Contacts of the helix formed by residues 16 - 34 (chain A) in PDB entry 2J3R
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 SER 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A MET 3.9 0.2 + - - -
15A SER* 1.3 74.6 + - - +
17A GLU* 1.3 68.4 + - - +
19A PHE* 2.9 18.1 + - - +
20A THR* 2.9 21.2 + - - +
114A ASP* 4.9 9.0 - - - -
22B THR* 3.0 45.7 + - - +
24B VAL* 3.8 17.5 - - - +
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Residues in contact with GLU 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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15A SER* 3.3 16.6 - - - +
16A SER* 1.3 77.9 - - - +
18A LEU* 1.3 59.3 + - - +
20A THR* 3.0 7.4 - - - +
21A LEU* 2.8 36.1 + - - +
114A ASP* 3.8 11.3 - - - +
115A PHE* 2.9 30.2 - - + -
65B LEU* 4.9 6.9 - - + +
72B ARG* 3.2 30.7 + - - +
96B ALA* 3.5 26.7 - - + +
97B LEU* 5.3 2.0 - - + -
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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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14A MET* 3.6 11.7 - - + -
15A SER* 4.0 2.4 + - - +
16A SER 3.1 2.2 + - - -
17A GLU* 1.3 77.3 - - - +
19A PHE* 1.3 54.1 + - - +
21A LEU* 4.1 6.5 - - + -
22A THR* 2.7 51.6 + - - +
29B PHE* 3.5 33.2 - - + -
96B ALA 4.5 1.2 + - - -
97B LEU* 3.4 51.8 + - + +
98B PHE* 3.9 16.2 - - + -
127B TYR* 3.8 21.3 - - + +
142B PHE* 4.9 6.3 - - + -
146B ILE* 5.4 0.9 - - + -
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Residues in contact with PHE 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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14A MET* 3.6 17.6 - - + +
16A SER* 2.9 11.2 + - - +
18A LEU* 1.3 79.3 - - - +
20A THR* 1.3 61.5 + - - +
22A THR* 3.8 0.9 - - - -
23A TYR* 3.0 32.0 + + + +
87A LEU* 4.5 11.4 - - + -
111A PRO 4.9 4.7 - - - -
112A LEU* 3.6 33.2 - - + -
130A LEU* 6.3 1.3 - - + -
1068A PLM 3.9 17.5 - - + -
24B VAL* 4.4 18.4 - - + -
28B ALA* 3.3 35.9 - - + -
29B PHE* 3.5 26.0 - - + -
32B LEU* 4.0 18.6 - - + -
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Residues in contact with THR 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 SER* 2.9 15.9 + - - +
17A GLU* 3.0 15.5 - - - +
19A PHE* 1.3 84.6 - - - +
21A LEU* 1.3 60.4 + - - +
23A TYR* 3.5 4.3 + - - +
24A GLY* 3.0 24.9 + - - -
111A PRO 5.4 1.6 - - - -
112A LEU 3.2 24.9 + - - +
113A VAL* 3.8 0.2 - - - -
114A ASP* 2.6 56.1 + - - +
115A PHE* 4.1 3.4 - - + -
116A VAL* 4.6 5.2 - - - +
127A TYR* 4.9 0.9 + - - -
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Residues in contact with LEU 21 (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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17A GLU 2.8 22.2 + - - +
18A LEU* 3.5 7.0 - - + +
20A THR* 1.3 76.0 - - - +
22A THR* 1.3 69.6 + - - +
24A GLY* 3.1 4.0 + - - -
25A ALA* 3.0 20.4 + - - +
115A PHE* 4.0 16.2 - - + -
116A VAL* 3.5 25.8 - - + -
61B VAL* 3.5 35.4 - - + +
65B LEU* 4.6 10.5 - - + -
97B LEU* 4.0 18.2 - - + -
142B PHE* 4.7 1.1 - - + -
146B ILE* 3.7 30.7 - - + -
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Residues in contact with THR 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* 2.7 32.7 + - - +
19A PHE 3.8 3.6 - - - -
21A LEU* 1.3 73.2 - - - +
23A TYR* 1.3 59.1 + - - +
25A ALA* 2.9 23.2 + - - +
26A LEU 3.1 5.7 + - - -
29B PHE* 3.1 32.1 - - + -
32B LEU* 3.8 9.4 - - + -
33B PHE* 4.5 5.8 - - + -
36B MET* 3.4 30.1 - - + +
142B PHE* 3.6 22.5 - - + -
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Residues in contact with TYR 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 PHE* 3.0 23.0 + + + +
20A THR* 3.8 6.1 - - - +
22A THR* 1.3 76.7 - - - +
24A GLY* 1.3 61.1 + - - +
26A LEU* 3.4 8.9 + - + +
27A VAL* 3.1 47.8 + - + +
44A LEU* 3.7 11.6 - - + +
112A LEU* 3.6 47.6 - - + +
127A TYR* 2.5 39.8 + + - -
128A SER* 3.5 6.9 - - - -
130A LEU* 3.8 30.1 - - + +
32B LEU* 3.6 27.3 - - + +
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Residues in contact with GLY 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 THR 3.0 13.9 + - - -
21A LEU 3.1 5.8 + - - -
23A TYR* 1.3 74.2 - - - +
25A ALA* 1.3 60.2 + - - +
27A VAL* 3.9 1.7 - - - +
28A THR* 2.8 35.7 + - - -
116A VAL* 3.7 10.5 - - - -
118A LEU* 4.8 0.2 - - - +
127A TYR* 3.5 22.9 - - - -
61B VAL* 3.9 4.9 - - - -
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Residues in contact with ALA 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 LEU 3.0 10.8 + - - +
22A THR 2.9 11.1 + - - +
