Contacts of the helix formed by residues 26 - 37 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR* 4.9 3.2 - - - +
32D THR* 4.0 19.2 + - + +
22E ASN 3.6 2.0 + - - +
23E ALA 3.1 15.8 + - - +
24E PHE 3.0 0.8 + - - -
25E SER* 1.3 77.9 + - - +
27E PRO* 1.4 66.6 - - - +
28E THR* 2.7 34.0 + - - +
29E VAL* 2.7 33.5 + - + -
30E ALA* 2.9 12.2 + - - -
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Residues in contact with PRO 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E SER 3.2 6.4 - - - +
26E ASN* 1.4 93.4 - - - +
28E THR* 1.3 64.3 + - + +
30E ALA* 3.8 2.7 + - + +
31E SER* 2.8 29.9 + - - -
27F PRO* 3.5 32.7 - - + +
28F THR* 5.7 0.2 - - - -
31F SER* 3.5 20.4 - - - +
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Residues in contact with THR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR* 3.1 30.2 - - + +
29D VAL* 4.8 1.1 - - - -
26E ASN* 2.7 20.2 + - - +
27E PRO* 1.3 79.7 - - + +
29E VAL* 1.3 58.4 + - - +
31E SER* 3.2 6.0 + - - -
32E THR* 2.4 40.1 + - - -
27F PRO* 5.5 1.3 - - + -
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Residues in contact with VAL 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D THR 4.5 0.2 - - - +
29D VAL* 3.9 27.4 - - + -
32D THR* 3.7 25.6 - - - +
33D ILE* 4.9 7.4 - - + -
23E ALA 3.5 19.1 - - - +
24E PHE* 4.0 8.1 - - - -
26E ASN* 2.7 31.3 + - + +
28E THR* 1.3 74.7 - - - +
30E ALA* 1.3 65.4 + - - +
32E THR* 3.4 0.7 + - - -
33E ILE* 3.0 43.2 + - + +
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E PHE* 3.3 39.8 + - + +
25E SER 5.0 0.7 - - - -
26E ASN 2.9 11.0 + - - +
27E PRO* 4.1 2.5 - - + +
29E VAL* 1.3 77.4 - - - +
31E SER* 1.3 57.1 + - - +
33E ILE* 3.9 0.7 - - - +
34E LEU* 2.9 37.5 + - + +
30F ALA* 3.6 28.0 - - + -
34F LEU* 4.5 2.7 - - + -
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E PRO 2.8 21.1 + - - -
28E THR* 3.2 9.7 + - - -
30E ALA* 1.3 76.4 - - - +
32E THR* 1.3 60.7 + - - +
34E LEU* 4.5 0.4 - - - +
35E SER* 2.6 40.5 + - - -
25F SER 3.4 24.2 - - - -
27F PRO* 3.5 25.2 - - - +
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Residues in contact with THR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 3.6 34.1 - - + +
26D ASN* 4.0 18.8 + - + +
29D VAL* 3.8 14.4 - - + +
28E THR* 2.4 26.2 + - - -
29E VAL 3.7 3.8 - - - -
31E SER* 1.3 78.3 + - - +
33E ILE* 1.3 63.3 + - - +
35E SER* 3.2 3.7 + - - -
36E ASN* 3.0 36.1 + - - +
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Residues in contact with ILE 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3177 A 3.6 43.3 - - - +
3187 T 4.7 8.1 - - - +
238 A 5.4 2.0 - - - +
20D LYS* 3.9 15.9 - - + -
23D ALA* 3.8 23.6 - - + -
29D VAL* 4.9 7.9 - - + -
33D ILE* 5.3 6.1 - - + -
24E PHE* 4.3 14.1 - - + -
29E VAL* 3.0 34.4 + - + +
30E ALA 3.9 2.2 - - - +
32E THR* 1.3 77.7 - - - +
34E LEU* 1.3 59.9 - - + +
36E ASN* 3.1 2.9 + - - +
37E VAL* 3.0 28.8 + - + +
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Residues in contact with LEU 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3167 T 4.6 6.3 - - + -
3177 A 4.2 23.8 - - - +
24E PHE* 4.0 15.0 - - + -
30E ALA* 2.9 28.4 + - + +
31E SER 4.3 0.2 - - - +
33E ILE* 1.3 77.0 - - + +
35E SER* 1.3 51.7 + - - +
37E VAL* 3.4 6.1 + - + +
38E SER* 2.6 37.1 + - - -
21F PHE* 3.9 23.5 - - + -
24F PHE* 3.5 39.3 - - + +
25F SER* 3.8 26.0 - - - -
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Residues in contact with SER 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E SER* 2.6 25.7 + - - -
32E THR* 3.2 6.2 + - - -
34E LEU* 1.3 77.6 - - - +
36E ASN* 1.3 70.2 + - - +
38E SER* 3.3 19.9 + - - -
39E PRO* 4.0 3.5 - - - +
25F SER* 4.5 10.0 - - - -
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Residues in contact with ASN 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ALA* 3.4 30.6 + - + +
22D ASN* 4.0 10.6 - - - +
23D ALA* 3.5 31.1 - - - +
32E THR* 3.0 27.1 + - - +
33E ILE* 3.6 4.3 - - - +
35E SER* 1.3 88.1 + - - +
37E VAL* 1.3 57.0 - - - +
38E SER 3.3 1.1 + - - -
39E PRO* 3.6 12.0 - - - +
40E VAL* 4.3 1.9 - - - +
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3167 T 3.9 22.7 - - - +
3177 A 3.9 5.2 - - - +
16D LYS* 4.7 10.8 - - + -
19D ALA* 3.7 17.9 - - + -
20D LYS* 3.6 30.5 - - + -
33E ILE 3.0 20.4 + - - +
34E LEU* 3.5 15.0 - - + +
36E ASN* 1.3 75.8 - - - +
38E SER* 1.3 68.5 + - - +
39E PRO* 3.5 1.6 - - - -
40E VAL* 3.9 7.6 - - + -
41E ALA* 2.9 20.9 + - + +
21F PHE* 4.5 9.4 - - + -
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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