Contacts of the helix formed by residues 11 - 27 (chain A) in PDB entry 2JBG
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 THR 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 1.3 76.8 - - - +
12A GLU* 1.3 66.7 + - - +
13A ALA* 3.5 8.5 + - - +
14A GLU* 3.0 38.7 + - - +
15A PHE* 3.0 19.9 + - - +
84A PHE* 4.2 1.6 - - - -
85A LYS* 3.6 39.3 - - + +
86A GLN 4.4 6.1 - - - +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 1.3 73.6 - - - +
13A ALA* 1.3 62.7 + - - +
15A PHE* 3.2 4.9 + - - +
16A VAL* 3.1 27.5 + - - +
69A VAL* 3.4 17.8 - - + +
73A LYS* 2.7 38.7 + - - +
84A PHE* 3.7 31.2 - - + +
85A LYS 4.6 1.6 + - - +
505D LYS* 4.8 4.6 + - - +
522D LYS* 2.7 39.7 + - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A THR* 3.2 8.4 + - - +
12A GLU* 1.3 79.8 - - - +
14A GLU* 1.3 63.0 + - + +
16A VAL* 3.3 7.8 + - - +
17A GLN* 3.3 26.4 + - - +
501D GLU* 4.7 8.1 - - - +
522D LYS 4.1 8.2 + - - +
523D VAL* 4.0 35.0 - - + +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 6.1 0.5 - - - +
4A LYS* 3.3 16.0 + - - -
9A ASP 3.3 16.6 - - - +
10A TYR* 3.4 14.1 - - + -
11A THR* 3.0 43.9 + - - +
13A ALA* 1.3 74.4 - - + +
15A PHE* 1.3 64.8 - - - +
17A GLN* 3.2 28.1 + - - +
18A LEU* 3.2 11.8 + - - +
85A LYS* 3.7 8.8 + - - -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.4 22.2 - - + -
10A TYR* 4.0 18.8 - + + -
11A THR 3.0 7.8 + - - +
12A GLU 3.6 7.6 - - - +
14A GLU* 1.3 76.9 - - - +
16A VAL* 1.3 62.8 + - - +
18A LEU* 3.1 14.3 + - + +
19A LEU* 2.9 32.8 + - + +
41A PHE* 3.6 31.2 - + - -
44A ILE* 3.8 16.2 - - + -
45A THR* 3.6 11.9 - - + -
69A VAL* 3.8 18.2 - - + -
72A ILE* 3.5 19.5 - - + -
84A PHE* 3.5 30.3 - + + -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.1 14.6 + - - +
13A ALA* 3.5 10.1 - - - +
14A GLU 3.2 0.2 - - - -
15A PHE* 1.3 77.6 - - - +
17A GLN* 1.3 57.6 + - - +
19A LEU* 3.1 10.0 + - - +
20A LYS* 2.9 28.4 + - + +
65A PRO* 4.2 23.8 - - + +
66A GLU* 4.9 3.8 - - - +
69A VAL* 3.8 19.1 - - + -
27C VAL* 4.0 25.8 - - + -
519D ASP* 5.0 1.8 - - - +
522D LYS* 3.8 26.2 - - + -
523D VAL* 4.6 4.9 - - + -
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.4 11.0 - - + +
13A ALA* 3.3 10.5 + - - +
14A GLU* 3.2 30.8 + - - +
16A VAL* 1.3 77.0 - - - +
18A LEU* 1.3 59.5 + - - +
20A LYS* 3.2 3.1 + - - +
21A GLU* 2.9 27.4 + - - +
24C LYS* 5.7 1.7 - - - +
27C VAL* 3.4 41.8 + - + +
28C ALA* 3.8 13.9 - - - +
29C ALA* 4.2 6.3 - - - +
523D VAL* 5.5 0.2 - - - -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.8 32.6 - - + -
3A LEU* 4.0 11.2 - - + -
10A TYR* 4.1 23.1 - - + +
14A GLU 3.2 8.2 + - - +
15A PHE* 3.1 36.4 + - + +
17A GLN* 1.3 81.0 - - - +
19A LEU* 1.3 57.3 + - + +
21A GLU* 3.0 3.1 + - + +
22A ILE* 2.9 50.2 + - + +
37A LEU* 4.9 7.9 - - + +
40A HIS* 4.5 5.8 - - - +
41A PHE* 5.0 6.5 - - + -
44A ILE* 4.3 9.2 - - + -
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 2.9 29.3 + - + +
16A VAL* 3.1 8.7 + - - +
18A LEU* 1.3 77.8 - - + +
20A LYS* 1.3 58.0 + - - +
22A ILE* 3.3 10.3 + - + +
