Contacts of the helix formed by residues 21 - 42 (chain B) in PDB entry 2W5J
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 21 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU 2.9 14.6 + - - -
20A ALA* 3.1 25.1 - - - -
23A GLY 3.6 0.2 + - - -
24A PRO* 2.9 23.6 - - - +
63A LEU* 3.7 22.4 + - - -
18B GLY* 3.7 11.5 + - - -
19B LEU 3.0 0.4 - - - -
20B ALA* 1.3 78.8 - - - +
22B ILE* 1.3 70.4 + - - +
25B GLY* 2.8 22.7 + - - -
64B THR* 4.8 0.2 - - - -
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.1 2.0 - - + +
22A ILE* 5.3 5.6 - - + -
23A GLY* 3.3 18.7 - - - +
18B GLY 4.2 1.6 + - - +
19B LEU* 3.0 19.5 + - + +
21B SER* 1.3 84.1 - - - +
23B GLY* 1.3 67.5 + - - +
25B GLY 3.1 4.7 + - - -
26B VAL* 3.2 11.7 + - - +
22C ILE* 5.6 4.9 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 3.8 0.2 + - - -
22B ILE* 1.3 79.9 - - - +
24B PRO* 1.3 71.7 - - - +
26B VAL* 3.3 6.3 + - - +
27B GLY 3.1 15.4 + - - -
21C SER* 3.7 4.2 + - - -
22C ILE* 3.6 28.9 - - - +
25C GLY* 3.4 12.4 - - - -
26C VAL* 3.5 7.7 + - - +
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Residues in contact with PRO 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.8 7.2 - - + -
20B ALA 3.5 4.5 - - - +
22B ILE 3.8 0.4 - - - -
23B GLY* 1.3 84.6 - - - +
25B GLY* 1.3 69.3 + - - +
26B VAL 3.1 0.2 - - - -
27B GLY* 2.5 19.1 + - - -
28B GLN* 3.3 10.9 + - + +
60B MET* 3.9 16.6 - - + +
63B LEU* 3.2 23.6 - - + -
64B THR* 3.1 33.9 - - + -
21C SER* 2.9 22.7 - - - +
25C GLY* 3.4 11.0 - - - +
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 3.2 7.4 - - - +
24A PRO* 3.2 27.4 - - - +
27A GLY* 3.3 18.0 - - - -
28A GLN 4.4 0.7 + - - -
60A MET* 5.5 4.1 - - - +
63A LEU* 4.3 5.4 - - - +
21B SER 2.8 24.2 + - - -
24B PRO* 1.3 72.9 - - - +
26B VAL* 1.3 60.3 + - - +
28B GLN* 5.4 0.8 - - - +
29B GLY* 3.9 6.6 + - - -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY* 3.2 10.3 + - - +
26A VAL* 3.5 28.6 - - + +
27A GLY* 4.0 8.4 - - - -
30A THR* 5.6 0.3 - - - +
22B ILE 3.2 9.4 + - - +
23B GLY* 3.4 7.4 - - - +
24B PRO 2.8 3.0 + - - -
25B GLY* 1.3 75.6 - - - +
27B GLY* 1.3 69.9 + - - +
29B GLY* 3.6 1.4 + - - -
30B THR* 3.1 23.9 + - + +
26C VAL* 3.8 25.8 - - + +
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.1 3.6 + - - -
24B PRO 2.5 11.1 + - - -
26B VAL* 1.3 72.6 - - - +
28B GLN* 1.3 53.5 + - - -
29B GLY 2.9 1.6 - - - -
30B THR* 2.4 50.8 + - - +
25C GLY 3.4 18.2 - - - -
26C VAL 4.1 9.0 - - - -
29C GLY* 4.1 5.6 - - - -
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Residues in contact with GLN 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 6.2 0.2 - - - -
59A PHE* 5.6 6.7 - - + +
60A MET* 6.4 1.8 - - + -
63A LEU* 6.5 0.9 - - + -
24B PRO* 3.3 10.0 + - + +
25B GLY 5.4 0.4 - - - +
27B GLY* 1.3 67.4 - - - -
29B GLY* 1.3 50.9 + - - +
31B ALA* 2.9 14.3 + - - +
32B ALA* 2.7 35.8 + - - +
57B LEU* 3.9 22.0 - - + +
60B MET* 3.6 29.6 - - + +
61B GLU* 6.4 0.9 - - + -
25C GLY 4.5 0.6 + - - -
29C GLY* 4.1 6.5 - - - -
