Contacts of the helix formed by residues 43 - 63 (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 ILE 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 4.3 14.4 - - + +
41A GLY 3.1 12.4 - - - +
42A ASP* 1.3 79.8 - - - +
44A ASN* 1.3 59.9 + - - +
45A ALA* 3.8 9.2 - - + +
46A VAL* 3.6 36.8 - - + +
47A HIS* 3.1 32.0 + - - -
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Residues in contact with ASN 44 (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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42A ASP 4.0 2.2 + - - -
43A ILE* 1.3 71.9 - - - +
45A ALA* 1.3 58.2 + - - +
47A HIS* 3.4 8.9 + - - +
48A THR* 2.7 47.5 + - - -
51A ARG* 5.7 3.4 - - - +
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Residues in contact with ALA 45 (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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43A ILE* 3.4 9.0 - - + +
44A ASN* 1.3 76.4 - - - +
46A VAL* 1.3 62.0 + - + +
48A THR* 3.3 6.2 + - - -
49A ILE* 3.0 37.7 + - + +
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Residues in contact with VAL 46 (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* 3.5 35.6 - - + +
40A ALA* 3.7 24.5 - - + +
43A ILE* 3.6 36.6 + - + +
44A ASN 3.3 0.2 - - - -
45A ALA* 1.3 77.7 - - + +
47A HIS* 1.3 59.1 + - + +
49A ILE* 3.4 11.0 + - + +
50A ALA* 3.0 27.2 + - - +
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Residues in contact with HIS 47 (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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37A GLY* 3.8 18.1 + - - -
40A ALA 3.2 24.4 + - - -
41A GLY* 3.7 3.7 - - - -
42A ASP* 3.7 24.7 + - - -
43A ILE 3.1 18.9 + - - +
44A ASN* 3.8 10.5 + - - +
46A VAL* 1.3 77.5 - - + +
48A THR* 1.3 54.5 + - - +
50A ALA* 3.7 5.5 - - - +
51A ARG* 2.7 42.4 + - - +
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Residues in contact with THR 48 (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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44A ASN* 2.7 40.9 + - - -
45A ALA* 3.6 7.1 - - - -
46A VAL 3.3 0.2 - - - -
47A HIS* 1.3 71.6 - - - +
49A ILE* 1.3 61.7 + - + +
51A ARG* 3.5 31.1 + - - +
52A VAL* 2.9 41.6 + - + +
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Residues in contact with ILE 49 (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* 4.6 15.0 - - + -
45A ALA* 3.0 26.1 + - + +
46A VAL* 3.7 9.4 - - + +
48A THR* 1.3 76.0 - - + +
50A ALA* 1.3 59.6 + - - +
52A VAL* 4.0 4.5 - - - +
53A MSE 3.0 53.6 + - + +
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Residues in contact with ALA 50 (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* 3.2 27.2 - - - +
36A ILE* 4.1 5.8 - - + -
37A GLY* 3.6 22.4 - - - +
46A VAL 3.0 17.0 + - - +
47A HIS* 3.7 5.4 - - - +
49A ILE* 1.3 76.8 - - - +
51A ARG* 1.3 59.7 + - - +
53A MSE 3.6 5.4 - - - +
54A GLU* 2.9 32.2 + - - +
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Residues in contact with ARG 51 (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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44A ASN* 5.6 3.8 + - - +
47A HIS* 2.7 29.0 + - - +
48A THR* 3.5 44.3 + - - +
50A ALA* 1.3 71.1 - - - +
52A VAL* 1.3 69.8 + - - +
54A GLU* 4.0 8.6 - - - +
55A ASP* 3.0 28.9 + - + +
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Residues in contact with VAL 52 (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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48A THR* 2.9 32.7 + - + +
49A ILE* 4.0 4.9 - - - +
51A ARG* 1.3 80.4 - - + +
53A MSE 1.3 64.3 + - - +
55A ASP* 3.2 6.0 + - - +
56A ILE* 3.0 44.6 + - + +
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Residues in contact with MSE 53 (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 3.2 70.2 - - + +
32A ILE* 3.6 31.9 - - - -
33A GLY* 4.0 6.3 - - - -
36A ILE* 4.1 17.3 - - + -
49A ILE* 3.0 44.0 + - + +
50A ALA* 3.6 4.5 - - - +
51A ARG 3.3 0.2 - - - -
52A VAL* 1.3 76.7 - - - +
54A GLU* 1.3 62.8 + - - +
