Contacts of the helix formed by residues 17 - 32 (chain L) in PDB entry 1JJ2
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 GLU 17 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14L ARG* 3.0 47.3 + - + +
16L LYS* 1.3 98.4 - - + +
18L GLY* 1.3 71.0 + - - +
20L ILE* 3.2 21.8 - - - +
21L ALA* 3.2 2.4 + - - -
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Residues in contact with GLY 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L GLU* 1.3 80.9 - - - +
19L GLN* 1.3 63.7 + - - +
21L ALA* 3.2 12.3 + - - +
22L GLU* 3.6 4.9 + - - +
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Residues in contact with GLN 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F VAL* 3.2 34.3 + - + +
3F TYR* 3.5 15.7 - - - +
61F MET* 3.2 47.6 + - + +
64F PRO* 6.2 1.0 - - - +
17L GLU 3.7 0.2 + - - -
18L GLY* 1.3 69.5 - - - -
20L ILE* 1.3 66.5 + - - +
22L GLU* 3.0 19.6 + - - +
23L LEU* 3.0 15.3 + - - +
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Residues in contact with ILE 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F GLU* 4.2 10.1 - - + +
61F MET* 4.2 13.4 - - + +
11L ALA* 3.8 15.9 - - + +
12L TRP* 3.2 56.1 - - + +
14L ARG 3.8 15.3 - - - +
15L PRO* 3.8 13.5 - - + -
17L GLU 3.2 13.7 - - - +
19L GLN* 1.3 79.0 - - - +
21L ALA* 1.3 68.1 + - - +
23L LEU* 3.1 11.6 + - + -
24L MET* 2.9 33.1 + - + +
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Residues in contact with ALA 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PRO 3.5 11.2 - - - -
16L LYS* 3.4 25.4 - - - +
17L GLU 3.2 11.2 + - - +
18L GLY 3.3 12.3 - - - +
19L GLN 3.1 0.4 - - - -
20L ILE* 1.3 83.5 - - - +
22L GLU* 1.3 61.1 + - - +
24L MET* 3.5 3.7 + - - +
25L TRP* 3.1 21.3 + - - +
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Residues in contact with GLU 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F VAL* 4.3 20.1 - - + +
18L GLY 3.6 4.1 + - - +
19L GLN* 3.0 12.1 + - - +
21L ALA* 1.3 77.1 - - - +
23L LEU* 1.3 66.2 + - - +
25L TRP* 3.4 8.7 + - + +
26L HIS* 3.0 45.7 + - + +
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Residues in contact with LEU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F VAL* 3.4 31.4 - - + -
57F GLU* 3.4 30.7 - - + +
58F GLU* 3.7 27.6 - - - +
61F MET* 3.7 24.0 - - - -
19L GLN 3.0 16.2 + - - +
20L ILE* 3.1 9.6 + - - +
22L GLU* 1.3 75.3 - - - +
24L MET* 1.3 53.8 + - - +
26L HIS* 2.8 12.7 + - + +
27L ARG* 2.6 56.8 + - + +
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Residues in contact with MET 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L TRP* 3.7 21.8 - - + -
15L PRO* 4.2 14.6 - - + +
20L ILE* 2.9 29.5 + - + +
21L ALA* 3.6 6.3 - - - +
23L LEU* 1.3 77.7 - - - +
25L TRP* 1.3 62.4 + - - +
27L ARG* 3.9 17.9 - - - -
28L MET* 2.9 63.8 + - + +
31L TRP* 4.2 11.0 - - + -
120L VAL 3.0 28.0 - - - +
121L GLY* 3.8 6.7 - - - -
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Residues in contact with TRP 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21330 U 3.9 29.2 + - - +
21340 G 6.0 0.4 + - - -
22430 C 3.7 41.5 + + - -
22440 A 3.3 46.3 + - - -
22580 A 5.6 0.8 + - - -
21L ALA 3.1 12.1 + - - +