23A GLU* 2.9 33.0 + - + +
41A PHE* 3.9 30.5 - - + -
54A ILE* 4.2 17.0 - - + -
65A PRO* 3.8 35.0 - - + +
68A ILE* 3.8 30.3 - - + -
69A VAL* 4.2 3.6 - - + -
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Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 2.9 15.5 + - + +
17A GLN 3.5 8.1 - - - +
19A LEU* 1.3 73.6 - - - +
21A GLU* 1.3 67.2 + - - +
23A GLU* 3.0 31.0 + - - +
24A LYS* 3.0 22.5 + - - +
65A PRO* 3.7 14.0 - - + +
20C LYS 5.2 1.3 - - - +
23C GLU* 2.9 57.5 + - + +
24C LYS* 3.8 17.9 - - + +
27C VAL* 3.9 18.4 - - + -
519D ASP* 2.9 27.2 + - - +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.8 35.5 + - + +
17A GLN 2.9 13.8 + - - +
18A LEU* 3.4 8.5 - - + +
20A LYS* 1.3 76.8 - - - +
22A ILE* 1.3 63.1 + - - +
24A LYS* 3.3 11.1 + - - +
25A GLU* 3.2 40.4 + - - +
33A VAL* 5.3 1.6 - - - +
37A LEU* 3.7 18.4 - - + +
24C LYS* 3.2 38.8 + - + +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 2.9 31.0 + - + +
19A LEU* 3.3 18.2 - - + +
21A GLU* 1.3 78.8 - - - +
23A GLU* 1.3 56.8 + - - +
25A GLU 3.4 0.9 + - - -
26A ASN* 2.9 25.8 + - - +
34A LEU* 3.4 11.1 - - + +
37A LEU* 3.9 30.5 - - + +
38A LEU* 3.8 22.9 - - + -
41A PHE* 4.0 26.7 - - + -
54A ILE* 4.2 22.9 - - + -
55A TYR* 4.4 4.7 - - - +
516B ASN* 5.0 3.1 - - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 2.9 18.6 + - - +
20A LYS* 3.0 41.9 + - + +
21A GLU 3.3 0.4 - - - -
22A ILE* 1.3 74.1 - - - +
24A LYS* 1.3 65.8 + - - +
26A ASN* 3.0 22.0 + - - +
27A VAL* 3.4 9.5 + - - +
65A PRO* 3.5 17.3 - - - +
516B ASN* 3.3 30.1 - - - +
519B ASP* 4.6 1.7 - - - +
20C LYS* 2.8 42.6 + - - +
23C GLU* 3.5 0.5 - - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS 3.0 13.2 + - - +
21A GLU* 3.6 17.1 + - - +
23A GLU* 1.3 76.2 - - - +
25A GLU* 1.3 78.9 + - - +
27A VAL* 3.0 22.9 + - + +
28A ALA* 3.5 6.1 + - - +
1C MET* 5.8 6.3 - - - +
17C GLN 5.8 1.6 - - - +
20C LYS* 4.1 22.4 + - + +
21C GLU* 2.9 38.6 - - + +
24C LYS* 3.9 26.3 - - + +
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 3.2 25.7 + - - +
22A ILE 4.0 2.2 - - - +
24A LYS* 1.3 97.2 + - - +
26A ASN* 1.3 60.2 + - - +
27A VAL 3.0 2.7 - - - -
28A ALA* 3.0 38.9 + - - +
30A THR 3.9 4.7 - - - +
33A VAL* 3.5 40.9 + - + +
34A LEU* 3.7 24.4 + - + +
37A LEU* 3.9 5.2 - - + -
525B LYS* 3.3 10.2 + - - -
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE 2.9 14.5 + - - +
23A GLU* 3.0 18.4 - - - +
25A GLU* 1.3 78.2 - - - +
27A VAL* 1.3 56.9 + - + +
34A LEU* 3.5 7.1 - - - +
55A TYR* 2.6 29.5 + - - -
516B ASN* 2.8 42.8 + - - +
519B ASP* 4.5 3.2 - - + +
520B ARG* 3.3 38.6 - - - +
525B LYS* 3.1 20.3 + - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 3.8 4.3 - - - +
24A LYS* 3.0 17.7 - - + +
26A ASN* 1.3 78.1 - - - +
28A ALA* 1.3 61.6 + - - +
519B ASP* 3.6 38.8 - - + +
523B VAL* 3.5 23.8 - - + +
16C VAL* 3.9 10.5 - - + -
17C GLN* 3.2 32.9 + - + +
20C LYS* 3.3 37.7 - - + -
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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