Contacts of the helix formed by residues 46 - 61 (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 LEU 46 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B G 3.3 17.0 - - - +
492B A 3.2 34.3 - - + +
7S HIS* 3.1 43.1 - - + +
10S ALA* 3.9 15.9 - - + +
44S ALA 3.5 3.0 + - - -
45S VAL* 1.3 77.2 - - + +
47S VAL* 1.3 55.3 + - - +
49S LYS* 3.1 38.0 - - + +
50S VAL* 2.7 41.1 + - + +
103S ILE* 4.3 2.9 - - + +
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Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S VAL* 4.1 12.3 - - + -
20S VAL* 3.8 17.5 - - + +
21S ALA* 4.9 12.1 - - + -
24S ILE* 6.5 0.2 - - + -
36S LEU* 3.7 24.9 - - + -
43S ALA 3.3 19.5 - - - +
44S ALA* 3.9 7.6 - - - -
45S VAL 2.6 19.2 + - - +
46S LEU* 1.3 71.5 - - - +
48S LYS* 1.3 66.6 + - - +
49S LYS 2.9 0.9 - - - -
50S VAL* 3.0 23.8 - - + +
51S LEU* 3.0 13.4 + - + +
74S ILE* 6.2 1.3 - - + -
103S ILE* 4.7 7.0 - - + -
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Residues in contact with LYS 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 4.3 20.1 - - + +
36S LEU* 3.4 21.4 - - + +
37S THR* 4.2 37.5 - - - +
44S ALA* 3.9 14.6 + - + +
47S VAL* 1.3 79.9 - - - +
49S LYS* 1.3 60.0 + - + +
51S LEU* 3.8 4.4 + - - +
52S GLU* 3.0 45.6 + - + +
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Residues in contact with LYS 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B G 3.2 41.8 + - - +
489B G 4.0 15.3 + - - -
491B G 3.7 14.8 - - - +
492B A 4.5 6.3 - - + +
46S LEU* 3.1 46.6 - - + +
47S VAL 2.9 0.4 - - - +
48S LYS* 1.3 80.4 - - + +
50S VAL* 1.3 61.2 + - - +
51S LEU 3.1 1.3 - - - -
52S GLU* 2.9 36.2 + - - +
53S SER* 2.9 14.8 + - - -
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Residues in contact with VAL 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B G 6.3 0.7 - - - +
5S ALA* 3.2 17.9 - - + +
6S LYS 4.2 3.6 - - - +
7S HIS* 3.9 27.8 - - + +
46S LEU* 2.7 35.2 + - + +
47S VAL* 3.0 24.0 - - + +
49S LYS* 1.3 73.3 - - + +
51S LEU* 1.3 51.8 + - + +
53S SER* 3.0 7.4 + - - -
54S ALA* 2.4 37.6 + - - +
103S ILE* 3.8 13.7 - - + -
105S VAL* 3.3 26.0 - - + -
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Residues in contact with LEU 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S ILE 6.0 0.2 - - - +
29S VAL* 4.6 0.7 - - + +
32S ALA* 3.5 25.6 - - + -
33S LEU* 3.4 34.5 - - + +
36S LEU* 4.4 14.1 - - + -
47S VAL* 3.0 15.7 + - + +
48S LYS* 3.9 5.8 - - - +
50S VAL* 1.3 77.7 - - + +
52S GLU* 1.3 57.5 + - - +
54S ALA* 3.6 1.9 - - + -
55S ILE* 2.8 38.1 + - + +
71S VAL* 3.6 27.6 - - + -
105S VAL* 4.1 18.8 - - + -
107S VAL* 4.2 9.2 - - + -
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Residues in contact with GLU 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3959 LYS* 5.8 1.6 + - - -
487B C 3.6 16.5 + - - +
488B G 4.4 13.0 + - - +
33S LEU* 4.7 12.6 - - + -
48S LYS* 3.0 31.9 + - + +
49S LYS* 2.9 41.4 + - - +
51S LEU* 1.3 80.5 - - - +
53S SER* 1.3 53.9 - - - +
55S ILE* 3.7 7.8 - - - +
56S ALA* 2.9 28.8 + - - +
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Residues in contact with SER 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B C 2.6 30.6 + - - +
493B G 3.2 14.3 + - - -
494B G 5.6 4.3 - - - -
5S ALA* 4.1 9.6 - - - -
49S LYS 2.9 11.4 + - - -
50S VAL* 3.4 9.8 - - - -
52S GLU* 1.3 74.2 - - - +
54S ALA* 1.3 56.4 + - - +
55S ILE 2.9 5.1 + - - -
56S ALA* 4.0 5.6 - - - -
