Contacts of the helix formed by residues 26 - 37 (chain a) 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 a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28Z THR* 4.9 3.0 - - - +
32Z THR* 4.0 19.2 + - + +
22a ASN 3.6 2.0 + - - +
23a ALA 3.1 15.5 + - - +
24a PHE 3.0 0.8 + - - +
25a SER* 1.3 78.7 + - - +
27a PRO* 1.4 67.4 - - - +
28a THR* 2.7 31.6 + - - +
29a VAL* 2.7 35.5 + - + -
30a ALA* 2.9 11.5 + - - -
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Residues in contact with PRO 27 (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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25a SER 3.2 6.6 - - - +
26a ASN* 1.4 92.5 - - - +
28a THR* 1.3 63.3 + - + +
30a ALA* 4.1 2.2 - - + +
31a SER* 2.8 30.3 + - - -
27b PRO* 3.5 33.5 - - + +
28b THR* 5.7 0.2 - - - -
31b SER* 3.5 20.0 - - - +
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Residues in contact with THR 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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28Z THR* 3.1 29.1 - - + +
29Z VAL* 4.8 0.9 - - - -
26a ASN* 2.7 20.4 + - - +
27a PRO* 1.3 79.3 - - + +
29a VAL* 1.3 58.7 + - - +
31a SER* 3.2 6.4 + - - -
32a THR* 2.4 40.7 + - - -
27b PRO* 5.5 1.6 - - + -
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Residues in contact with VAL 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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28Z THR 4.5 0.2 - - - +
29Z VAL* 3.9 27.1 - - + -
32Z THR* 3.7 25.1 - - - +
33Z ILE* 4.9 8.1 - - + -
23a ALA 3.5 20.0 - - - +
24a PHE* 4.0 8.1 - - - -
26a ASN* 2.7 30.7 + - + +
28a THR* 1.3 75.5 - - - +
30a ALA* 1.3 64.6 + - - +
32a THR* 3.4 0.7 + - - -
33a ILE* 3.0 43.6 + - + +
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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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24a PHE* 3.3 39.2 + - + +
25a SER 5.0 0.7 - - - -
26a ASN 2.9 10.6 + - - +
27a PRO* 4.1 2.7 - - + +
29a VAL* 1.3 78.4 - - - +
31a SER* 1.3 58.0 + - - +
33a ILE* 3.9 0.2 - - - +
34a LEU* 2.9 37.5 + - + +
30b ALA* 3.6 28.5 - - + -
34b LEU* 4.5 2.2 - - + -
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Residues in contact with SER 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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27a PRO 2.8 21.4 + - - -
28a THR* 3.2 9.9 + - - -
30a ALA* 1.3 76.8 - - - +
32a THR* 1.3 59.7 + - - +
34a LEU* 4.5 0.4 - - - +
35a SER* 2.6 39.8 + - - -
25b SER 3.4 24.0 - - - -
27b PRO* 3.5 24.8 - - - +
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Residues in contact with THR 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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23Z ALA* 3.6 34.3 - - + +
26Z ASN* 4.0 18.4 + - + +
29Z VAL* 3.8 13.4 - - + +
28a THR* 2.4 26.3 + - - -
29a VAL 3.7 3.6 - - - -
30a ALA 3.3 0.2 - - - -
31a SER* 1.3 77.9 + - - +
33a ILE* 1.3 63.5 + - - +
35a SER* 3.2 3.4 + - - -
36a ASN* 3.0 36.3 + - - +
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Residues in contact with ILE 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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1857 A 3.6 42.4 - - - +
1867 T 4.7 8.3 - - - +
1558 A 5.4 2.0 - - - +
20Z LYS* 3.9 16.6 - - + -
23Z ALA* 3.8 22.2 - - + -
29Z VAL* 4.9 7.4 - - + -
33Z ILE* 5.3 5.8 - - + -
24a PHE* 4.3 14.4 - - + -
29a VAL* 3.0 34.5 + - + +
30a ALA 3.9 2.0 - - - +
32a THR* 1.3 77.7 - - - +
34a LEU* 1.3 60.2 + - + +
36a ASN* 3.1 3.1 + - - +
37a VAL* 3.0 29.0 + - + +
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Residues in contact with LEU 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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1847 T 4.6 6.3 - - + -
1857 A 4.2 24.0 - - - +
24a PHE* 4.0 15.3 - - + -
30a ALA* 2.9 29.4 + - + +
31a SER 4.3 0.4 - - - +
33a ILE* 1.3 77.2 - - - +
35a SER* 1.3 52.8 + - - +
37a VAL* 3.4 6.6 + - + +
38a SER* 2.6 37.1 + - - -
21b PHE* 3.9 23.4 - - + -
24b PHE* 3.5 39.3 - - + +
25b SER* 3.8 25.8 - - - -
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Residues in contact with SER 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 SER* 2.6 26.5 + - - -
32a THR* 3.2 6.4 + - - -
34a LEU* 1.3 77.5 - - - +
36a ASN* 1.3 69.1 + - - +
38a SER* 3.3 20.2 + - - -
39a PRO* 4.0 3.6 - - - +
25b SER* 4.5 9.1 - - - -
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Residues in contact with ASN 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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19Z ALA* 3.4 30.0 + - + +
22Z ASN* 4.0 9.5 - - - +
23Z ALA* 3.5 30.5 - - - +
32a THR* 3.0 28.3 + - - +
33a ILE* 3.6 4.0 - - - +
35a SER* 1.3 91.1 + - - +
37a VAL* 1.3 58.1 + - - +
38a SER 3.3 0.7 + - - -
39a PRO* 3.6 11.8 - - - +
40a VAL* 4.3 2.3 - - - +
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Residues in contact with VAL 37 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1847 T 3.9 22.2 - - - +
1857 A 3.9 4.7 - - - +
16Z LYS* 4.7 9.6 - - + -
19Z ALA* 3.7 18.6 - - + -
20Z LYS* 3.6 31.2 - - + -
33a ILE 3.0 20.2 + - - +
34a LEU* 3.5 15.9 - - + +
36a ASN* 1.3 75.9 - - - +
38a SER* 1.3 69.7 + - - +
39a PRO* 3.5 1.3 - - - -
40a VAL* 3.3 8.7 + - + +
41a ALA* 2.9 19.5 + - + +
21b 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