Contacts of the helix formed by residues 25 - 46 (chain B) in PDB entry 4EOZ
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 MSE 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 1.3 80.5 - - - +
26B ASP* 1.3 64.8 + - - +
27B GLU 3.3 1.1 - - - -
28B LYS* 3.6 28.6 + - - +
29B TYR* 3.3 20.4 + - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MSE 1.3 76.4 - - - +
27B GLU* 1.3 67.5 + - - +
28B LYS 3.3 0.2 - - - -
29B TYR* 3.5 19.5 + - - -
30B VAL* 3.1 21.1 + - - +
67B HIS* 6.0 1.7 - - - +
69B HIS* 4.4 18.7 + - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 3.6 36.8 - - + +
25B MSE 4.0 0.4 - - - +
26B ASP* 1.3 77.8 - - - +
28B LYS* 1.3 58.8 + - + +
30B VAL* 3.1 13.8 - - - +
31B ASN* 2.9 47.4 + - - +
69B HIS* 6.1 0.7 - - - -
72B LYS* 5.9 0.7 - - - +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 3.8 19.7 + - - +
25B MSE 3.6 30.7 + - - +
26B ASP 3.3 0.6 - - - -
27B GLU* 1.3 81.1 - - + +
29B TYR* 1.3 57.8 + - - +
31B ASN* 3.5 11.2 + - - +
32B SER* 2.8 31.5 + - - -
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Residues in contact with TYR 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MSE 3.3 15.3 + - - +
26B ASP* 3.8 19.7 - - - +
27B GLU 3.3 0.4 - - - -
28B LYS* 1.3 77.6 - - - +
30B VAL* 1.3 61.9 + - + +
32B SER* 3.1 23.1 - - - -
33B ILE* 3.1 32.1 + - + +
63B THR* 3.7 19.1 - - - +
67B HIS* 4.3 22.2 - + - -
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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
----------------------------------------------------------
26B ASP* 3.1 15.7 + - - +
27B GLU* 3.1 29.9 + - - +
29B TYR* 1.3 76.4 - - + +
31B ASN* 1.3 67.1 + - - +
33B ILE* 3.2 9.0 + - + +
34B TRP* 3.0 22.9 + - - +
64B MSE 3.6 32.5 - - + -
69B HIS* 3.8 42.8 - - + +
72B LYS* 4.1 13.0 - - + -
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 2.9 38.1 + - - +
28B LYS* 3.6 12.2 - - - +
30B VAL* 1.3 74.3 - - - +
32B SER* 1.3 58.1 + - - +
34B TRP* 3.3 2.4 + - - +
35B ASP* 2.9 41.1 + - - +
72B LYS* 3.1 31.0 + - - +
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Residues in contact with SER 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 LYS 2.8 15.2 + - - -
29B TYR* 3.1 20.2 - - - -
31B ASN* 1.3 76.5 - - - +
33B ILE* 1.3 59.5 + - - +
35B ASP* 3.4 16.2 + - - +
36B LEU* 3.4 12.1 + - - +
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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 TYR* 3.1 49.6 + - + +
30B VAL* 3.2 10.3 + - + +
32B SER* 1.3 73.7 - - - +
34B TRP* 1.3 67.5 + - - +
36B LEU* 3.2 13.0 + - - +
37B LEU* 3.3 12.7 + - + +
60B ASN* 3.4 48.7 - - + +
63B THR* 4.2 17.5 - - + -
64B MSE 3.7 19.1 - - + -
67B HIS* 5.8 0.2 - - - +
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Residues in contact with TRP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL 3.0 16.1 + - - +
31B ASN 3.6 3.4 - - - +
33B ILE* 1.3 77.9 - - - +
35B ASP* 1.3 72.8 + - - +
36B LEU 3.2 0.2 + - - -
37B LEU* 3.2 19.9 + - + -
38B LYS* 2.9 57.5 + - + +
41B ILE* 4.2 10.8 - - + -
64B MSE 3.8 12.5 - - + -
72B LYS* 3.8 31.2 - - + -
73B LEU* 3.7 33.2 - - + -
76B GLY* 3.3 44.6 - - - -
77B LEU* 3.6 6.7 - - + -
79B GLU* 5.1 5.0 + - + -
80B VAL* 4.1 9.9 - - + -
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Residues in contact with ASP 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 ASN* 2.9 22.4 + - - +
32B SER* 3.5 13.7 - - - +
33B ILE 3.2 0.4 - - - -
34B TRP* 1.3 87.4 - - - +
36B LEU* 1.3 61.0 + - - +
38B LYS* 3.9 9.2 - - - +
39B ASN* 3.2 32.4 + - - +
