Contacts of the helix formed by residues 19 - 35 (chain Y) 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 GLY 19 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17710 U 3.4 18.6 + - - -
18850 A 3.5 14.5 + - - -
18860 A 3.7 6.7 - - - -
17Y ARG 3.2 6.9 + - - -
18Y TYR* 1.3 81.1 - - - +
20Y LEU* 1.3 63.9 + - - -
21Y LYS 3.7 1.1 - - - -
22Y ILE 4.4 0.4 - - - -
23Y ARG* 3.0 33.5 + - - +
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Residues in contact with LEU 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17710 U 3.4 34.8 + - - +
17720 C 3.3 32.1 - - - +
18860 A 3.0 24.3 + - - +
18870 U 4.1 20.9 - - - +
19Y GLY* 1.3 67.6 - - - +
21Y LYS* 1.3 58.2 + - + +
23Y ARG* 3.3 5.8 + - - +
24Y VAL* 2.7 50.5 + - + +
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Residues in contact with LYS 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18860 A 3.8 13.6 + - - +
18870 U 2.8 40.7 + - - +
18880 C 5.2 4.8 + - - -
19Y GLY 3.7 0.2 - - - -
20Y LEU* 1.3 77.4 - - + +
22Y ILE* 1.3 66.6 + - + +
24Y VAL* 4.4 4.7 - - - -
25Y ARG* 3.0 59.4 + - - +
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Residues in contact with ILE 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18290 A 6.2 0.4 - - - +
18470 A 3.1 33.9 - - + +
18480 G 4.1 11.7 - - - +
18850 A 3.5 24.5 - - - +
18860 A 5.4 4.4 - - - -
168A PRO* 3.8 22.8 - - + +
170A VAL* 3.4 39.0 - - + +
18Y TYR* 3.6 24.0 + - + +
19Y GLY 3.9 0.8 + - - -
20Y LEU 3.4 0.8 - - - -
21Y LYS* 1.3 81.0 - - + +
23Y ARG* 1.3 62.1 + - + +
26Y VAL* 3.1 28.1 + - + +
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Residues in contact with ARG 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17710 U 2.6 52.1 + - - +
17720 C 3.4 12.2 + - - +
17730 G 3.3 12.1 + - - -
11Y THR* 2.6 53.7 + - + +
14Y PHE* 3.9 13.2 - - + -
15Y GLY 3.3 17.0 + - - -
16Y PRO 3.5 12.7 + - - -
17Y ARG 2.9 26.9 + - - +
19Y GLY* 3.0 24.1 + - - +
20Y LEU* 3.3 5.3 + - - +
22Y ILE* 1.3 79.0 - - + +
24Y VAL* 1.3 68.1 + - + +
25Y ARG 3.2 1.6 - - - -
26Y VAL* 4.2 2.9 - - - -
27Y ALA* 3.1 12.8 + - - +
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Residues in contact with VAL 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17720 C 5.5 3.6 - - - +
11Y THR* 5.7 0.4 - - - -
20Y LEU* 2.7 40.7 + - + +
21Y LYS* 3.9 4.9 - - - +
23Y ARG* 1.3 75.2 - - + +
25Y ARG* 1.3 63.2 + - + +
27Y ALA* 3.5 4.5 + - - +
28Y ASP* 3.0 42.7 + - - +
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Residues in contact with ARG 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18490 G 4.9 9.9 + - - -
166A ASP 4.9 9.6 + - - +
168A PRO* 4.3 21.0 - - + +
21Y LYS* 3.0 49.6 + - - +
22Y ILE* 4.0 3.8 - - - +
24Y VAL* 1.3 81.5 - - + +
26Y VAL* 1.3 59.0 + - - +
28Y ASP* 4.2 8.1 - - - +
29Y VAL* 2.9 41.4 + - + +
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Residues in contact with VAL 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LYS* 4.2 19.5 - - + +
168A PRO* 4.3 6.5 - - + -
170A VAL* 3.7 26.9 - - + -
11Y THR* 3.7 15.3 - - - +
13Y ARG* 3.8 6.1 - - - +
14Y PHE* 3.8 22.0 - - + -
22Y ILE 3.1 18.1 + - - +
24Y VAL 3.4 0.2 - - - -
25Y ARG* 1.3 75.7 - - - +
27Y ALA* 1.3 57.7 + - - +
29Y VAL* 4.7 0.4 - - - -
30Y GLU* 2.9 62.2 + - + +
