Contacts of the helix formed by residues 22 - 40 (chain A) in PDB entry 5IWS
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 VAL 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A VAL 3.1 22.4 - - - +
19A VAL* 3.7 13.0 - - + +
20A VAL 3.1 0.2 - - - -
21A ALA* 1.3 80.5 - - + +
23A MSE 1.3 53.6 + - - +
24A PRO 3.5 1.3 - - - -
25A ALA* 3.2 9.3 + - + +
26A ALA* 2.7 32.6 + - - +
60A ILE* 3.6 37.7 - - + -
67A LEU* 5.9 5.4 - - + -
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Residues in contact with MSE 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 VAL* 3.3 31.4 + - + +
20A VAL* 4.2 7.6 - - + +
22A VAL* 1.3 74.3 - - + +
24A PRO* 1.3 68.1 - - + +
26A ALA* 3.0 8.8 + - + +
27A GLY 2.7 26.9 + - - -
60A ILE* 5.3 5.4 - - + -
64A LEU* 3.8 36.1 - - + -
68A PHE* 4.2 9.2 - - + -
238A GLY* 6.2 0.4 - - - -
240A HIS* 5.9 1.1 - - + -
241A HIS* 5.1 0.2 - - - +
353A VAL* 3.3 19.4 - - + +
355A GLU* 3.6 35.2 - - + +
359A PHE* 6.5 0.2 - - + -
2B GLC 3.7 17.3 - - - +
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Residues in contact with PRO 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 VAL 3.0 26.5 - - - +
21A ALA* 4.4 2.9 - - - -
22A VAL 3.7 2.0 - - - +
23A MSE 1.3 83.3 - - + +
25A ALA* 1.3 57.5 + - - +
27A GLY 3.5 0.2 + - - -
28A LEU* 2.9 29.2 + - - +
347A ALA* 4.3 15.3 - - + -
351A THR* 3.4 20.3 - - + +
353A VAL* 3.8 18.8 - - + +
356A PRO* 3.7 28.0 - - + -
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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 ALA 4.7 7.1 + - - +
22A VAL* 3.2 14.8 + - + +
24A PRO* 1.3 76.6 - - - +
26A ALA* 1.3 65.9 + - - +
28A LEU* 3.3 11.6 + - + +
29A MSE 3.0 32.2 + - + +
60A ILE* 5.3 0.9 - - + -
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Residues in contact with ALA 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 VAL 2.7 17.2 + - - +
23A MSE 3.0 14.1 + - - +
25A ALA* 1.3 75.3 - - - +
27A GLY* 1.3 62.4 + - - +
29A MSE 3.2 14.3 + - - +
30A ILE* 3.3 19.4 + - - +
57A GLY* 3.6 12.7 - - - +
60A ILE* 3.6 36.3 - - + +
61A ILE* 6.5 0.4 - - + -
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Residues in contact with GLY 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 MSE 2.7 18.0 + - - -
24A PRO 3.8 1.6 - - - -
26A ALA* 1.3 73.0 - - - +
28A LEU* 1.3 56.9 + - - +
30A ILE* 3.4 9.6 + - - +
31A SER* 2.9 36.0 + - - -
351A THR* 4.7 6.5 - - - -
353A VAL* 4.7 2.5 - - - -
393A PHE* 4.4 23.2 - - - -
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Residues in contact with LEU 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 PRO 2.9 19.4 + - - +
25A ALA* 3.5 12.3 - - + +
26A ALA 3.2 0.2 - - - -
27A GLY* 1.3 77.4 - - - +
29A MSE 1.3 64.9 + - + +
31A SER* 4.5 3.4 - - - +
32A ILE* 3.0 62.6 + - + +
350A LEU* 6.4 0.2 - - + -
351A THR* 4.2 13.0 - - + +
396A ILE* 3.7 22.9 - - + -
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Residues in contact with MSE 29 (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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25A ALA* 3.0 18.9 + - + +
26A ALA* 3.2 8.9 + - - +
28A LEU* 1.3 80.0 - - - +
30A ILE* 1.3 57.0 + - - +
32A ILE* 4.4 6.1 - - - -
33A GLY* 3.0 21.0 + - - -
53A MSE 3.2 67.5 - - + +
56A ILE* 3.6 41.1 - - + -
57A GLY 4.2 4.7 - - - +
60A ILE* 6.0 0.4 - - + -
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Residues in contact with ILE 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 ALA* 3.3 13.3 + - + +
27A GLY* 3.9 8.5 - - - +
28A LEU 3.2 0.6 - - - -
29A MSE 1.3 76.6 - - - +
31A SER* 1.3 67.5 + - - +
34A LYS* 3.0 50.9 + - + +
54A GLU* 3.7 28.7 - - + +
57A GLY* 3.6 26.2 - - - +
58A TRP* 3.8 26.0 - - + +
61A ILE* 5.7 2.0 - - + -
393A PHE* 6.5 1.6 - - + -
397A GLU* 5.5 0.9 - - - +
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Residues in contact with SER 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 GLY 2.9 21.3 + - - -
28A LEU* 4.0 4.3 - - - -
30A ILE* 1.3 78.1 - - - +
32A ILE* 1.3 60.0 + - - +
34A LYS* 3.3 4.2 + - - +
35A LEU* 3.0 23.7 + - - +
350A LEU 5.3 0.8 + - - -
