact with LEU 34 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407 T 4.6 6.1 - - + -
417 A 4.2 24.2 - - - -
24y PHE* 4.0 13.5 - - + -
30y ALA* 2.9 29.9 + - + +
31y SER 4.3 0.2 - - - +
33y ILE* 1.3 77.7 - - - +
35y SER* 1.3 50.6 + - - +
37y VAL* 3.5 6.1 - - + +
38y SER* 2.6 37.6 + - - -
21z PHE* 3.9 23.9 - - + -
24z PHE* 3.5 38.4 - - + +
25z SER* 3.8 27.4 - - - -
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Residues in contact with SER 35 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31y SER* 2.6 26.6 + - - -
32y THR* 3.2 6.9 + - - -
34y LEU* 1.3 77.8 - - - +
36y ASN* 1.3 69.9 + - - +
38y SER* 3.3 19.9 + - - -
39y PRO* 4.0 3.8 - - - +
25z SER* 4.5 8.9 - - - -
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Residues in contact with ASN 36 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19x ALA* 3.4 29.6 + - + +
22x ASN* 4.0 10.5 - - - +
23x ALA* 3.5 30.1 - - - +
32y THR* 3.0 27.0 + - - +
33y ILE* 3.1 4.7 + - - +
35y SER* 1.3 89.0 + - - +
37y VAL* 1.3 58.0 - - - +
38y SER 3.3 0.8 + - - -
39y PRO* 3.6 11.8 - - - +
40y VAL* 4.3 1.9 - - - +
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Residues in contact with VAL 37 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407 T 3.9 22.0 - - - +
417 A 3.9 4.5 - - - +
16x LYS* 4.7 10.1 - - + -
19x ALA* 3.7 17.9 - - + -
20x LYS* 3.6 31.2 - - + -
33y ILE 3.0 21.1 + - - +
34y LEU* 3.5 15.7 - - + +
36y ASN* 1.3 74.8 - - - +
38y SER* 1.3 70.2 + - - +
39y PRO* 3.5 1.8 - - - -
40y VAL* 3.3 8.4 + - + +
41y ALA* 2.9 20.0 + - + +
21z 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