Contacts of the helix formed by residues 26 - 37 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L THR* 4.9 3.0 - - - +
32L THR* 4.0 19.8 + - + +
22M ASN 4.6 2.0 - - - +
23M ALA 3.1 14.9 + - - +
24M PHE 3.0 0.6 + - - -
25M SER* 1.3 78.8 + - - +
27M PRO* 1.4 68.1 - - - +
28M THR* 2.7 32.0 + - - +
29M VAL* 2.7 34.7 + - + -
30M ALA* 2.9 12.1 + - - -
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Residues in contact with PRO 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M SER 3.2 6.8 - - - +
26M ASN* 1.4 93.0 - - - +
28M THR* 1.3 62.9 + - + +
30M ALA* 4.1 2.5 - - + +
31M SER* 2.8 30.1 + - - -
27N PRO* 3.5 33.1 - - + +
28N THR* 5.7 0.2 - - - -
31N SER* 3.5 19.1 - - - +
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Residues in contact with THR 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L THR* 3.1 29.9 - - + +
29L VAL* 4.8 0.9 - - - -
26M ASN* 2.7 20.1 + - - +
27M PRO* 1.3 81.5 - - + +
29M VAL* 1.3 58.7 + - - +
31M SER* 3.2 5.9 + - - -
32M THR* 2.4 40.5 + - - -
27N PRO* 5.5 1.3 - - + -
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Residues in contact with VAL 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L THR 4.5 0.2 - - - +
29L VAL* 3.9 28.0 - - + -
32L THR* 3.7 25.4 - - - +
33L ILE* 4.9 7.9 - - + -
23M ALA 3.5 19.7 - - - +
24M PHE* 4.0 8.5 - - - -
26M ASN* 2.7 31.1 + - + +
28M THR* 1.3 75.7 - - - +
30M ALA* 1.3 64.7 + - - +
32M THR* 3.4 0.7 + - - -
33M ILE* 3.0 43.2 + - + +
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Residues in contact with ALA 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M PHE* 3.3 38.9 + - + +
25M SER 5.0 0.7 - - - -
26M ASN 2.9 10.9 + - - +
27M PRO* 4.1 2.2 - - + +
29M VAL* 1.3 78.2 - - - +
31M SER* 1.3 57.0 + - - +
33M ILE* 3.9 0.3 - - - +
34M LEU* 2.9 37.4 + - + +
30N ALA* 3.6 28.3 - - + -
34N LEU* 4.5 3.1 - - + -
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Residues in contact with SER 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M PRO 2.8 21.4 + - - -
28M THR* 3.2 9.4 + - - -
30M ALA* 1.3 76.1 - - - +
32M THR* 1.3 60.9 + - - +
34M LEU* 4.6 0.4 - - - -
35M SER* 2.6 40.0 + - - -
25N SER 3.4 24.5 - - - -
27N PRO* 3.5 24.9 - - - +
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Residues in contact with THR 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L ALA* 3.6 35.2 - - + +
26L ASN* 4.0 18.8 + - + +
29L VAL* 3.8 12.9 - - + +
28M THR* 2.4 26.5 + - - -
29M VAL 3.7 3.6 - - - -
30M ALA 3.3 0.2 - - - -
31M SER* 1.3 78.6 + - - +
33M ILE* 1.3 63.8 + - - +
35M SER* 3.2 3.6 + - - -
36M ASN* 3.0 36.5 + - - +
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Residues in contact with ILE 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2697 A 3.6 42.8 - - - +
2707 T 4.7 8.7 - - - +
718 A 5.4 1.8 - - - +
20L LYS* 3.9 16.8 - - + -
23L ALA* 3.8 21.8 - - + -
29L VAL* 4.9 7.9 - - + -
33L ILE* 5.3 5.8 - - + -
24M PHE* 4.3 14.8 - - + -
29M VAL* 3.0 33.6 + - + +
30M ALA 3.9 1.8 - - - +
32M THR* 1.3 77.9 - - - +
34M LEU* 1.3 60.0 + - + +
36M ASN* 3.1 2.8 + - - +
37M VAL* 3.0 29.2 + - + +
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2687 T 4.6 6.3 - - + -
2697 A 4.2 23.8 - - - +
24M PHE* 4.0 15.3 - - + -
30M ALA* 2.9 28.6 + - + +
31M SER 4.3 0.2 - - - +
33M ILE* 1.3 77.6 - - - +
35M SER* 1.3 53.1 + - - +
37M VAL* 3.4 6.5 + - + +
38M SER* 2.6 36.9 + - - -
21N PHE* 3.9 24.0 - - + -
24N PHE* 3.5 38.8 - - + +
25N SER* 3.8 26.5 - - - -
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Residues in contact with SER 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M SER* 2.6 26.4 + - - -
32M THR* 3.2 6.2 + - - -
34M LEU* 1.3 78.2 - - - +
36M ASN* 1.3 69.8 + - - +
38M SER* 3.3 20.5 + - - -
39M PRO* 4.0 3.6 - - - +
25N SER* 4.5 8.5 - - - -
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Residues in contact with ASN 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ALA* 3.4 30.3 + - + +
22L ASN* 4.0 9.9 - - - +
23L ALA* 3.5 30.7 - - - +
32M THR* 3.0 26.8 + - - +
33M ILE* 3.1 4.7 + - - +
35M SER* 1.3 88.5 + - - +
37M VAL* 1.3 59.1 + - - +
38M SER 3.3 0.8 + - - -
39M PRO* 3.6 12.1 - - - +
40M VAL* 4.3 2.3 - - - +
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Residues in contact with VAL 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2687 T 3.9 22.0 - - - +
2697 A 3.9 4.7 - - - +
16L LYS* 4.7 11.2 - - + -
19L ALA* 3.7 18.8 - - + -
20L LYS* 3.6 30.3 - - + -
33M ILE 3.0 19.8 + - - +
34M LEU* 3.5 15.5 - - + +
36M ASN* 1.3 75.9 - - - +
38M SER* 1.3 68.8 + - - +
39M PRO* 3.5 1.3 - - - -
40M VAL* 3.3 7.5 + - + -
41M ALA* 2.9 21.0 + - + +
21N 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