Contacts of the helix formed by residues 29 - 39 (chain S) in PDB entry 2J28
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 VAL 29 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27S LYS 3.1 1.2 + - - -
28S LYS* 1.3 77.7 - - - +
30S SER* 1.3 63.7 + - - +
31S GLN 3.1 0.4 - - - -
32S ALA* 3.6 13.3 - - - +
33S LEU* 2.9 37.0 + - + +
51S LEU* 5.4 0.2 - - + -
55S ILE* 3.3 32.1 - - + -
66S ILE* 5.2 6.7 - - + +
68S ASP 4.5 2.7 - - - +
69S LEU* 3.0 41.3 - - + +
70S LYS* 3.3 12.6 - - - -
71S VAL* 3.3 22.7 - - + +
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Residues in contact with SER 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S LYS 2.6 17.6 + - - -
29S VAL* 1.3 76.1 - - - +
31S GLN* 1.3 60.4 + - - -
33S LEU* 3.8 5.4 + - - +
34S ASP* 2.9 25.5 + - - +
66S ILE* 3.7 38.1 + - - +
67S ASP* 5.4 1.2 - - - -
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Residues in contact with GLN 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250 THR* 5.6 7.0 - - - +
28S LYS* 3.5 41.1 + - + +
29S VAL 3.1 0.4 - - - -
30S SER* 1.3 80.6 - - - +
32S ALA* 1.3 53.3 + - - +
34S ASP* 2.6 15.8 + - - +
35S ILE* 2.5 46.5 + - + +
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Residues in contact with ALA 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S ILE* 4.1 18.6 - - + +
25S ARG 5.5 0.2 - - - +
27S LYS 5.4 0.2 - - - +
28S LYS* 3.6 5.2 - - + +
29S VAL* 3.5 20.7 + - - +
30S SER 3.5 0.2 - - - -
31S GLN* 1.3 78.4 - - - +
33S LEU* 1.3 54.9 + - - +
35S ILE* 3.1 12.9 + - - -
36S LEU* 2.7 41.9 + - + +
51S LEU* 3.5 23.1 - - + -
71S VAL* 5.1 3.4 - - + -
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Residues in contact with LEU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 2.9 32.5 + - + +
30S SER* 3.9 6.5 - - - +
32S ALA* 1.3 77.9 - - - +
34S ASP* 1.3 59.3 + - - +
36S LEU* 4.1 3.7 - - - +
37S THR* 3.0 30.4 + - - +
48S LYS* 4.3 36.3 - - + +
51S LEU* 3.4 31.9 - - + +
52S GLU* 4.7 10.8 - - + +
55S ILE* 5.5 3.8 - - + -
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Residues in contact with ASP 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340 GLY 5.6 3.0 - - - +
350 GLU* 5.2 5.7 - - - +
30S SER* 2.9 18.3 - - - +
31S GLN* 2.6 21.8 + - - +
33S LEU* 1.3 72.2 - - - +
35S ILE* 1.3 64.0 + - + +
37S THR* 3.0 25.4 - - - +
38S TYR* 3.1 24.3 + - + +
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Residues in contact with ILE 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210 LEU* 5.3 0.7 - - + -
230 ALA* 3.8 31.3 - - + +
250 THR* 6.4 2.2 - - - -
23S LEU 4.5 5.4 - - - +
24S ILE* 3.4 39.9 - - + -
28S LYS* 4.1 21.3 - - + +
31S GLN* 2.5 30.7 + - + +
32S ALA* 3.4 24.0 - - - +
34S ASP* 1.3 73.5 - - + +
36S LEU* 1.3 58.3 + - - +
38S TYR* 3.6 2.4 + - - +
39S THR* 3.1 27.5 + - + +
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Residues in contact with LEU 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20S VAL* 3.9 26.0 - - + +
24S ILE* 3.9 21.8 - - + -
32S ALA* 2.7 23.3 + - - +
33S LEU* 4.1 4.0 - - - +
35S ILE* 1.3 70.2 - - - +
37S THR* 1.3 60.4 - - - +
38S TYR 3.1 4.5 - - - -
39S THR* 2.9 27.2 + - + +
44S ALA* 4.4 12.0 - - + +
47S VAL* 3.7 22.2 - - + +
48S LYS* 3.4 44.9 - - + +
51S LEU* 4.4 14.4 - - + -
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Residues in contact with THR 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350 GLU* 5.7 2.4 + - - +
33S LEU 3.0 24.4 + - - +
34S ASP* 3.0 20.0 - - - +
36S LEU* 1.3 76.8 - - - +
38S TYR* 1.3 82.0 + - + +
39S THR 5.4 0.2 - - - -
40S ASN* 5.3 1.9 - - - +
48S LYS* 4.2 23.5 - - - +
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Residues in contact with TYR 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230 ALA* 6.5 1.8 - - + -
280 SER* 5.1 9.2 - - - -
340 GLY 5.2 1.8 - - - -
350 GLU* 3.2 28.4 + - - +
360 LYS* 3.1 28.3 + - - -
370 HIS* 3.5 62.4 + + + -
34S ASP* 3.1 25.6 + - + +
35S ILE* 4.0 2.2 - - - +
36S LEU 3.1 1.0 - - - -
37S THR* 1.3 107.6 - - + +
39S THR* 1.3 61.6 + - - +
40S ASN* 3.4 11.7 + - - +
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Residues in contact with THR 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210 LEU* 5.8 5.5 - - - +
220 THR* 5.4 7.7 + - - -
230 ALA* 5.8 4.9 - - - -
20S VAL* 4.6 17.0 - - + +
24S ILE* 6.1 1.6 - - + -
35S ILE* 3.1 19.6 + - + +
36S LEU* 2.9 29.0 + - + +
37S THR 5.4 0.2 - - - -
38S TYR* 1.3 75.3 - - - +
40S ASN* 1.3 63.3 + - - +
41S LYS* 3.3 27.5 + - - +
44S ALA* 4.5 4.9 - - + +
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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