Contacts of the helix formed by residues 26 - 37 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F THR* 4.9 3.2 - - - +
32F THR* 4.0 19.4 + - + +
22G ASN 4.6 1.8 - - - +
23G ALA 3.1 15.6 + - - +
24G PHE 3.0 1.0 + - - -
25G SER* 1.3 78.3 + - - +
27G PRO* 1.4 67.8 - - - +
28G THR* 2.7 33.3 + - - +
29G VAL* 2.7 34.3 + - + -
30G ALA* 2.9 11.8 + - - -
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Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G SER 3.2 6.2 - - - +
26G ASN* 1.4 93.0 - - - +
28G THR* 1.3 63.1 + - + +
30G ALA* 4.1 1.7 - - + +
31G SER* 2.8 30.7 + - - -
27H PRO* 3.5 33.1 - - + +
28H THR* 5.7 0.2 - - - -
31H SER* 3.5 19.3 - - - +
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Residues in contact with THR 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F THR* 3.1 29.8 - - + +
29F VAL* 4.8 0.7 - - - -
26G ASN* 2.7 20.8 + - - +
27G PRO* 1.3 80.2 - - + +
29G VAL* 1.3 58.0 + - - +
31G SER* 3.2 5.7 + - - -
32G THR* 2.4 40.3 + - - -
27H PRO* 5.5 1.8 - - + -
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Residues in contact with VAL 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F VAL* 3.9 28.5 - - + -
32F THR* 3.7 24.9 - - - +
33F ILE* 4.9 7.4 - - + -
23G ALA 3.5 19.7 - - - +
24G PHE* 4.0 9.0 - - - -
26G ASN* 2.7 30.8 + - + +
28G THR* 1.3 74.7 - - - +
30G ALA* 1.3 65.5 + - - +
32G THR* 3.4 0.7 + - - -
33G ILE* 3.0 42.7 + - + +
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G PHE* 3.3 39.8 + - + +
25G SER 5.0 0.7 - - - -
26G ASN 2.9 11.3 + - - +
27G PRO* 4.1 2.2 - - + +
29G VAL* 1.3 77.8 - - - +
31G SER* 1.3 57.4 + - - +
33G ILE* 3.9 0.5 - - - +
34G LEU* 2.9 37.9 + - + +
30H ALA* 3.6 28.5 - - + -
34H LEU* 4.5 2.2 - - + -
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Residues in contact with SER 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO 2.8 20.8 + - - -
28G THR* 3.2 9.4 + - - -
30G ALA* 1.3 76.2 - - - +
32G THR* 1.3 61.1 + - - +
34G LEU* 4.6 0.4 - - - -
35G SER* 2.6 40.0 + - - -
25H SER 3.4 23.6 - - - -
27H PRO* 3.5 24.8 - - - +
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Residues in contact with THR 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ALA* 3.6 35.0 - - + +
26F ASN* 4.0 19.3 + - + +
29F VAL* 3.8 14.0 - - + +
28G THR* 2.4 28.2 + - - -
29G VAL 3.7 3.1 - - - -
31G SER* 1.3 78.5 + - - +
33G ILE* 1.3 63.5 + - - +
35G SER* 3.2 3.4 + - - -
36G ASN* 3.0 35.0 + - - +
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Residues in contact with ILE 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3057 A 3.6 43.3 - - - +
3067 T 4.7 8.3 - - - +
358 A 5.4 2.0 - - - +
20F LYS* 3.9 16.2 - - + -
23F ALA* 3.8 21.8 - - + -
29F VAL* 4.9 8.1 - - + -
33F ILE* 5.3 6.1 - - + -
24G PHE* 4.3 14.4 - - + -
29G VAL* 3.0 34.6 + - + +
30G ALA 3.9 1.8 - - - +
32G THR* 1.3 79.0 - - - +
34G LEU* 1.3 59.0 + - + +
36G ASN* 3.1 2.9 + - - +
37G VAL* 3.0 29.8 + - + +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3047 T 4.6 6.7 - - + -
3057 A 4.2 23.3 - - - -
24G PHE* 4.0 13.7 - - + -
30G ALA* 2.9 29.9 + - + +
31G SER 4.3 0.2 - - - +
33G ILE* 1.3 77.0 - - - +
35G SER* 1.3 52.1 + - - +
37G VAL* 3.4 6.7 + - + +
38G SER* 2.6 37.7 + - - -
21H PHE* 3.9 23.9 - - + -
24H PHE* 3.5 39.0 - - + +
25H SER* 3.8 26.2 - - - -
30H ALA* 4.6 0.2 - - + -
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Residues in contact with SER 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G SER* 2.6 26.7 + - - -
32G THR* 3.2 6.4 + - - -
34G LEU* 1.3 78.2 - - - +
36G ASN* 1.3 69.6 + - - +
38G SER* 3.3 20.8 + - - -
39G PRO* 4.0 3.5 - - - +
25H SER* 4.5 9.8 - - - -
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Residues in contact with ASN 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA* 3.4 30.2 + - + +
22F ASN* 4.0 10.7 - - - +
23F ALA* 3.5 31.1 - - - +
32G THR* 3.0 27.0 + - - +
33G ILE* 3.6 4.7 - - - +
35G SER* 1.3 89.4 + - - +
37G VAL* 1.3 58.9 + - - +
38G SER 3.3 1.1 + - - -
39G PRO* 3.6 11.6 - - - +
40G VAL* 4.3 1.9 - - - +
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3047 T 3.9 21.5 - - - +
3057 A 3.9 4.9 - - - +
16F LYS* 4.7 10.8 - - + -
19F ALA* 3.7 18.8 - - + -
20F LYS* 3.6 30.3 - - + -
33G ILE 3.0 20.1 + - - +
34G LEU* 3.5 15.7 - - + +
36G ASN* 1.3 76.2 - - - +
38G SER* 1.3 68.1 + - - +
39G PRO* 3.5 1.3 - - - -
40G VAL* 3.3 7.9 + - + -
41G ALA* 2.9 21.0 + - + +
21H 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