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Residues in contact with GLY 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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27A GLY* 3.9 19.3 - - - -
28A GLN* 3.9 6.5 - - - -
30A THR* 2.7 22.7 + - - -
31A ALA* 3.5 5.9 + - - +
60A MET* 5.9 3.7 - - - +
25B GLY 3.9 5.0 + - - -
26B VAL 3.6 7.9 + - - -
27B GLY 2.6 6.6 + - - -
28B GLN* 1.3 74.6 - - - +
30B THR* 1.3 51.5 + - - -
32B ALA* 4.3 6.1 - - - -
33B GLY 3.1 17.0 + - - -
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 4.0 11.4 - - + +
26B VAL* 3.1 21.1 - - + +
27B GLY* 2.4 33.4 + - - +
29B GLY* 1.3 63.9 - - - -
31B ALA* 1.3 65.6 + - - -
33B GLY* 3.0 1.3 + - - -
34B GLN* 2.5 40.6 + - - +
26C VAL 5.8 0.9 - - - +
29C GLY 2.8 21.9 + - - -
30C THR* 4.1 7.9 + - + +
33C GLY* 4.7 1.6 - - - -
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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
----------------------------------------------------------
27B GLY 3.4 0.6 + - - -
28B GLN* 2.9 12.7 + - - +
30B THR* 1.3 82.1 + - - +
32B ALA* 1.3 64.9 + - - +
34B GLN* 3.1 1.6 + - - +
35B ALA* 2.8 26.5 + - - +
53B LEU* 4.8 5.2 - - - -
56B SER* 5.1 1.1 - - - -
57B LEU* 4.0 14.4 - - + -
29C GLY 3.5 13.9 - - - +
32C ALA* 3.8 21.3 - - + -
33C GLY* 3.7 11.7 - - - +
36C VAL* 4.0 2.4 - - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 3.6 17.0 - - + -
52A THR* 5.7 0.3 - - - +
53A LEU* 5.8 1.1 - - - -
56A SER* 3.2 35.0 - - - +
28B GLN 2.7 19.2 + - - +
29B GLY* 3.8 3.6 - - - +
31B ALA* 1.3 72.8 - - - +
33B GLY* 1.3 65.5 + - - +
35B ALA* 2.9 1.9 + - - +
36B VAL* 2.9 25.1 + - - +
53B LEU* 3.8 14.7 - - - +
57B LEU* 4.3 2.7 - - + +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 4.5 1.6 - - - -
31A ALA* 3.5 23.7 - - - +
34A GLN* 3.3 20.7 - - - +
29B GLY 3.1 7.6 + - - -
30B THR* 3.0 6.9 + - - -
32B ALA* 1.3 79.5 - - - +
34B GLN* 1.3 58.9 + - - +
36B VAL* 2.9 23.2 - - - +
37B GLU* 3.3 5.2 + - - +
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Residues in contact with GLN 34 (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 GLN* 5.4 0.4 - - - -
30B THR* 2.5 20.2 + - - +
33B GLY* 1.3 71.9 - - - -
35B ALA* 1.3 59.5 + - - +
37B GLU* 4.1 4.8 + - - +
38B GLY* 3.5 15.9 + - - -
33C GLY* 3.5 31.9 - - - +
36C VAL* 3.6 6.9 - - - +
37C GLU* 4.2 12.3 - - + +
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Residues in contact with ALA 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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52A THR* 5.3 2.0 - - + -
31B ALA 2.8 15.2 + - - +
32B ALA 3.5 3.4 - - - +
34B GLN* 1.3 75.3 - - - +
36B VAL* 1.3 66.9 + - - +
37B GLU 3.2 1.8 - - - -
38B GLY* 3.1 2.9 + - - -
39B ILE* 2.9 29.9 + - + +
49B ILE* 4.8 4.7 - - + -
50B ARG 5.8 0.2 - - - +
53B LEU* 4.0 20.6 - - + -
36C VAL* 3.1 33.6 - - + +
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Residues in contact with VAL 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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31A ALA* 3.8 6.1 - - + +
