Contacts of the helix formed by residues 22 - 37 (chain B) in PDB entry 1WZN
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 ARG 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ARG* 3.4 19.4 + - - +
19B ARG* 3.6 32.5 + - - +
20B ILE 3.0 0.4 - - - -
21B GLU* 1.3 78.1 - - - +
23B VAL* 1.3 65.2 + - - +
24B LYS* 3.2 3.9 + - - +
25B ALA* 3.3 13.2 + - + +
26B GLU* 2.5 52.9 + - - +
113B PHE* 4.6 13.1 - - - -
242B ARG* 4.2 11.9 - - - +
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Residues in contact with VAL 23 (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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19B ARG* 3.5 12.3 + - - +
20B ILE* 3.2 20.9 + - + +
22B ARG* 1.3 77.6 - - - +
24B LYS* 1.3 67.3 + - + +
26B GLU* 3.2 7.4 + - + +
27B ILE* 2.9 31.2 + - + +
54B ILE* 3.7 24.2 - - + +
55B PRO* 3.7 33.2 - - + -
58B GLU* 3.9 21.8 - - + +
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Residues in contact with LYS 24 (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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21B GLU 5.3 2.4 + - - +
22B ARG* 3.2 1.1 - - - -
23B VAL* 1.3 82.9 - - + +
25B ALA* 1.3 62.6 + - - +
28B ASP* 3.0 25.2 + - - +
58B GLU* 3.0 37.5 + - - +
61B GLU* 3.6 17.2 + - - -
62B ARG* 3.0 20.2 + - - +
86B ARG* 5.5 1.4 - - - +
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Residues in contact with ALA 25 (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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22B ARG* 3.3 16.3 + - + +
24B LYS* 1.3 78.7 - - - +
26B GLU* 1.3 62.0 + - - +
28B ASP* 3.3 14.3 + - - +
29B PHE* 3.2 19.2 + - - +
232B LEU* 4.2 19.6 - - + +
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Residues in contact with GLU 26 (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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19B ARG* 3.1 30.0 + - - -
22B ARG* 2.5 44.4 + - + +
23B VAL* 3.2 9.8 + - + +
24B LYS 3.2 0.4 - - - -
25B ALA* 1.3 79.8 - - - +
27B ILE* 1.3 62.2 + - + +
29B PHE* 3.2 6.6 + - - +
30B VAL* 3.0 28.3 + - + +
55B PRO* 5.7 0.7 - - - +
112B PHE* 5.1 3.6 - - + -
144B ASP* 5.3 0.9 - - - +
232B LEU* 3.9 14.6 - - + -
242B ARG* 3.0 34.9 + - - +
244B TRP* 4.1 12.7 - - + -
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Residues in contact with ILE 27 (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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23B VAL* 2.9 24.3 + - + +
26B GLU* 1.3 78.4 - - + +
28B ASP* 1.3 65.6 + - - +
30B VAL* 4.0 14.8 - - + -
31B GLU* 2.9 25.5 + - + +
55B PRO* 4.0 24.0 - - + +
58B GLU* 3.3 25.1 - - + -
59B LEU* 3.7 34.8 - - + -
62B ARG* 3.5 32.5 - - - +
112B PHE* 4.3 6.3 - - + -
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Residues in contact with ASP 28 (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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24B LYS* 3.0 19.5 + - - +
25B ALA* 3.3 15.5 - - - +
27B ILE* 1.3 77.6 - - - +
29B PHE* 1.3 62.3 + - - +
31B GLU* 3.4 5.3 + - - +
32B GLU* 3.2 19.2 + - - +
62B ARG* 2.7 36.0 + - - +
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Residues in contact with PHE 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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25B ALA 3.2 4.9 + - - +
26B GLU 3.2 8.4 + - - +
27B ILE 3.1 0.2 - - - -
28B ASP* 1.3 78.6 - - - +
30B VAL* 1.3 65.9 + - - +
32B GLU* 3.0 28.3 + - - +
33B ILE* 3.0 31.2 + - + +
229B TYR* 4.0 12.1 - + + -
232B LEU* 3.5 44.2 - - + +
233B LYS 3.4 38.4 - - - -
234B ARG* 3.7 14.1 - - + -
244B TRP* 3.6 41.1 - + - -
