Contacts of the helix formed by residues 27 - 44 (chain B) in PDB entry 6WPJ
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 THR 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A ILE* 3.7 26.0 - - + +
384A GLY 3.3 15.5 - - - +
385A LYS* 4.8 4.3 - - - -
386A THR* 5.5 2.7 - - - +
26B LEU* 1.3 77.2 - - - +
28B GLU* 1.3 65.8 + - - +
29B GLU* 3.9 12.0 + - - +
30B LYS* 3.3 31.1 + - - +
31B ILE* 3.0 21.4 + - - +
135B ILE* 4.4 0.2 - - - -
404B GLU* 4.4 18.8 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 4.8 12.0 + - - -
319A TYR* 5.5 2.9 + - - -
383A TRP 4.0 12.6 - - - +
384A GLY* 2.9 18.3 + - - +
385A LYS* 5.8 3.5 - - - +
27B THR* 1.3 69.7 - - - +
29B GLU* 1.3 67.9 + - - +
31B ILE* 3.8 1.7 - - - +
32B LYS* 2.9 58.2 + - + +
135B ILE* 3.9 29.3 - - + +
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 3.3 10.6 + - - +
28B GLU* 1.3 77.6 - - - +
30B LYS* 1.3 63.7 + - - +
32B LYS* 3.4 6.1 + - - +
33B ALA* 3.0 24.1 + - - +
64B LYS* 5.1 7.8 + - - +
71B TRP* 3.7 34.3 + - + -
404B GLU* 5.5 2.3 - - - +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.3 18.4 - - + -
27B THR* 3.3 23.4 + - - +
28B GLU 3.3 0.6 - - - -
29B GLU* 1.3 75.6 - - - +
31B ILE* 1.3 57.7 + - - +
33B ALA* 3.4 2.9 + - - +
34B LEU* 2.9 34.8 + - - +
61B PHE* 4.3 8.1 - - + -
62B ALA* 3.4 43.6 + - + +
63B ILE* 5.6 0.2 - - - +
71B TRP* 4.0 14.8 - - + -
403B THR* 2.9 46.5 + - - -
404B GLU* 3.1 23.9 + - - +
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Residues in contact with ILE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.7 22.9 - - + +
27B THR 3.0 19.5 + - - +
28B GLU* 3.8 5.2 - - + +
30B LYS* 1.3 76.0 - - - +
32B LYS* 1.3 59.0 + - + +
34B LEU* 3.3 7.7 + - - +
35B VAL* 2.9 41.0 + - + +
132B ILE* 4.6 2.9 - - + -
133B PRO* 3.7 41.7 - - + +
134B SER* 4.1 4.7 - - - -
135B ILE* 3.5 35.9 - - + +
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 2.9 55.5 + - + +
29B GLU* 3.8 5.8 - - - +
31B ILE* 1.3 78.8 - - + +
33B ALA* 1.3 61.4 + - - +
35B VAL* 3.2 6.1 + - - +
36B GLU* 3.0 24.4 + - - +
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Residues in contact with ALA 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 GLU 3.0 17.3 + - - +
30B LYS* 3.7 4.3 - - - +
32B LYS* 1.3 77.1 - - - +
34B LEU* 1.3 56.7 + - - +
36B GLU* 3.3 6.5 + - - +
37B ILE* 2.9 38.1 + - + +
62B ALA* 4.6 3.4 - - + -
71B TRP* 3.5 47.3 - - + +
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Residues in contact with LEU 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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26B LEU* 3.5 32.3 - - + -
30B LYS 2.9 19.8 + - - +
31B ILE* 3.7 5.4 - - - +
33B ALA* 1.3 76.1 - - - +
35B VAL* 1.3 57.5 + - - +
37B ILE* 3.9 3.1 - - + +
38B CYS* 2.8 35.4 + - - +
60B VAL* 4.2 12.3 - - + -
61B PHE* 3.4 35.2 - - - +
62B ALA* 4.0 7.0 - - + +
73B LYS* 3.6 34.3 - - + -
132B ILE* 3.9 18.2 - - + -
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Residues in contact with VAL 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 ILE* 2.9 27.3 + - + +
32B LYS* 3.8 6.1 - - - +
33B ALA 3.2 0.4 - - - -
34B LEU* 1.3 77.0 - - - +
36B GLU* 1.3 59.1 + - - +
38B CYS* 3.9 4.1 - - - +
39B THR* 2.8 39.5 + - - +
132B ILE* 3.9 23.1 - - + -
144B TYR* 5.7 0.2 + - - -
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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 LYS 3.0 16.1 + - - +
33B ALA* 3.8 5.8 - - - +
35B VAL* 1.3 78.7 - - - +
37B ILE* 1.3 68.3 + - - +
