Contacts of the helix formed by residues 41 - 59 (chain B) 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 ALA 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A TYR* 4.2 8.7 + - - +
37B ALA* 3.1 22.3 + - + +
38B MET* 5.2 0.7 - - - +
40B THR* 1.4 72.7 - - - +
42B ILE* 1.4 60.5 + - + +
43B GLY 3.2 0.4 - - - -
44B PHE* 3.6 12.3 - - - +
45B ALA* 2.9 28.4 + - - +
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Residues in contact with ILE 42 (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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38B MET 4.8 7.4 - - - +
39B ALA 5.8 0.4 - - - +
40B THR 2.7 10.5 + - - +
41B ALA* 1.4 73.0 - - + +
43B GLY* 1.4 55.6 + - - +
45B ALA* 3.5 7.0 + - + +
46B ILE* 3.0 33.2 + - + +
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 5.3 3.4 - - - +
458A PHE* 6.6 0.2 - - - -
39B ALA 4.9 2.8 + - - -
40B THR* 3.4 20.1 + - - -
41B ALA 3.2 0.4 - - - -
42B ILE* 1.4 76.8 - - - +
44B PHE* 1.4 60.4 + - - +
46B ILE* 3.6 12.9 - - - +
47B MET* 3.5 25.3 - - - +
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A CYS* 4.0 30.8 - - + +
191A ILE* 3.8 34.8 - - + -
248A THR* 4.7 15.7 - - + -
450A ALA* 5.6 4.7 - - + -
451A VAL* 5.0 15.9 - - + -
454A ILE* 4.7 12.1 - - + -
455A TYR* 5.0 12.6 - + - +
40B THR* 3.7 14.2 - - + +
41B ALA* 3.4 19.0 + - - +
43B GLY* 1.4 75.8 - - - +
45B ALA* 1.4 63.9 + - - +
47B MET* 3.8 3.3 + - - +
48B GLY* 3.6 15.1 + - - -
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Residues in contact with ALA 45 (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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41B ALA 2.9 18.1 + - - +
42B ILE* 3.6 9.0 - - + +
44B PHE* 1.4 78.0 - - - +
46B ILE* 1.4 59.1 + - - +
48B GLY* 3.3 2.6 + - - -
49B PHE* 3.0 56.2 + - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.0 20.7 + - + +
43B GLY* 3.6 18.4 - - - +
45B ALA* 1.4 73.0 - - - +
47B MET* 1.4 73.6 + - + +
49B PHE* 3.8 6.2 - - + +
50B ILE* 3.0 44.7 + - + +
53B PHE* 4.8 14.1 - - + -
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Residues in contact with MET 47 (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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39A LEU* 4.7 25.6 - - + -
185A THR* 4.5 23.9 - - + +
188A CYS* 3.7 27.4 - - + -
189A GLU* 3.3 16.3 - - - +
454A ILE* 5.0 12.3 - - + -
43B GLY* 3.5 17.5 - - - +
44B PHE 3.8 2.6 + - - +
45B ALA 3.4 0.2 - - - -
46B ILE* 1.4 86.2 - - + +
48B GLY* 1.4 61.5 + - - +
50B ILE* 3.3 27.6 - - - +
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Residues in contact with GLY 48 (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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188A CYS* 3.4 30.7 - - - +
189A GLU* 3.7 8.2 - - - +
192A VAL* 3.5 22.2 - - - +
44B PHE 3.6 6.6 + - - -
45B ALA 3.3 6.6 + - - -
46B ILE 3.3 0.4 - - - -
47B MET* 1.4 79.2 - - - +
49B PHE* 1.4 59.4 + - - +
51B GLY 4.0 0.5 + - - -
52B PHE* 3.7 13.0 + - - +
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 4.3 21.5 - - + -
209A PHE* 4.7 5.4 - + - -
210A GLU* 3.3 39.5 - - - -
45B ALA* 3.0 40.3 + - + +
46B ILE* 4.0 8.3 - - + +
47B MET 3.3 0.2 - - - -
48B GLY* 1.4 78.8 - - - +
50B ILE* 1.4 59.3 + - - +
51B GLY 3.4 0.7 - - - -
52B PHE* 3.4 19.6 + + + +
53B PHE* 3.0 54.1 + + + -
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Residues in contact with ILE 50 (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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39A LEU* 6.2 4.3 - - + -
43A LEU* 3.6 35.1 - - + +
185A THR* 5.5 4.7 - - + -
189A GLU* 4.5 4.3 - - - +
46B ILE* 3.0 32.4 + - + +
47B MET* 3.3 32.8 - - - +
49B PHE* 1.4 78.1 - - - +
51B GLY* 1.4 57.8 + - - +
53B PHE* 3.3 24.0 + - + +
54B VAL* 3.1 23.0 + - - +
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Residues in contact with GLY 51 (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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43A LEU* 3.7 9.8 - - - +
46A CYS* 4.9 3.2 - - - +
75A THR* 5.4 0.3 + - - +