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Residues in contact with VAL 30 (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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26B GLU 3.0 19.6 + - - +
27B ILE* 3.2 14.6 + - + +
29B PHE* 1.3 77.3 - - + +
31B GLU* 1.3 56.9 + - - +
33B ILE* 3.1 12.6 + - - +
34B PHE* 3.0 58.3 + - + -
59B LEU* 4.5 10.1 - - + -
110B THR* 5.0 0.9 - - + -
112B PHE* 3.7 35.9 - - + -
142B ILE* 4.1 10.3 - - + -
244B TRP* 4.3 12.8 - - + -
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Residues in contact with GLU 31 (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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27B ILE* 2.9 23.9 + - + +
28B ASP* 3.7 5.8 - - - +
30B VAL* 1.3 73.6 - - - +
32B GLU* 1.3 65.4 + - - +
34B PHE* 3.2 12.4 + - + +
35B LYS* 3.0 23.6 + - - +
62B ARG* 2.8 41.0 + - - +
64B TYR* 2.6 36.2 + - + +
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Residues in contact with GLU 32 (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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28B ASP 3.2 11.5 + - - +
29B PHE* 3.0 23.7 + - + +
31B GLU* 1.3 76.7 - - - +
33B ILE* 1.3 57.9 + - - +
35B LYS* 3.2 9.7 + - + +
36B GLU* 2.8 38.8 + - + +
232B LEU 5.1 2.6 - - - +
233B LYS* 5.5 1.1 - - - -
234B ARG* 3.2 37.2 + - - +
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Residues in contact with ILE 33 (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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29B PHE* 3.0 50.8 + - + +
30B VAL* 3.1 9.2 + - - +
32B GLU* 1.3 75.2 - - - +
34B PHE* 1.3 60.0 + - - +
37B ASP* 2.8 49.1 + - + +
38B ALA 3.2 5.2 + - - -
140B VAL* 4.9 3.6 - - + -
142B ILE* 3.5 34.3 - - + -
229B TYR* 4.4 3.1 - - + -
234B ARG* 4.7 2.5 - - + +
244B TRP* 5.0 0.9 - - + -
246B VAL* 3.8 35.9 - - + -
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Residues in contact with PHE 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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30B VAL* 3.0 35.9 + - + -
31B GLU* 3.5 10.1 - - - +
33B ILE* 1.3 75.4 - - - +
35B LYS* 1.3 61.4 + - - +
38B ALA* 3.0 28.4 - - - +
40B ARG 4.5 2.3 - - - +
42B VAL* 3.7 40.7 - - + +
45B VAL* 4.4 7.6 - - + -
59B LEU* 4.2 11.0 - - + -
64B TYR* 3.5 33.2 - + - +
108B ALA* 3.6 23.3 - - + -
110B THR* 4.7 7.6 - - + -
140B VAL* 3.9 9.4 - - + -
142B ILE* 3.7 20.9 - - + -
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Residues in contact with LYS 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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31B GLU 3.0 16.5 + - - +
32B GLU* 3.5 9.4 - - + +
33B ILE 3.1 0.2 - - - -
34B PHE* 1.3 80.6 - - - +
36B GLU* 1.3 83.2 + - + +
38B ALA 4.2 6.6 - - - +
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Residues in contact with GLU 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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32B GLU* 2.8 27.9 + - + +
35B LYS* 1.3 107.7 + - + +
37B ASP* 1.3 60.1 + - - +
38B ALA 4.7 0.9 - - - -
39B LYS* 4.3 13.2 + - - -
234B ARG* 3.2 45.9 + - - +
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Residues in contact with ASP 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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33B ILE* 2.8 35.7 + - + +
36B GLU* 1.3 73.0 - - - +
38B ALA* 1.3 65.5 + - - +
39B LYS* 3.6 11.0 + - - +
140B VAL* 4.1 1.8 - - + -
227B LYS* 3.2 20.0 - - - +
229B TYR* 2.9 33.3 + - - -
234B ARG* 3.0 31.6 + - - -
246B VAL* 4.3 5.4 - - + -
248B ILE* 3.7 30.5 - - + +
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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