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Residues in contact with ALA 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y ARG* 4.2 33.2 - - + +
11Y THR* 4.0 14.5 + - - +
23Y ARG 3.1 17.5 + - - +
24Y VAL* 3.7 6.1 - - - +
26Y VAL* 1.3 75.7 - - - +
28Y ASP* 1.3 58.5 + - - +
30Y GLU* 4.7 2.2 - - - -
31Y ILE* 2.7 38.6 + - - +
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Residues in contact with ASP 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y VAL* 3.0 35.8 + - - +
25Y ARG* 3.7 9.5 - - + +
27Y ALA* 1.3 78.4 - - - +
29Y VAL* 1.3 63.8 + - + +
31Y ILE* 2.9 27.1 - - - +
32Y LYS* 3.3 9.7 + - - +
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Residues in contact with VAL 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 4.7 21.1 - - + +
167A LYS* 4.4 18.4 - - + -
25Y ARG* 2.9 29.0 + - + +
26Y VAL* 4.1 3.4 - - - +
28Y ASP* 1.3 74.6 - - + +
30Y GLU* 1.3 61.5 + - + +
32Y LYS* 3.4 5.9 + - - +
33Y HIS* 2.9 26.9 + - - +
69Y TYR* 3.5 44.1 - - + +
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Residues in contact with GLU 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16510 C 3.8 11.2 + - - -
167A LYS* 2.7 35.3 + - - +
10Y ARG* 4.7 7.9 - - - -
13Y ARG* 3.1 31.0 + - - -
26Y VAL* 2.9 33.0 + - - +
27Y ALA* 4.2 2.5 - - - +
29Y VAL* 1.3 75.3 - - + +
31Y ILE* 1.3 59.4 + - - +
33Y HIS* 3.0 15.6 - - + +
34Y LYS* 2.8 63.7 + - - +
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Residues in contact with ILE 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7980 G 5.1 12.6 - - - +
10Y ARG* 6.5 0.7 - - + -
27Y ALA 2.7 20.9 + - - +
28Y ASP* 2.9 30.5 - - - +
30Y GLU* 1.3 73.6 - - - +
32Y LYS* 1.3 71.6 + - + +
34Y LYS* 3.2 8.1 + - - +
35Y LYS* 3.0 36.3 + - + +
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Residues in contact with LYS 32 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Y ASP 3.3 8.5 + - - +
29Y VAL* 3.6 9.0 - - - +
31Y ILE* 1.3 82.1 - - + +
33Y HIS* 1.3 62.5 + - - +
35Y LYS* 3.1 38.4 + - - +
37Y HIS* 3.0 30.8 - - - -
69Y TYR 4.5 2.2 - - - +
70Y GLN* 2.8 49.8 + - + +
71Y PRO* 5.9 0.4 - - - +
72Y GLU 5.1 1.6 + - - -
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Residues in contact with HIS 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16510 C 4.1 13.1 + - - -
16520 C 5.1 0.2 + - - -
167A LYS* 5.4 0.6 + - - -
29Y VAL 2.9 20.1 + - - +
30Y GLU* 3.0 29.6 - - + +
32Y LYS* 1.3 75.8 - - - +
34Y LYS* 1.3 61.4 + - + -
37Y HIS* 3.0 20.2 + - - -
49Y ARG* 3.0 64.5 + - + +
55Y TRP* 3.7 8.7 - - - -
69Y TYR* 3.2 41.7 + + + +
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Residues in contact with LYS 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7970 A 3.2 31.3 + - - +
7980 G 5.1 14.4 - - - +
16500 C 5.2 13.2 - - - +
10Y ARG* 4.2 11.1 - - - +
13Y ARG* 6.1 0.2 - - - +
30Y GLU* 2.8 55.1 + - - +
31Y ILE* 3.2 5.8 + - - +
33Y HIS* 1.3 80.3 - - + +
35Y LYS* 1.3 66.6 + - - +
36Y LYS* 3.8 0.9 + - - +
48Y LYS* 5.4 7.8 - - - -
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Residues in contact with LYS 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Y ILE* 3.0 28.3 + - + +
32Y LYS* 3.1 46.9 + - + +
34Y LYS* 1.3 81.3 - - - +
36Y LYS* 1.3 65.4 + - - +
37Y HIS* 3.0 28.9 + - + -
47Y LEU 4.4 1.9 - - - +
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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