Contacts of the helix formed by residues 12 - 38 (chain B) in PDB entry 4WOL
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 1.3 79.1 - - - +
13B PRO* 1.3 67.7 - - - +
14B GLY* 3.4 5.5 + - - -
15B VAL* 3.0 28.1 + - - +
16B LEU* 3.0 28.0 + - - +
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Residues in contact with PRO 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 5.8 3.8 - - - +
11B VAL 4.3 2.9 - - - +
12B SER* 1.3 85.4 - - - +
14B GLY* 1.3 60.0 + - - +
15B VAL 3.3 0.2 - - - -
16B LEU* 4.1 4.7 - - + -
17B ALA* 2.8 26.7 + - - +
101B OLC 2.9 31.6 + - - +
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Residues in contact with GLY 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 3.1 6.5 + - - -
13B PRO* 1.3 78.5 - - - +
15B VAL* 1.3 63.8 + - - +
17B ALA* 3.6 6.5 + - - +
18B GLY* 3.3 16.3 + - - -
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Residues in contact with VAL 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.6 25.4 - - + -
12B SER* 3.0 25.6 + - - +
14B GLY* 1.3 75.7 - - - +
16B LEU* 1.3 59.5 + - - +
18B GLY* 3.1 4.4 + - - -
19B ILE* 2.9 32.6 + - + +
16C LEU* 4.0 16.4 - - + -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.9 28.0 - - + +
12B SER 3.0 17.3 + - - +
13B PRO* 4.6 3.1 - - + -
14B GLY 3.3 0.2 - - - -
15B VAL* 1.3 78.6 - - - +
17B ALA* 1.3 56.6 + - - +
19B ILE* 3.6 4.2 - - + +
20B VAL* 2.9 35.9 + - - +
101B OLC 3.5 25.6 - - - +
11C VAL* 5.2 4.7 - - + -
16C LEU* 4.4 17.7 - - + -
101C OLC 3.8 52.7 - - + +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO 2.8 18.3 + - - +
14B GLY* 3.8 7.4 - - - +
16B LEU* 1.3 77.8 - - - +
18B GLY* 1.3 61.7 + - - +
20B VAL* 4.1 3.5 - - - +
21B VAL* 3.1 34.0 + - + +
101B OLC 3.6 13.2 + - - +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY 3.3 7.6 + - - -
15B VAL* 3.1 7.4 + - - -
17B ALA* 1.3 79.3 - - - +
19B ILE* 1.3 53.5 + - - +
21B VAL* 5.0 2.0 - - - -
22B GLY* 2.7 33.6 + - - -
101C OLC 4.7 4.0 - - - +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 2.9 32.2 + - + +
16B LEU* 3.2 9.8 + - + +
18B GLY* 1.3 76.9 - - - +
20B VAL* 1.3 53.0 + - + +
23B ASP* 2.7 33.8 + - - +
16C LEU* 4.2 22.4 - - + -
20C VAL* 4.0 20.4 - - + -
101C OLC 3.3 58.9 - - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 2.9 21.0 + - - +
17B ALA* 4.2 3.6 - - - +
19B ILE* 1.3 75.5 - - - +
21B VAL* 1.3 68.0 + - + +
23B ASP* 3.1 9.6 + - - +
24B LEU* 3.1 30.9 + - + +
101B OLC 3.7 58.8 - - + +
101C OLC 4.2 27.8 - - + -
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Residues in contact with VAL 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 3.1 19.5 + - + +
18B GLY* 4.3 2.0 - - - +
20B VAL* 1.3 79.2 - - + +
22B GLY* 1.3 63.1 + - - +
24B LEU* 3.2 16.3 + - + +
25B VAL* 3.1 34.5 + - + +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLY 2.7 24.3 + - - -
19B ILE 3.7 0.7 - - - -
21B VAL* 1.3 73.8 - - - +
23B ASP* 1.3 57.1 + - - +
25B VAL* 3.3 5.6 + - - +
26B LEU* 2.9 34.3 + - - +
101C OLC 3.9 25.6 - - - +
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Residues in contact with ASP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 2.5 23.6 - - - +
101A K 3.0 20.4 - - - -
19B ILE 2.7 20.8 + - - +
20B VAL* 3.1 6.7 + - - +
22B GLY* 1.3 73.4 - - - +
24B LEU* 1.3 63.6 + - - +
26B LEU* 4.1 1.9 - - - +
27B THR* 2.7 35.0 + - - -
101B OLC 3.7 13.0 - - - +
23C ASP* 3.6 6.9 - - - +
24C LEU* 5.0 2.6 - - - +
101C OLC 3.6 39.3 - - + +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.8 28.9 - - + -
30A ILE* 5.1 1.9 - - + +
20B VAL* 3.1 23.1 + - + +
21B VAL* 3.5 16.4 - - + +
23B ASP* 1.3 83.7 - - - +
25B VAL* 1.3 66.0 + - + +
27B THR* 3.8 4.4 - - - -
28B VAL* 3.2 29.5 + - + +
101B OLC 4.5 13.0 - - + -
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 3.1 28.6 + - + +
22B GLY* 3.8 5.6 - - - +
24B LEU* 1.3 77.1 - - + +
26B LEU* 1.3 62.2 + - + +
28B VAL* 3.2 7.3 + - - +
