Contacts of the helix formed by residues 29 - 44 (chain B) in PDB entry 1WKM
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 LEU 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B GLY 3.3 4.5 + - - +
28B MET* 1.3 78.1 - - - +
30B LEU* 1.3 67.7 + - - +
31B LEU* 3.1 16.6 - - + +
32B GLU* 2.9 26.3 + - + +
33B LEU* 2.9 19.8 + - - +
69B ASP 4.3 9.2 - - - +
70B THR* 3.8 19.7 - - - +
71B THR 3.6 15.7 - - - +
72B VAL* 4.3 8.7 - - + -
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Residues in contact with LEU 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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28B MET 3.5 3.8 + - - -
29B LEU* 1.3 69.5 - - - +
31B LEU* 1.3 59.0 + - - +
33B LEU* 3.2 9.3 + - + +
34B ALA* 2.9 25.6 + - - +
54B LEU* 3.6 39.5 - - + +
56B ILE* 4.2 6.7 - - + -
63B TYR* 3.8 25.4 - - + -
65B PRO* 3.3 16.9 - - + +
69B ASP* 4.8 0.9 - - - +
71B THR* 3.1 44.5 + - + +
73B LEU* 3.2 32.1 - - + -
79B LEU* 4.3 6.1 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.1 12.4 - - + +
30B LEU* 1.3 78.7 - - - +
32B GLU* 1.3 57.5 + - - +
34B ALA* 3.3 1.6 + - - +
35B GLU* 2.8 50.9 + - + +
65B PRO* 3.6 13.1 - - + +
66B TYR 3.6 21.3 - - - +
67B LYS* 4.1 19.5 - - + +
68B GLY* 4.2 5.6 - - - +
69B ASP 4.2 17.0 + - - +
71B THR 4.7 0.4 + - - -
238B ARG* 3.5 32.3 - - + -
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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 MET* 3.6 27.6 - - + +
29B LEU* 2.9 27.4 + - + +
31B LEU* 1.3 77.1 - - - +
33B LEU* 1.3 65.6 + - - +
35B GLU* 3.4 8.0 + - - +
36B SER* 2.9 38.9 + - - +
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Residues in contact with LEU 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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20B ALA* 4.0 9.2 - - - +
23B LEU* 3.6 37.7 - - + +
24B ALA* 4.4 5.4 - - + -
28B MET* 4.0 10.3 - - + -
29B LEU 2.9 11.9 + - - +
30B LEU* 3.4 11.9 - - + +
32B GLU* 1.3 78.3 - - - +
34B ALA* 1.3 62.1 + - - +
36B SER* 3.6 4.1 + - - -
37B ILE* 3.1 46.1 + - + +
54B LEU* 4.0 24.2 - - + -
73B LEU* 4.3 13.9 - - + -
79B LEU* 4.1 19.1 - - + -
81B ILE* 5.2 2.0 - - + -
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Residues in contact with ALA 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 LEU 2.9 16.8 + - - +
31B LEU* 3.5 5.6 - - - +
33B LEU* 1.3 76.9 - - - +
35B GLU* 1.3 61.8 + - - +
37B ILE* 3.3 5.1 + - - +
38B GLU* 3.1 26.3 + - - +
52B VAL* 3.7 20.5 - - + +
54B LEU* 3.9 3.3 - - + +
65B PRO* 3.6 24.0 - - + -
238B ARG* 4.0 17.3 - - - +
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Residues in contact with GLU 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 LEU* 2.8 48.7 - - + +
32B GLU* 3.6 7.9 - - - +
34B ALA* 1.3 71.9 - - - +
36B SER* 1.3 57.9 + - - +
38B GLU* 2.9 9.0 + - - +
39B LYS* 2.6 39.6 + - + +
67B LYS* 4.3 16.8 + - - -
238B ARG* 3.5 18.6 + - - +
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Residues in contact with SER 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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23B LEU* 4.3 22.1 - - - +
32B GLU* 2.9 29.0 + - - +
33B LEU* 3.6 6.2 - - - -
35B GLU* 1.3 81.4 - - - +
37B ILE* 1.3 57.7 + - - +
39B LYS* 3.4 10.4 + - - +
40B MET* 2.9 31.1 + - - +
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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