24A GLY* 1.3 75.2 - - - +
26A LEU* 1.3 66.6 + - - +
28A THR* 3.3 3.4 + - - -
29A GLN* 2.9 26.6 + - - +
36B MET* 4.3 1.1 - - + -
57B MET* 3.4 28.3 - - + +
61B VAL* 3.6 14.1 - - + +
142B PHE* 3.8 22.4 - - + -
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Residues in contact with LEU 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 THR 3.1 3.4 + - - +
23A TYR* 3.6 12.8 - - + +
25A ALA* 1.3 79.9 - - - +
27A VAL* 1.3 58.0 + - - +
29A GLN* 3.1 2.4 + - - +
30A LEU* 2.8 60.1 + - + +
44A LEU* 4.3 7.9 - - + -
47A MET* 3.9 30.7 - - + -
130A LEU* 4.3 15.5 - - + -
32B LEU* 3.9 23.1 - - + -
36B MET* 3.3 21.7 - - + +
39B TYR* 4.7 1.1 - - + -
57B MET* 3.8 20.0 - - + -
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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
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23A TYR* 3.1 55.3 + - + +
24A GLY 4.0 3.6 - - - +
26A LEU* 1.3 77.9 - - - +
28A THR* 1.3 61.3 + - - +
30A LEU* 3.5 7.6 + - - +
31A CYS* 3.2 25.3 + - - -
40A VAL* 5.1 1.3 - - + +
44A LEU* 4.4 10.1 - - + -
118A LEU* 3.5 24.2 - - + -
125A LEU* 4.4 14.1 - - + -
127A TYR* 3.6 22.9 - - + +
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Residues in contact with THR 28 (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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24A GLY 2.8 22.3 + - - -
25A ALA* 3.6 6.3 - - - -
27A VAL* 1.3 76.7 - - - +
29A GLN* 1.3 61.3 + - + +
31A CYS* 3.6 11.6 - - - +
32A LYS* 3.4 37.6 - - - +
116A VAL* 4.8 2.1 - - - +
117A GLU 5.6 0.5 + - - -
118A LEU* 3.8 23.9 - - + +
119A PRO* 6.4 1.6 - - + -
60B GLY* 4.8 17.0 - - - +
61B VAL* 4.4 6.5 - - - +
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Residues in contact with GLN 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA 2.9 13.9 + - - +
26A LEU 3.6 3.1 - - - +
28A THR* 1.3 74.3 - - + +
30A LEU* 1.3 60.6 + - - +
31A CYS 3.0 2.0 - - - -
32A LYS* 2.8 43.9 + - - +
33A ASP* 2.7 49.8 + - - +
53B ARG* 4.2 9.4 + - - +
56B ASP* 4.2 23.3 + - - +
57B MET* 3.2 46.0 - - + -
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Residues in contact with LEU 30 (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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26A LEU* 2.8 39.2 + - + +
27A VAL 3.9 4.9 - - - +
29A GLN* 1.3 72.5 - - + +
31A CYS* 1.3 57.0 + - - +
32A LYS 3.1 0.2 - - - -
33A ASP* 3.8 2.5 - - - -
34A TYR* 3.0 47.0 + - + +
40A VAL* 3.7 16.2 - - + +
43A GLN* 4.3 10.3 - - + -
44A LEU* 3.2 38.4 - - + -
47A MET* 4.3 7.4 - - - -
39B TYR* 3.5 42.6 - - + +
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Residues in contact with CYS 31 (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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27A VAL* 3.2 26.0 + - - +
28A THR* 3.6 9.6 - - - +
29A GLN 3.0 0.4 - - - -
30A LEU* 1.3 77.5 - - - +
32A LYS* 1.3 59.1 + - + +
34A TYR 3.0 17.5 - - - +
35A GLU* 5.1 0.7 - - - -
37A ASP* 4.6 3.1 - - - -
40A VAL* 4.4 12.8 - - - -
118A LEU* 4.1 14.8 - - - -
122A HIS* 3.8 37.4 - - + +
125A LEU* 4.4 10.5 - - - -
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Residues in contact with LYS 32 (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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28A THR* 3.4 36.0 - - - +
29A GLN* 2.8 35.0 + - - +
31A CYS* 1.3 80.9 - - + +
33A ASP* 1.3 62.0 + - - +
34A TYR 3.1 7.8 + - - -
35A GLU* 5.6 0.2 - - - -
56B ASP 5.7 1.2 + - - -
60B GLY* 4.8 12.7 - - - -
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Residues in contact with ASP 33 (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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29A GLN* 2.7 40.5 + - - +
30A LEU* 3.8 0.9 - - - -
32A LYS* 1.3 78.5 - - - +
34A TYR* 1.3 69.7 + - + +
35A GLU 4.3 0.2 - - - -
39B TYR* 2.6 38.4 + - - +
43B ARG* 3.2 27.1 + - - +
53B ARG* 3.7 16.1 + - - -
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Residues in contact with TYR 34 (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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30A LEU* 3.0 39.0 + - + +
31A CYS* 3.0 22.5 - - - +
32A LYS 4.5 2.9 - - - -
33A ASP* 1.3 88.4 - - + +
35A GLU* 1.3 64.0 + - - +
36A ASN 3.4 7.5 + - - +
39A ASP* 4.0 27.6 - - + -
40A VAL* 3.8 19.4 - - + +
43A GLN* 3.4 35.8 + - + -
39B TYR* 3.6 25.4 - - - -
43B ARG* 4.3 7.0 + - - -
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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