57S ASN* 2.8 45.8 + - - +
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Residues in contact with ALA 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S THR* 2.5 39.0 + - + -
5S ALA* 3.4 17.0 - - + +
50S VAL 2.4 21.6 + - - +
51S LEU* 3.8 9.2 - - + +
53S SER* 1.3 72.4 - - - +
55S ILE* 1.3 56.9 + - - +
57S ASN* 4.7 0.4 - - - -
58S ALA* 3.6 2.1 - - - +
105S VAL* 4.0 11.0 - - + +
107S VAL* 3.0 31.0 - - + +
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Residues in contact with ILE 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S VAL* 3.3 34.1 - - + -
33S LEU* 5.5 3.4 - - + -
51S LEU* 2.8 21.0 + - + +
52S GLU* 3.7 10.5 - - - +
54S ALA* 1.3 79.0 - - - +
56S ALA* 1.3 69.0 + - - +
57S ASN 3.3 0.4 - - - -
58S ALA* 3.4 5.5 + - - +
59S GLU* 3.1 25.2 + - + +
65S ASP 5.3 2.9 - - - +
69S LEU* 3.9 27.4 - - + -
107S VAL* 4.3 14.1 - - + -
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Residues in contact with ALA 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B C 4.5 3.4 - - - +
487B C 3.0 40.4 - - - +
52S GLU 2.9 19.7 + - - +
53S SER 3.6 3.1 - - - +
55S ILE* 1.3 78.2 - - + +
57S ASN* 1.3 58.8 + - - +
59S GLU* 2.9 14.7 + - - +
60S HIS* 2.7 37.7 + - - +
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Residues in contact with ASN 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B C 4.2 7.3 + - - -
487B C 5.5 1.2 + - - -
494B G 3.4 25.6 + - - +
495B G 2.9 42.0 + - - +
3S THR* 2.9 30.7 + - - +
4S ILE 3.7 2.9 - - - +
5S ALA* 5.0 0.2 - - - +
53S SER* 2.8 29.2 + - - +
56S ALA* 1.3 69.9 - - - +
58S ALA* 1.3 49.8 + - - +
59S GLU 2.7 15.2 + - - -
60S HIS* 5.0 1.3 - - - -
61S ASN* 2.5 37.1 + - - +
62S ASP* 5.0 0.2 - - - -
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Residues in contact with ALA 58 (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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2S GLU* 5.7 1.8 - - + -
3S THR* 3.0 23.7 + - - +
54S ALA 3.6 9.4 - - - +
55S ILE* 3.4 7.4 + - - +
56S ALA 3.3 0.2 - - - -
57S ASN* 1.3 73.1 - - - +
59S GLU* 1.3 55.8 + - - +
62S ASP* 2.9 34.3 - - + +
63S GLY 2.9 13.5 - - - +
64S ALA* 3.7 6.7 - - + +
69S LEU* 4.3 23.8 - - + -
107S VAL* 4.5 2.0 - - + -
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Residues in contact with GLU 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3979 SER* 2.9 30.4 + - - -
4009 ARG* 3.9 16.3 + - - +
486B C 5.4 1.3 + - - -
487B C 5.8 0.7 - - - +
55S ILE* 3.1 14.8 + - + +
56S ALA* 2.9 18.1 + - - +
57S ASN 2.7 2.8 + - - -
58S ALA* 1.3 79.5 - - - +
60S HIS* 1.3 69.9 + - - +
62S ASP 2.8 22.0 - - - +
63S GLY 4.1 4.3 - - - -
64S ALA* 5.4 1.8 - - - +
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Residues in contact with HIS 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009 ARG* 2.1 45.4 + - - +
485B C 2.8 37.7 + - - -
486B C 3.0 36.7 + - - +
495B G 3.9 5.5 + - - -
496B G 5.4 3.4 - - - -
56S ALA 2.7 14.7 + - - +
57S ASN* 4.3 1.1 - - - +
59S GLU* 1.3 82.8 - - - +
61S ASN* 1.3 76.9 + - + +
62S ASP 3.7 0.9 + - - -
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Residues in contact with ASN 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B G 3.6 34.2 + - - +
496B G 3.8 27.6 + - - +
3S THR* 5.7 0.7 - - - -
57S ASN* 2.5 34.2 + - - +
60S HIS* 1.3 95.4 + - + +
62S ASP* 1.3 77.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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