56A ILE* 3.3 10.3 + - - +
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Residues in contact with GLU 54 (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 3.8 9.8 + - - +
30A ILE* 3.7 18.1 - - + +
33A GLY* 4.6 6.7 - - - -
34A LYS* 3.8 24.7 - - - +
50A ALA 2.9 17.5 + - - +
51A ARG* 4.1 7.6 - - - +
53A MSE 1.3 75.6 - - - +
55A ASP* 1.3 62.6 + - - +
57A GLY 3.3 3.1 + - - -
58A TRP* 3.1 50.3 + - + +
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Residues in contact with ASP 55 (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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51A ARG* 3.0 23.3 + - + +
52A VAL* 3.7 6.3 - - - +
54A GLU* 1.3 74.4 - - - +
56A ILE* 1.3 60.9 + - + +
58A TRP* 3.4 12.2 + - - +
59A ALA* 2.9 29.9 + - - +
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Residues in contact with ILE 56 (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 3.6 35.9 - - + -
52A VAL* 3.0 34.9 + - + +
53A MSE 3.5 7.6 - - - +
54A GLU 3.2 0.2 - - - -
55A ASP* 1.3 76.0 - - - +
57A GLY* 1.3 62.4 + - - +
59A ALA* 3.2 15.2 + - - +
60A ILE* 3.3 26.7 + - + +
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Residues in contact with GLY 57 (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* 3.6 37.0 - - - +
29A MSE 4.2 1.0 - - - +
30A ILE* 3.6 16.5 - - - +
53A MSE 3.6 4.8 + - - -
54A GLU 3.3 4.2 + - - -
56A ILE* 1.3 79.2 - - - +
58A TRP* 1.3 60.8 + - - +
60A ILE* 3.4 11.1 + - - +
61A ILE* 3.5 13.7 + - - +
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Residues in contact with TRP 58 (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* 3.9 21.0 - - + +
34A LYS* 5.7 2.5 - - - -
54A GLU* 3.1 53.0 + - + +
55A ASP* 3.9 14.4 - - - +
56A ILE 3.3 0.4 - - - -
57A GLY* 1.3 74.4 - - - +
59A ALA* 1.3 61.3 + - - +
61A ILE* 3.3 21.1 - - + +
62A THR* 2.8 40.3 + - - +
245A ILE* 4.2 22.2 - - + -
249A TYR* 3.6 49.8 - + - -
1B GLC 5.5 3.6 - - - -
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Residues in contact with ALA 59 (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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55A ASP* 2.9 20.6 + - - +
56A ILE* 3.2 10.0 + - - +
58A TRP* 1.3 75.2 - - - +
60A ILE* 1.3 63.2 + - + +
62A THR* 4.4 2.9 - - - -
63A ASN* 2.9 39.7 + - - +
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Residues in contact with ILE 60 (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* 3.6 37.7 - - + -
23A MSE 5.3 5.4 - - + +
25A ALA* 5.3 0.7 - - + -
26A ALA* 3.6 33.0 - - + +
29A MSE 6.0 0.4 - - + -
56A ILE* 3.3 25.8 + - + +
57A GLY 3.7 5.8 - - - +
58A TRP 3.2 0.8 - - - -
59A ALA* 1.3 80.2 - - + +
61A ILE* 1.3 63.7 + - - +
64A LEU* 3.3 24.2 + - + +
67A LEU* 3.6 24.8 - - + +
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Residues in contact with ILE 61 (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* 6.5 0.7 - - + -
30A ILE* 5.7 2.0 - - + -
57A GLY 3.5 11.1 + - - +
58A TRP* 3.3 32.5 - - + +
60A ILE* 1.3 78.1 - - - +
62A THR* 1.3 69.3 + - - +
64A LEU* 3.3 21.1 + - + +
241A HIS* 3.5 25.1 - - + +
245A ILE* 3.7 20.2 - - + -
1B GLC 3.4 33.9 - - - +
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Residues in contact with THR 62 (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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58A TRP* 2.8 31.6 + - - +
59A ALA* 4.0 5.2 - - - -
61A ILE* 1.3 81.7 - - - +
63A ASN* 1.3 66.8 + - - +
64A LEU 3.3 3.6 + - - -
65A HIS* 3.6 14.1 + - + -
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Residues in contact with ASN 63 (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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59A ALA* 2.9 34.2 + - - +
60A ILE 3.7 4.5 - - - +
61A ILE 3.3 0.2 - - - -
62A THR* 1.3 84.6 - - - +
64A LEU* 1.3 58.1 + - - +
65A HIS* 3.2 17.1 - - - -
66A ILE* 3.2 15.7 - - + +
67A LEU* 3.0 32.9 + - + +
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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