39B THR* 3.2 7.9 + - - -
40B GLU* 3.0 24.0 + - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 2.9 24.0 + - + +
34B LEU* 3.9 5.8 - - + +
36B GLU* 1.3 83.2 - - + +
38B CYS* 1.3 58.5 + - - +
40B GLU* 3.4 5.5 + - - +
41B MET* 2.9 51.2 + - + +
62B ALA* 5.9 0.4 - - + -
71B TRP* 3.9 28.9 - - + +
72B ARG* 4.5 0.4 - - - -
73B LYS* 3.9 40.2 - - + +
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Residues in contact with CYS 38 (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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34B LEU 2.8 24.6 + - - +
35B VAL* 4.0 4.5 - - - +
37B ILE* 1.3 73.5 - - - +
39B THR* 1.3 60.4 + - - +
41B MET* 3.3 3.8 + - - +
42B GLU* 2.9 30.8 + - - +
47B ILE* 3.8 15.7 - - + +
73B LYS* 4.5 15.3 - - - -
130B PHE* 3.9 24.5 - - - -
132B ILE* 3.7 23.8 - - + -
144B TYR* 4.0 18.1 + - + +
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Residues in contact with THR 39 (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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173A LYS* 5.6 10.7 - - - -
35B VAL* 2.8 29.8 + - - +
36B GLU* 3.2 8.0 + - - -
38B CYS* 1.3 76.2 - - - +
40B GLU* 1.3 65.0 + - - +
42B GLU* 3.1 12.8 + - - +
43B LYS* 3.0 22.3 + - + +
144B TYR* 5.0 4.2 + - - -
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Residues in contact with GLU 40 (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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36B GLU* 3.0 13.3 + - + +
37B ILE* 3.7 8.3 - - - +
39B THR* 1.3 76.8 - - - +
41B MET* 1.3 66.7 + - + +
42B GLU 3.0 0.9 + - - -
43B LYS* 3.1 17.5 + - - +
44B GLU* 2.8 28.0 + - - +
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Residues in contact with MET 41 (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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37B ILE* 2.9 39.6 + - + +
38B CYS* 3.7 4.9 - - - +
39B THR 3.3 0.2 - - - -
40B GLU* 1.3 73.0 - - + +
42B GLU* 1.3 59.4 + - - +
44B GLU* 3.5 8.7 + - - +
45B GLY 3.4 2.3 + - - -
46B LYS* 3.0 54.2 + - + +
47B ILE* 3.6 28.6 + - + -
73B LYS* 3.7 27.1 - - - -
116B PHE* 3.8 34.5 - - + -
146B TYR* 4.2 9.0 - - + +
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Residues in contact with GLU 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 CYS 2.9 16.1 + - - +
39B THR* 3.6 8.6 - - - +
40B GLU 3.1 0.2 - - - -
41B MET* 1.3 75.0 - - - +
43B LYS* 1.3 64.6 + - - +
44B GLU 3.0 1.8 - - - -
45B GLY* 3.0 13.9 + - - -
47B ILE* 3.9 24.9 - - + +
48B SER* 5.2 1.9 - - - -
49B LYS* 3.0 45.7 + - - +
144B TYR* 4.2 13.1 + - + -
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Residues in contact with LYS 43 (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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39B THR* 3.0 13.7 + - + +
40B GLU* 3.1 11.2 + - - +
42B GLU* 1.3 76.4 - - - +
44B GLU* 1.3 61.3 + - + +
45B GLY 3.6 0.3 + - - -
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Residues in contact with GLU 44 (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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40B GLU* 2.8 36.7 + - - +
41B MET* 3.5 5.4 + - - +
42B GLU 3.0 1.0 - - - -
43B LYS* 1.3 78.1 - - + +
45B GLY* 1.3 61.9 + - - +
46B LYS* 3.3 26.4 + - + +
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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
------------------------------------------------------------
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