22L GLU* 3.6 13.0 - - + +
24L MET* 1.3 78.7 - - - +
26L HIS* 1.3 89.7 + + - +
28L MET* 4.8 4.3 - - - +
29L GLN* 3.0 41.1 + - - +
32L ARG* 5.1 2.7 + - - +
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Residues in contact with HIS 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F PRO* 6.3 1.1 - - + -
2F VAL* 4.0 21.7 - - + +
57F GLU* 5.5 1.8 + - - -
22L GLU* 3.0 42.7 + - + +
23L LEU* 2.8 13.1 + - - +
25L TRP* 1.3 100.5 - + - +
27L ARG* 1.3 67.5 + - + +
29L GLN* 3.2 26.7 + - - +
30L GLU* 4.0 10.9 + - - +
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Residues in contact with ARG 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F GLN* 5.3 5.5 - - - +
56F PRO* 3.6 17.2 - - - +
57F GLU* 4.1 3.8 - - - +
58F GLU* 2.2 49.7 + - - -
12L TRP* 4.0 0.6 - - - -
20L ILE* 4.9 0.4 - - - +
23L LEU* 2.6 42.8 + - + +
24L MET* 3.9 23.6 - - - +
26L HIS* 1.3 69.4 - - + +
28L MET* 1.3 67.1 + - - +
29L GLN 3.0 2.2 - - - -
30L GLU* 2.8 25.6 + - - +
31L TRP* 2.9 45.1 + - + +
44L THR* 3.4 18.0 + - - +
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Residues in contact with MET 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21320 C 6.1 0.4 - - - +
21330 U 5.9 2.2 - - - -
24L MET* 2.9 59.2 + - + +
25L TRP* 4.8 2.7 - - - +
27L ARG* 1.3 73.6 - - - +
29L GLN* 1.3 54.8 + - - +
31L TRP* 3.6 16.4 - - + -
32L ARG* 2.7 70.9 + - - +
122L GLU 3.2 35.7 - - - +
123L ASP* 4.0 2.2 - - - -
128L TRP* 3.5 23.6 - - + -
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Residues in contact with GLN 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22440 A 3.5 45.9 + - - +
22450 C 3.7 16.2 + - - +
25L TRP* 3.0 50.4 + - - +
26L HIS* 3.3 11.9 + - - +
27L ARG 3.0 0.2 - - - -
28L MET* 1.3 78.5 - - - +
30L GLU* 1.3 63.1 + - + +
32L ARG* 3.9 4.6 + - - +
33L ASN* 3.1 27.5 + - - -
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Residues in contact with GLU 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L HIS* 4.3 13.1 - - - +
27L ARG* 2.8 13.5 + - - +
29L GLN* 1.3 78.8 - - + +
31L TRP* 1.3 65.0 + - + +
33L ASN* 3.0 17.8 + - - +
34L GLU* 2.9 28.8 + - - +
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Residues in contact with TRP 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L MET* 4.2 13.2 - - + -
27L ARG* 2.9 49.1 + - + +
28L MET* 3.6 16.6 - - + +
30L GLU* 1.3 79.8 - - + +
32L ARG* 1.3 54.2 + - - +
33L ASN 3.0 0.2 - - - -
34L GLU* 2.7 42.3 + - - +
35L PRO 5.1 0.7 - - - +
44L THR* 4.4 10.1 - - + -
64L ARG* 3.1 49.0 - - - +
120L VAL* 3.3 43.7 - - + -
128L TRP* 3.4 49.6 + + + +
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Residues in contact with ARG 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21320 C 4.7 9.6 + - - -
21330 U 4.9 2.6 + - - -
22440 A 3.1 23.8 + - - -
22450 C 2.9 39.4 + - - +
25L TRP* 5.1 2.8 + - - +
28L MET* 2.7 46.7 + - - +
29L GLN* 3.9 16.8 - - - +
31L TRP* 1.3 71.5 - - - +
33L ASN* 1.3 62.4 + - - +
34L GLU 3.3 4.7 + - - +
123L ASP* 3.0 41.8 + - - +
126L HIS* 4.0 19.3 + - + -
128L TRP* 3.9 10.9 - - + -
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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