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16B VAL* 4.1 11.8 - - + +
20B ALA* 3.8 31.9 - - + -
23B LEU* 5.8 2.0 - - + -
33B LEU* 3.1 34.2 + - + +
34B ALA 3.5 6.7 - - - +
35B GLU 3.1 0.4 - - - -
36B SER* 1.3 80.4 - - - +
38B GLU* 1.3 62.7 + - - +
40B MET* 3.2 9.6 + - - +
41B ILE* 3.0 33.5 + - + +
52B VAL* 3.6 40.4 - - + -
54B LEU* 4.4 2.9 - - + -
81B ILE* 4.2 7.0 - - + -
83B VAL* 4.4 11.2 - - + -
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Residues in contact with GLU 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 ALA 3.1 6.6 + - - +
35B GLU* 2.9 9.7 + - - +
37B ILE* 1.3 77.2 - - - +
39B LYS* 1.3 63.6 + - - +
41B ILE* 3.3 18.5 + - + +
42B MET* 3.2 28.4 + - - +
48B PRO* 4.7 13.0 - - + +
51B PRO* 3.4 7.3 - - - +
52B VAL* 3.1 34.0 + - + +
238B ARG* 2.3 36.0 + - - -
239B TRP* 2.8 22.7 + - - -
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Residues in contact with LYS 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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35B GLU 2.6 22.3 + - - +
36B SER* 3.6 9.0 - - - +
38B GLU* 1.3 73.7 - - - +
40B MET* 1.3 58.8 + - - +
42B MET* 3.4 8.6 + - + +
43B GLU* 3.0 53.9 + - + +
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Residues in contact with MET 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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15B LYS* 3.1 38.8 - - + +
16B VAL* 3.4 21.5 - - + +
19B LYS* 3.4 33.4 - - + -
36B SER 2.9 19.0 + - - +
37B ILE* 3.4 7.6 - - - +
39B LYS* 1.3 77.0 - - - +
41B ILE* 1.3 64.4 + - - +
43B GLU* 3.4 16.7 + - + +
44B LEU* 3.1 39.6 + - + +
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Residues in contact with ILE 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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12B ILE* 4.2 4.9 - - - +
16B VAL* 3.9 14.6 - - + -
37B ILE* 3.0 24.7 + - + +
38B GLU* 3.5 22.9 - - + +
39B LYS 3.3 0.4 - - - -
40B MET* 1.3 75.7 - - - +
42B MET* 1.3 62.1 + - - +
44B LEU* 3.4 8.3 + - - +
45B GLY 3.4 0.3 + - - -
46B GLY* 2.9 45.5 + - - +
47B LYS* 3.6 18.4 - - - +
48B PRO* 3.7 9.4 - - + -
50B PHE 5.9 0.2 - - - +
52B VAL* 5.8 1.6 - - + -
83B VAL* 4.2 12.8 - - + -
84B GLY 4.0 16.8 - - - +
85B VAL* 3.7 21.5 - - + -
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Residues in contact with MET 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 GLU* 3.2 16.4 - - + +
39B LYS* 3.6 9.4 - - - +
40B MET 3.2 0.2 - - - -
41B ILE* 1.3 72.5 - - - +
43B GLU* 1.3 54.4 + - + +
44B LEU 3.0 4.5 - - - -
45B GLY* 2.7 26.3 + - - -
46B GLY 3.2 24.2 + - - +
47B LYS* 4.0 13.7 - - + -
48B PRO* 3.9 25.6 - - + -
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Residues in contact with GLU 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 LYS* 3.0 52.9 + - + +
40B MET* 3.4 20.9 + - + +
42B MET* 1.3 75.3 - - + +
44B LEU* 1.3 63.7 + - + +
45B GLY* 3.3 0.6 + - - -
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Residues in contact with LEU 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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8B LYS* 5.5 2.3 - - - +
12B ILE* 3.8 35.6 - - + +
15B LYS* 3.9 46.2 - - + +
16B VAL* 4.1 9.9 - - + -
40B MET* 3.1 27.8 + - + +
41B ILE 3.6 6.7 - - - +
42B MET 3.0 0.8 - - - -
43B GLU* 1.3 81.2 - - + +
45B GLY* 1.3 59.9 + - - +
46B GLY 3.5 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