29B LEU* 3.0 46.5 + - + +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLY 2.9 14.6 + - - +
23B ASP 4.1 1.8 - - - +
25B VAL* 1.3 81.9 - - + +
27B THR* 1.3 58.1 + - - +
29B LEU* 3.8 16.9 - - + +
30B ILE* 2.8 45.8 + - + +
24C LEU* 3.8 33.7 - - + -
101C OLC 3.6 37.9 - - + -
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Residues in contact with THR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 4.2 1.2 + - - +
26A LEU* 6.2 0.7 - - + -
27A THR* 3.5 35.9 - - + +
30A ILE* 3.8 24.2 - - + -
101A K 2.7 19.2 - - - -
23B ASP* 2.7 28.2 + - - -
24B LEU* 3.8 4.5 - - - -
26B LEU* 1.3 74.9 - - - +
28B VAL* 1.3 66.0 + - - +
30B ILE* 3.5 1.0 + - - +
31B ALA* 3.0 25.2 + - + +
24C LEU* 5.5 1.7 - - - +
27C THR* 3.9 12.7 - - + +
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.1 30.3 - - + -
34A VAL* 6.4 0.2 - - + -
24B LEU* 3.2 15.0 + - + +
25B VAL* 3.7 7.6 - - - +
27B THR* 1.3 77.9 - - - +
29B LEU* 1.3 68.0 + - + +
31B ALA* 3.4 1.9 + - - +
32B LEU* 3.1 42.6 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B VAL* 3.0 37.3 + - + +
26B LEU* 3.8 17.5 - - + +
28B VAL* 1.3 82.2 - - + +
30B ILE* 1.3 60.4 + - + +
32B LEU* 3.3 9.2 + - + +
33B ALA* 2.8 32.3 + - - +
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 2.8 33.3 + - + +
27B THR 3.9 2.7 - - - +
29B LEU* 1.3 71.1 - - + +
31B ALA* 1.3 67.8 + - - +
33B ALA* 3.3 5.1 + - - -
34B VAL* 2.9 36.3 + - + +
24C LEU* 4.1 28.7 - - + +
27C THR* 3.9 19.1 - - + +
28C VAL* 3.6 44.9 - - + -
31C ALA* 4.9 0.4 - - + -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 5.7 1.3 - - + +
30A ILE* 3.7 24.5 - - + -
31A ALA* 4.5 6.7 - - + -
34A VAL* 4.3 5.8 - - + -
27B THR* 3.0 19.2 + - + +
28B VAL 3.7 2.9 - - - +
29B LEU 3.4 0.2 - - - -
30B ILE* 1.3 76.8 - - - +
32B LEU* 1.3 57.9 + - - +
35B TYR* 3.1 18.4 + - - +
27C THR* 5.4 0.6 - - + +
31C ALA* 4.1 13.5 - - + -
35C TYR* 2.7 30.7 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.8 31.2 - - + -
28B VAL* 3.1 38.8 + - + +
29B LEU* 3.9 9.9 - - + +
31B ALA* 1.3 75.9 - - - +
33B ALA* 1.3 64.6 + - - +
35B TYR* 3.5 1.7 - - + +
36B PHE* 3.0 54.7 + - + -
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU 2.8 22.5 + - - +
30B ILE* 3.8 5.8 - - - +
32B LEU* 1.3 74.7 - - - +
34B VAL* 1.3 58.0 + - + +
36B PHE* 3.4 2.9 + - - +
37B LEU* 2.9 39.8 + - + +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 2.9 36.8 + - + +
31B ALA 4.1 3.1 - - - +
33B ALA* 1.3 74.2 - - + +
35B TYR* 1.3 66.0 + - - +
37B LEU* 3.3 15.9 + - + +
38B GLY* 3.2 17.7 + - - -
28C VAL* 4.3 19.5 - - + +
31C ALA* 4.1 3.1 - - + -
32C LEU* 3.9 45.1 - - + +
35C TYR* 4.0 10.8 - - + -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.4 31.0 - - + -
35A TYR* 4.4 13.1 + + - -
38A GLY* 3.2 26.7 + - - -
39A ARG* 4.8 0.7 - - - +
31B ALA 3.1 19.8 + - - +
32B LEU* 3.5 4.9 - - + +
34B VAL* 1.3 76.4 - - - +
36B PHE* 1.3 87.3 + + - +
38B GLY* 3.1 13.9 + - - -
39B ARG* 2.6 57.0 + - + +
35C TYR* 3.4 28.6 - + + -
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.0 50.5 + - + +
33B ALA* 4.3 2.9 - - - +
35B TYR* 1.3 87.8 - + - +
37B LEU* 1.3 67.6 + - - +
39B ARG* 2.9 49.5 + - + +
40B LEU* 3.6 10.1 + - - +
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 2.9 33.2 + - + +
34B VAL* 3.5 15.0 - - + +
36B PHE* 1.3 77.4 - - - +
38B GLY* 1.3 59.6 + - - +
39B ARG 3.2 1.6 + - - -
40B LEU* 3.2 44.6 + - + +
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Residues in contact with GLY 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL 3.2 9.0 + - - -
35B TYR 3.1 12.6 + - - -
37B LEU* 1.3 75.4 - - - +
39B ARG* 1.3 59.4 + - - +
40B LEU* 3.4 3.9 + - - +
102C OLC 6.2 0.2 - - - -
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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
------------------------------------------------------------
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