Contacts of the helix formed by residues 27 - 48 (chain A) in PDB entry 2WWB
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 GLN 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.2 18.0 + - + -
26A ILE* 1.4 85.0 - - - +
28A PHE* 1.4 76.1 + - - +
29A LYS* 3.4 10.6 + - + +
30A GLU* 3.4 25.8 + - + +
31A LYS* 3.1 20.1 + - - +
173A TYR* 5.1 0.4 - - - -
538E U 4.7 13.2 + - - -
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Residues in contact with PHE 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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27A GLN* 1.4 82.9 - - - +
29A LYS* 1.4 63.1 + - - +
31A LYS* 3.3 33.6 + - + +
32A VAL* 3.9 3.1 + - - +
175A LEU* 5.5 3.6 - - + -
464A GLU 4.4 9.9 - - - -
465A GLN* 3.2 48.2 + - - +
466A SER* 3.3 20.2 - - - -
476A PHE 5.8 0.2 - - - +
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Residues in contact with LYS 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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27A GLN* 4.9 7.0 - - + -
28A PHE* 1.4 77.4 - - - +
30A GLU* 1.4 76.9 + - - +
32A VAL* 3.4 15.8 - - - +
33A LEU* 3.7 14.5 - - + +
475A LEU 5.1 3.0 - - - +
476A PHE 4.2 16.1 - - - +
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Residues in contact with GLU 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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25A LYS* 3.6 42.4 + - + +
27A GLN* 3.7 17.2 - - + +
28A PHE 3.3 0.6 - - - -
29A LYS* 1.4 99.8 + - - +
31A LYS* 1.4 62.0 + - - +
33A LEU* 3.2 24.8 + - - +
34A TRP* 2.9 28.4 + - - +
173A TYR* 3.6 27.7 + - + +
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Residues in contact with LYS 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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26A ILE* 3.5 28.7 - - - +
27A GLN* 3.1 35.4 + - - +
28A PHE* 3.3 24.3 + - + +
30A GLU* 1.4 75.4 - - - +
32A VAL* 1.4 61.8 + - - +
33A LEU 3.5 0.3 + - - -
34A TRP* 3.6 19.0 + - - +
35A THR* 3.3 16.6 + - - -
172A GLY 4.9 3.1 - - - -
173A TYR* 3.8 26.9 - - + +
174A GLY* 3.8 31.1 - - - +
175A LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 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 PHE 3.9 3.6 + - - +
29A LYS 3.4 18.4 - - - +
31A LYS* 1.4 74.9 - - - +
33A LEU* 1.4 67.4 + - + +
35A THR* 3.4 8.3 + - - -
36A ALA* 3.3 21.5 + - - +
175A LEU* 4.6 4.7 - - + -
461A PHE* 4.0 20.4 - - + -
465A GLN* 3.7 22.9 - - + +
473A ALA 3.7 22.4 - - - +
474A LEU 4.3 8.2 - - - +
475A LEU* 3.9 12.1 - - - -
476A PHE* 3.8 22.4 - - - +
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Residues in contact with LEU 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 LYS* 3.7 17.0 - - + +
30A GLU* 3.2 25.0 + - - +
32A VAL* 1.4 76.4 - - - +
34A TRP* 1.4 85.8 + - + +
36A ALA* 3.5 9.5 - - - +
37A ILE* 3.3 23.7 - - + +
475A LEU* 4.1 38.0 - - + +
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Residues in contact with TRP 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 GLU* 2.9 38.3 + - - -
31A LYS* 3.7 5.8 - - - +
32A VAL 3.3 0.4 - - - -
33A LEU* 1.4 90.4 - - + +
35A THR* 1.4 61.7 + - - +
37A ILE* 3.3 22.9 + - + +
38A THR* 3.0 19.5 + - - -
165A LEU* 4.7 11.0 - - + +
168A LEU* 5.1 14.1 - - + -