34A GLN 3.4 1.6 - - - -
35A ALA* 3.0 52.3 - - + +
38A GLY* 5.2 0.2 - - - -
49A ILE* 3.7 33.8 - - + +
52A THR* 5.5 7.1 - - - -
53A LEU* 4.9 9.2 - - + +
32B ALA 2.9 12.0 + - - +
33B GLY* 2.9 26.9 - - - +
35B ALA* 1.3 75.9 - - - +
37B GLU* 1.3 60.6 + - - +
39B ILE* 3.7 7.7 + - - +
40B ALA* 3.1 19.4 + - - +
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Residues in contact with GLU 37 (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 GLN* 3.9 20.4 - - + +
38A GLY* 4.8 3.8 - - - +
41A ARG* 6.0 3.1 - - - +
33B GLY 3.3 8.4 + - - +
34B GLN* 4.4 5.2 - - - +
35B ALA 3.2 0.2 - - - -
36B VAL* 1.3 79.8 - - - +
38B GLY* 1.3 58.4 + - - +
40B ALA* 2.8 34.0 + - - +
41B ARG* 3.1 12.7 + - - +
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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
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34B GLN 3.5 10.7 + - - -
35B ALA* 3.1 7.4 + - - -
37B GLU* 1.3 78.4 - - - +
39B ILE* 1.3 61.1 + - - +
41B ARG* 3.1 24.6 + - - +
42B GLN* 3.2 11.3 + - - +
36C VAL 5.3 0.2 - - - -
37C GLU* 5.0 4.7 - - - -
40C ALA* 3.6 30.2 - - - +
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Residues in contact with ILE 39 (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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45A ALA* 5.4 1.6 - - - +
48A LYS* 3.7 31.4 - - + +
49A ILE* 4.8 2.2 - - - +
52A THR* 5.3 6.5 - - + +
35B ALA* 2.9 21.3 + - + +
36B VAL* 3.9 7.2 - - - +
38B GLY* 1.3 73.0 - - - +
40B ALA* 1.3 67.4 + - - +
41B ARG 3.1 0.7 + - - -
42B GLN 4.3 3.8 - - - +
43B PRO* 3.2 30.1 - - + +
45B ALA* 4.3 4.5 - - + +
46B GLU* 3.7 38.8 - - + +
49B ILE* 2.9 36.6 - - + -
50B ARG* 6.0 1.8 - - + -
36C VAL* 5.6 0.2 - - + -
40C ALA* 5.4 4.3 - - + -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 3.4 41.7 - - - +
39A ILE* 5.2 5.4 - - + -
41A ARG* 5.6 3.1 - - + +
42A GLN* 3.1 27.3 - - - +
45A ALA* 4.2 10.0 - - + +
49A ILE* 6.0 0.9 - - - +
36B VAL 3.1 12.7 + - - +
37B GLU 2.8 19.8 + - - +
39B ILE* 1.3 72.8 - - - +
41B ARG* 1.3 60.3 + - - +
43B PRO* 3.8 5.7 - - - +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG* 4.4 26.7 - - - +
42A GLN* 4.3 15.5 + - - +
37B GLU* 3.1 10.3 + - - +
38B GLY* 3.1 21.3 + - - +
40B ALA* 1.3 81.1 - - - +
42B GLN* 1.3 85.8 + - - +
43B PRO* 3.2 7.3 - - - +
37C GLU* 6.1 3.0 - - - +
40C ALA* 5.7 2.9 - - + +
41C ARG* 4.7 22.0 - - - +
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 3.2 6.0 + - - +
39B ILE* 3.3 8.8 - - - +
41B ARG* 1.3 109.5 + - - +
43B PRO* 1.4 60.0 - - - +
44B GLU* 3.2 3.8 - - + +
45B ALA* 3.0 29.6 + - + +
46B GLU 3.7 2.1 + - - -
40C ALA 3.3 30.6 - - - +
41C ARG* 4.5 10.9 + - - +
43C PRO* 5.5 2.2 - - + -
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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
------------------------------------------------------------
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