Contacts of the helix formed by residues 26 - 37 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T THR* 4.9 3.2 - - - +
32T THR* 4.0 19.4 + - + +
22U ASN 3.6 2.4 + - - +
23U ALA 3.1 15.3 + - - +
24U PHE 3.0 1.2 + - - +
25U SER* 1.3 78.1 + - - +
27U PRO* 1.4 68.1 - - - +
28U THR* 2.7 33.4 + - - +
29U VAL* 2.7 35.3 + - + -
30U ALA* 2.9 11.7 + - - -
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Residues in contact with PRO 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U SER 3.2 6.6 - - - +
26U ASN* 1.4 92.5 - - - +
28U THR* 1.3 63.1 + - + +
30U ALA* 4.1 1.5 - - + +
31U SER* 2.8 30.7 + - - -
27V PRO* 3.5 33.5 - - + +
31V SER* 3.5 20.0 - - - +
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Residues in contact with THR 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T THR* 3.1 29.7 - - + +
29T VAL* 4.8 0.9 - - - -
26U ASN* 2.7 21.3 + - - +
27U PRO* 1.3 79.1 - - + +
29U VAL* 1.3 58.1 + - - +
31U SER* 3.2 5.2 + - - -
32U THR* 2.4 40.5 + - - -
27V PRO* 5.5 1.6 - - + -
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Residues in contact with VAL 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28T THR 4.5 0.2 - - - +
29T VAL* 3.9 27.8 - - + -
32T THR* 3.7 25.1 - - - +
33T ILE* 4.9 6.7 - - + -
23U ALA 3.5 20.0 - - - +
24U PHE* 4.0 8.7 - - - +
26U ASN* 2.7 30.4 + - + +
28U THR* 1.3 75.0 - - - +
30U ALA* 1.3 65.4 + - - +
32U THR* 3.4 0.7 + - - -
33U ILE* 3.0 43.4 + - + +
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Residues in contact with ALA 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U PHE* 3.3 40.2 + - + +
25U SER 5.0 0.7 - - - -
26U ASN 2.9 10.0 + - - +
27U PRO* 4.1 2.5 - - + +
29U VAL* 1.3 78.8 - - - +
31U SER* 1.3 56.8 + - - +
33U ILE* 3.9 0.3 - - - +
34U LEU* 2.9 38.0 + - + +
30V ALA* 3.6 28.0 - - + -
34V LEU* 4.5 3.1 - - + -
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Residues in contact with SER 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U PRO 2.8 21.5 + - - -
28U THR* 3.2 9.5 + - - -
30U ALA* 1.3 76.6 - - - +
32U THR* 1.3 60.8 + - - +
34U LEU 4.5 0.2 - - - +
35U SER* 2.6 39.6 + - - -
25V SER 3.4 24.0 - - - -
27V PRO* 3.5 24.5 - - - +
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Residues in contact with THR 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23T ALA* 3.6 35.0 - - + +
26T ASN* 4.0 19.0 + - + +
29T VAL* 3.8 13.0 - - + +
28U THR* 2.4 27.3 + - - -
29U VAL 3.7 3.4 - - - -
30U ALA 3.3 0.2 - - - -
31U SER* 1.3 78.4 + - - +
33U ILE* 1.3 62.8 + - - +
35U SER* 3.2 3.4 + - - -
36U ASN* 3.0 36.2 + - - +
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Residues in contact with ILE 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2217 A 3.6 42.6 - - - +
2227 T 4.7 8.5 - - - +
1198 A 5.3 1.8 - - - +
20T LYS* 3.9 16.8 - - + -
23T ALA* 3.8 21.8 - - + -
29T VAL* 4.9 7.6 - - + -
33T ILE* 5.3 6.1 - - + -
24U PHE* 4.3 14.8 - - + -
29U VAL* 3.0 35.0 + - + +
30U ALA 3.9 2.2 - - - +
32U THR* 1.3 77.2 - - - +
34U LEU* 1.3 58.6 + - + +
36U ASN* 3.1 2.8 + - - +
37U VAL* 3.0 29.4 + - + +
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2207 T 4.6 6.7 - - + -
2217 A 4.2 23.8 - - - +
24U PHE* 4.0 13.7 - - + -
30U ALA* 2.9 28.4 + - + +
31U SER 4.3 0.2 - - - +
33U ILE* 1.3 77.9 - - - +
35U SER* 1.3 51.8 + - - +
37U VAL* 3.4 6.5 + - + +
38U SER* 2.6 37.3 + - - -
21V PHE* 3.9 24.3 - - + -
24V PHE* 3.5 38.6 - - + +
25V SER* 3.8 25.8 - - - -
30V ALA* 4.6 0.2 - - + -
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Residues in contact with SER 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U SER* 2.6 26.1 + - - -
32U THR* 3.2 6.4 + - - -
34U LEU* 1.3 77.5 - - - +
36U ASN* 1.3 69.5 + - - +
38U SER* 3.3 21.1 + - - -
39U PRO* 4.0 4.0 - - - +
25V SER* 4.5 9.1 - - - -
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Residues in contact with ASN 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T ALA* 3.4 30.3 + - + +
22T ASN* 4.0 10.1 - - - +
23T ALA* 3.5 30.7 - - - +
32U THR* 3.0 27.3 + - - +
33U ILE* 3.1 4.9 + - - +
35U SER* 1.3 91.4 + - - +
37U VAL* 1.3 58.5 + - - +
38U SER 3.3 1.0 + - - -
39U PRO* 3.6 11.6 - - - +
40U VAL* 4.3 1.9 - - - +
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Residues in contact with VAL 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2207 T 3.9 21.8 - - - +
2217 A 3.9 5.4 - - - +
16T LYS* 4.7 10.1 - - + -
19T ALA* 3.7 19.1 - - + -
20T LYS* 3.6 29.8 - - + -
33U ILE 3.0 20.5 + - - +
34U LEU* 3.5 15.7 - - + +
36U ASN* 1.3 76.7 - - - +
38U SER* 1.3 68.1 + - - +
39U PRO* 3.5 1.6 - - - -
40U VAL* 3.3 8.9 + - + +
41U ALA* 2.9 19.9 + - + +
21V PHE* 4.5 9.9 - - + -
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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