189A GLU* 3.8 27.1 + - - -
193A TRP* 3.7 17.0 + - - -
47B MET 4.0 0.2 + - - -
48B GLY 4.0 2.8 + - - -
49B PHE 3.4 0.4 - - - -
50B ILE* 1.4 80.7 - - - +
52B PHE* 1.4 59.9 + - - +
54B VAL* 3.6 20.3 - - - +
55B LYS* 4.2 5.5 + - - +
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.6 50.0 - - + -
193A TRP* 3.5 17.9 - + - +
196A PHE* 4.4 3.1 - - + -
209A PHE* 3.7 31.4 - + + -
210A GLU* 3.1 21.3 - - + +
211A GLY* 3.5 28.8 - - - -
213A ILE* 3.8 31.2 - - + -
48B GLY 3.7 8.7 + - - +
49B PHE* 3.4 23.1 + + + +
51B GLY* 1.4 77.4 - - - +
53B PHE* 1.4 61.2 + - - +
55B LYS* 3.5 18.1 - - + +
56B LEU 3.8 0.2 + - - -
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Residues in contact with PHE 53 (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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210A GLU* 3.7 37.9 - - + -
46B ILE* 4.8 11.7 - - + -
49B PHE* 3.0 44.4 + + + +
50B ILE* 3.3 21.7 + - + +
52B PHE* 1.4 74.9 - - - +
54B VAL* 1.4 64.2 + - + +
55B LYS 3.3 0.2 - - - -
56B LEU* 3.4 18.8 + - + +
57B ILE* 4.0 7.3 + - - +
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Residues in contact with VAL 54 (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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43A LEU* 3.8 18.8 - - + -
46A CYS* 3.9 25.1 - - + +
47A GLN* 3.7 24.2 - - + +
75A THR* 5.8 2.2 - - + -
50B ILE 3.1 18.4 - - - +
51B GLY 3.6 11.7 - - - +
52B PHE 3.4 0.6 - - - -
53B PHE* 1.4 74.6 - - + +
55B LYS* 1.3 60.9 + - + +
57B ILE* 3.2 16.7 + - - +
58B HIS* 3.0 48.8 + - + +
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Residues in contact with LYS 55 (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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74A GLY 4.7 3.4 + - - -
75A THR* 3.4 41.0 + - + -
193A TRP* 3.6 34.8 - - - +
211A GLY* 4.4 7.9 - - - -
212A ALA* 3.9 17.0 - - + +
213A ILE* 4.6 18.5 - - + +
51B GLY 4.2 6.1 - - - +
52B PHE* 3.5 20.6 - - + +
54B VAL* 1.3 79.6 - - + +
56B LEU* 1.4 62.6 + - - +
57B ILE 3.3 0.2 - - - -
58B HIS* 3.4 15.5 + - - +
59B ILE* 3.6 20.2 + - + +
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Residues in contact with LEU 56 (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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209A PHE 5.7 1.6 - - - +
210A GLU* 4.2 11.7 - - - +
211A GLY* 3.3 26.4 - - - +
212A ALA* 4.7 0.4 - - - -
52B PHE 3.8 2.6 + - - -
53B PHE* 3.4 16.5 + - + +
54B VAL 3.3 0.2 - - - -
55B LYS* 1.4 77.1 - - - +
57B ILE* 1.4 79.5 + - + +
60B PRO* 3.4 10.4 - - - +
66B VAL* 4.2 16.7 - - + +
67B GLY 3.4 33.9 - - - +
68B GLY* 4.8 1.1 - - - -
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Residues in contact with ILE 57 (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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53B PHE 4.4 7.2 - - - +
54B VAL* 3.2 12.4 + - - +
56B LEU* 1.4 93.1 - - + +
58B HIS* 1.4 77.4 + - + +
59B ILE 3.7 0.2 - - - -
60B PRO* 3.4 6.2 - - - +
61B ILE* 3.5 13.0 - - + +
68B GLY* 3.2 42.1 - - - +
90C TRP* 5.9 0.4 - - + -
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Residues in contact with HIS 58 (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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46A CYS 4.3 2.8 + - - -
47A GLN* 3.4 43.9 + - + +
76A LEU* 5.1 3.3 - - + +
54B VAL* 3.0 40.2 + - + +
55B LYS* 3.4 8.2 + - - +
57B ILE* 1.4 90.3 - - + +
59B ILE* 1.4 66.8 + - - +
61B ILE* 3.5 20.7 + - - +
62B ASN* 4.4 1.0 + - - -
90C TRP* 3.3 48.1 + + + +
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Residues in contact with ILE 59 (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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212A ALA* 3.3 35.9 - - + +
55B LYS* 3.6 8.5 + - + +
58B HIS* 1.4 76.6 - - - +
60B PRO* 1.3 64.3 - - + +
61B ILE 3.1 5.2 + - - -
62B ASN* 3.1 38.4 + - - +
63B ASN 3.8 1.4 - - - +
65B ILE* 4.1 21.1 - - + -
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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