169A LEU* 4.1 13.6 - - + +
173A TYR* 3.3 65.3 - + - -
68C VAL* 4.7 10.5 - - + -
70C PRO* 4.0 38.1 - - + -
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Residues in contact with THR 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 LYS 3.3 13.4 + - - -
32A VAL* 3.4 12.6 + - - -
34A TRP* 1.4 76.7 - - - +
36A ALA* 1.4 61.7 + - - +
38A THR* 3.4 6.9 + - - -
39A LEU* 3.3 22.1 + - + +
169A LEU* 3.4 19.7 - - + +
175A LEU* 4.4 0.5 + - - +
176A GLY* 3.6 27.9 + - - -
177A SER 5.0 0.9 - - - +
181A LEU* 4.6 17.3 - - + +
457A TYR* 6.5 0.4 - - + -
461A PHE* 4.5 17.0 - - + -
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Residues in contact with ALA 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 VAL 3.3 4.9 + - - +
33A LEU 3.5 11.9 - - - +
34A TRP 3.3 0.4 - - - -
35A THR* 1.4 76.5 - - - +
37A ILE* 1.4 66.0 + - + +
39A LEU* 3.5 12.1 + - - +
40A PHE* 3.1 22.9 + - - +
474A LEU 4.6 4.9 - - - +
475A LEU* 3.7 26.0 - - + -
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Residues in contact with ILE 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 LEU* 3.3 19.7 - - + +
34A TRP* 3.3 20.6 + - + +
36A ALA* 1.4 79.8 - - + +
38A THR* 1.4 62.3 + - - +
40A PHE* 3.3 19.7 + - + +
41A ILE* 3.4 21.7 + - + +
165A LEU* 4.2 22.7 - - + -
475A LEU* 6.2 0.7 - - + -
73C VAL* 5.2 4.5 - - + -
74C LEU* 4.6 21.3 - - + -
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Residues in contact with THR 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 TRP 3.0 15.1 + - - -
35A THR 3.6 6.6 + - - -
36A ALA 3.3 0.4 - - - -
37A ILE* 1.4 77.3 - - - +
39A LEU* 1.4 59.1 + - - +
41A ILE* 3.4 10.2 + - - +
42A PHE* 3.0 28.8 - - + -
162A VAL* 3.9 20.2 - - + +
165A LEU* 3.5 32.4 - - + +
169A LEU* 3.8 14.6 - - + +
177A SER 5.1 2.2 - - - -
178A GLY* 3.9 27.8 - - - -
181A LEU* 5.9 0.7 - - - -
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Residues in contact with LEU 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 THR* 3.3 11.0 + - + +
36A ALA* 3.6 13.0 - - - +
37A ILE 3.4 0.2 - - - -
38A THR* 1.4 77.3 - - - +
40A PHE* 1.4 62.8 + - - +
42A PHE* 3.4 43.3 + - + +
43A LEU* 4.1 3.1 + - - +
181A LEU* 4.2 20.4 - - + +
185A THR* 4.0 18.5 - - + +
47B MET* 4.7 23.8 - - + -
50B ILE* 6.2 4.5 - - + -
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Residues in contact with PHE 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 ALA 3.1 13.5 + - - +
37A ILE* 3.3 16.8 + - + +
39A LEU* 1.4 74.6 - - - +
41A ILE* 1.4 69.2 + - + +
42A PHE 3.2 0.7 + - - -
43A LEU* 3.3 30.5 + - + +
44A VAL* 3.4 28.1 + - + +
47A GLN* 4.9 6.1 - - - -
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Residues in contact with ILE 41 (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 ILE* 3.4 23.8 - - + +
38A THR 3.8 8.7 - - - +
39A LEU 3.4 0.8 - - - -
40A PHE* 1.4 83.9 - - + +
42A PHE* 1.4 62.3 + - - +
44A VAL* 3.2 23.5 + - + +
45A CYS* 3.4 18.7 + - - -
158A ALA* 4.1 13.7 - - - +
161A ILE* 4.0 30.5 - - + -
162A VAL* 3.9 20.2 - - + -
165A LEU* 4.1 9.6 - - + -
74C LEU* 6.1 3.4 - - + -
77C SER* 4.5 10.1 - - - +
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Residues in contact with PHE 42 (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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38A THR* 3.0 28.7 - - + -