351A THR* 4.8 4.7 + - - -
393A PHE* 3.5 24.1 + - - -
396A ILE* 4.6 21.5 - - - +
397A GLU* 4.2 25.8 + - - +
400A THR* 5.6 1.0 + - - +
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Residues in contact with ILE 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 LEU* 3.0 50.2 + - + +
29A MSE 4.2 6.7 - - - +
31A SER* 1.3 71.6 - - - +
33A GLY* 1.3 61.6 + - - +
35A LEU* 3.4 17.1 - - + +
36A ILE* 2.8 39.1 + - + +
53A MSE 3.6 25.1 - - + -
396A ILE* 4.6 16.4 - - + -
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Residues in contact with GLY 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 MSE 3.0 24.2 + - - -
30A ILE* 3.8 0.4 - - - -
31A SER 3.2 0.6 - - - -
32A ILE* 1.3 79.2 - - - +
34A LYS* 1.3 56.8 + - - +
36A ILE* 4.8 0.2 - - - -
37A GLY* 3.0 21.1 + - - -
50A ALA* 3.2 22.0 - - - +
53A MSE 4.0 18.6 - - - -
54A GLU* 4.6 4.5 - - - -
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Residues in contact with LYS 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 ILE* 3.0 36.9 + - - +
31A SER 3.8 3.6 - - - +
33A GLY* 1.3 72.6 - - - +
35A LEU* 1.3 65.0 + - - +
37A GLY* 3.7 1.9 - - - +
38A MSE 3.1 32.2 + - - +
54A GLU* 3.8 24.5 - - - +
58A TRP* 5.5 2.5 - - - +
249A TYR* 4.4 6.5 + - - -
272A ASP* 4.3 14.3 + - - -
276A LEU* 6.0 1.8 - - - +
397A GLU* 3.8 24.0 + - - +
400A THR* 5.9 1.1 - - + -
401A ARG* 4.2 14.8 - - - +
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Residues in contact with LEU 35 (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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31A SER 3.0 14.7 + - - +
32A ILE* 3.2 19.9 + - + +
34A LYS* 1.3 77.1 - - - +
36A ILE* 1.3 63.7 + - + +
38A MSE 3.5 11.9 - - + +
39A SER* 3.1 29.0 + - - -
396A ILE* 4.9 12.6 - - + -
400A THR* 3.4 37.6 - - + +
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Residues in contact with ILE 36 (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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32A ILE* 2.8 25.4 + - + +
33A GLY 4.0 3.4 - - - +
35A LEU* 1.3 77.5 - - + +
37A GLY* 1.3 65.7 + - - +
38A MSE 3.5 0.2 + - - -
39A SER* 3.5 11.8 + - - -
40A ALA 3.7 3.6 + - - -
46A VAL* 3.5 42.2 - - + +
49A ILE* 4.6 9.6 - - + -
50A ALA* 4.2 6.7 - - + +
53A MSE 4.1 26.5 - - + -
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Residues in contact with GLY 37 (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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33A GLY 3.0 11.9 + - - -
34A LYS* 3.2 4.9 + - - -
35A LEU 3.2 0.4 - - - -
36A ILE* 1.3 79.8 - - - +
38A MSE 1.3 58.1 + - - +
40A ALA 3.8 3.5 - - - +
41A GLY* 5.0 0.5 - - - -
47A HIS* 3.8 25.4 + - - -
50A ALA* 3.6 17.4 - - - +
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Residues in contact with MSE 38 (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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34A LYS* 3.1 21.3 + - - +
35A LEU* 3.5 10.8 - - + +
37A GLY* 1.3 75.6 - - - +
39A SER* 1.3 70.2 + - - +
40A ALA* 3.4 3.3 + - - -
41A GLY* 4.5 2.6 + - - -
400A THR* 3.7 39.5 - - + +
404A MSE 5.4 18.4 - - + -
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Residues in contact with SER 39 (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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35A LEU* 3.1 24.6 + - - -
36A ILE* 4.0 6.7 - - - -
37A GLY 3.4 0.8 - - - -
38A MSE 1.3 81.4 - - - +
40A ALA* 1.3 59.7 + - - +
41A GLY 4.2 0.7 + - - -
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Residues in contact with ALA 40 (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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36A ILE 3.7 3.2 + - - -
37A GLY 3.8 4.7 - - - +
38A MSE 3.4 0.4 - - - -
39A SER* 1.3 79.1 - - - +
41A GLY* 1.3 61.7 + - - +
43A ILE* 4.3 13.5 + - + -
46A VAL* 3.7 32.9 - - + +
47A HIS* 3.2 22.2 + - - -
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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
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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