39A LEU* 3.4 31.6 - - + +
40A PHE 3.2 0.4 - - - -
41A ILE* 1.4 77.3 - - - +
43A LEU* 1.4 60.3 + - - +
45A CYS* 3.7 8.8 + - - +
72A ASN* 3.4 41.9 + - - +
81A ILE* 3.6 20.9 - - + -
162A VAL* 3.7 25.1 - - + -
178A GLY 3.7 14.4 - - - -
181A LEU* 4.0 11.4 - - + -
182A PHE* 3.6 34.1 - - + -
185A THR* 3.7 21.3 - - + -
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Residues in contact with LEU 43 (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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39A LEU 4.1 2.6 + - - +
40A PHE* 3.3 29.5 + - + +
42A PHE* 1.4 76.9 - - - +
44A VAL* 1.4 57.4 + - - +
46A CYS* 3.1 30.8 + - - +
47A GLN* 3.5 15.9 + - - +
185A THR* 5.9 0.6 - - - +
189A GLU* 4.1 7.4 - - - +
50B ILE* 3.6 60.3 - - + +
51B GLY* 3.7 11.2 - - - +
54B VAL* 3.8 15.7 - - + -
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Residues in contact with VAL 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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40A PHE* 3.4 42.0 - - + +
41A ILE* 3.2 20.5 + - + +
43A LEU* 1.4 72.7 - - - +
45A CYS* 1.4 59.1 + - - +
47A GLN* 3.1 24.2 + - + +
48A ILE* 2.9 42.1 + - + +
81C ILE* 4.6 15.3 - - + -
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Residues in contact with CYS 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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41A ILE* 3.4 20.9 - - - -
42A PHE 3.7 8.7 - - - +
44A VAL* 1.4 77.4 - - - +
46A CYS* 1.4 55.6 + - - +
48A ILE* 3.0 28.9 - - - +
71A SER* 3.6 24.0 - - - +
72A ASN 4.6 0.4 - - - +
76A LEU 3.4 13.0 - - - +
77A MET* 3.4 19.5 - - + +
81A ILE* 4.2 17.0 - - - -
158A ALA* 4.2 23.1 - - - -
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Residues in contact with CYS 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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42A PHE 4.2 1.6 - - - -
43A LEU* 3.1 15.3 + - - +
45A CYS* 1.4 73.9 - - - +
47A GLN* 1.4 61.3 + - - +
72A ASN* 3.2 29.8 - - - -
75A THR* 4.2 13.9 - - - +
76A LEU* 3.4 28.6 - - - +
189A GLU* 3.5 26.5 - - - -
193A TRP* 4.5 7.6 - - - -
51B GLY* 4.9 7.0 - - - +
54B VAL* 3.9 20.5 - - + +
58B HIS* 4.3 1.7 + - - -
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Residues in contact with GLN 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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40A PHE* 4.9 6.1 - - - -
43A LEU* 3.6 25.0 - - - +
44A VAL* 3.1 29.5 + - + +
46A CYS* 1.4 77.3 - - - +
48A ILE* 1.4 60.5 + - + +
76A LEU* 3.5 2.3 - - - +
54B VAL* 3.7 30.2 - - + +
58B HIS* 3.4 20.0 + - + +
90C TRP* 3.2 34.9 + - + -
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Residues in contact with ILE 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 VAL* 2.9 28.7 + - + +
45A CYS* 3.0 27.0 - - - +
47A GLN* 1.4 77.7 - - + +
49A PRO* 1.3 71.9 - - + +
76A LEU* 3.4 7.4 - - - +
77A MET* 4.2 13.4 + - + +
80C PHE* 4.7 9.4 - - + -
81C ILE* 3.6 36.3 - - + +
84C VAL* 3.8 13.2 - - + -
85C PHE* 3.5 35.4 - - + -
90C TRP* 5.9 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
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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