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Residues in contact with LEU 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 SER 3.4 7.1 + - - +
33B ILE 3.2 10.4 + - - +
35B ASP* 1.3 74.4 - - - +
37B LEU* 1.3 68.7 + - + +
39B ASN* 3.3 12.3 + - - +
40B ALA* 3.1 18.5 + - + +
56B GLU* 4.1 27.1 - - + +
57B LEU* 3.8 25.1 - - + -
60B ASN* 4.0 24.2 - - - +
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Residues in contact with LEU 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 3.3 10.7 + - - +
34B TRP* 3.5 18.2 - - + +
36B LEU* 1.3 77.6 - - + +
38B LYS* 1.3 55.2 + - - +
40B ALA* 2.8 23.9 + - + +
41B ILE* 2.8 27.6 + - + +
57B LEU* 3.5 40.2 - - + +
60B ASN* 3.8 14.1 - - + -
61B ALA* 3.9 20.6 - - + +
64B MSE 4.1 8.1 - - - -
73B LEU* 3.7 30.3 - - + -
122B ILE* 4.9 4.3 - - + -
123B LEU* 4.7 4.3 - - + -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TRP* 2.9 57.2 + - + +
35B ASP* 3.9 9.0 - - - +
37B LEU* 1.3 72.2 - - - +
39B ASN* 1.3 70.5 + - - +
41B ILE* 3.3 7.3 + - - +
42B GLN* 3.0 43.8 + - - +
79B GLU* 4.2 18.8 + - - +
80B VAL* 4.3 15.5 - - + +
83B GLU* 3.7 21.6 + - - -
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Residues in contact with ASN 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 ASP* 3.2 17.3 + - - +
36B LEU* 3.3 12.2 + - - +
38B LYS* 1.3 82.4 - - - +
40B ALA* 1.3 61.6 + - - +
42B GLN* 3.4 15.0 + - - +
43B GLU* 3.2 26.1 + - - +
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Residues in contact with ALA 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 LEU* 3.1 9.4 + - + +
37B LEU* 2.8 15.9 + - + +
39B ASN* 1.3 68.9 - - - +
41B ILE* 1.3 66.5 + - + +
43B GLU* 2.8 16.5 + - - +
44B ILE* 3.0 18.0 + - - +
52B LEU* 4.0 16.7 - - + +
57B LEU* 3.6 42.2 - - + -
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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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34B TRP* 4.2 28.3 - - + -
37B LEU* 2.8 23.2 + - + +
38B LYS* 3.5 7.2 - - - +
40B ALA* 1.3 72.3 - - + +
42B GLN* 1.3 57.7 + - - +
44B ILE* 3.2 15.3 + - + +
45B GLN* 2.9 39.4 + - - +
77B LEU* 4.6 13.5 - - + -
80B VAL* 3.6 29.4 - - + -
81B VAL* 5.1 1.1 - - + -
119B ILE* 4.1 25.6 - - + -
122B ILE* 6.1 6.1 - - + -
123B LEU* 5.2 10.3 - - + -
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Residues in contact with GLN 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 LYS* 3.0 36.4 + - - +
39B ASN* 3.7 16.1 - - - +
41B ILE* 1.3 75.7 - - - +
43B GLU* 1.3 60.5 + - - +
45B GLN* 3.3 15.4 + - - +
46B ARG* 3.1 54.1 + - - +
80B VAL* 3.8 17.5 + - + +
83B GLU* 3.7 23.6 + - - +
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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 ASN 3.2 14.8 + - - +
40B ALA 2.8 9.2 + - - +
42B GLN* 1.3 72.9 - - - +
44B ILE* 1.3 57.5 + - - +
46B ARG* 3.0 31.9 + - - +
47B LYS 3.0 8.1 + - - -
48B ASN* 2.2 70.6 + - + +
52B LEU* 4.4 21.3 - - + -
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Residues in contact with ILE 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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233A MET* 4.2 8.3 - - + -
40B ALA 3.0 14.5 + - - +
41B ILE* 3.3 17.7 - - + +
43B GLU* 1.3 75.8 - - - +
45B GLN* 1.3 57.9 + - - +
47B LYS* 2.9 20.9 + - - +
48B ASN 4.4 2.9 - - - +
49B ASN* 4.2 11.2 - - + -
52B LEU* 3.6 18.4 - - + +
57B LEU* 4.8 2.0 - - + -
115B ALA* 4.0 26.0 - - + +
118B MSE 3.6 28.9 - - + +
119B ILE* 4.3 15.0 - - + -
122B ILE* 3.7 29.6 - - + -
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Residues in contact with GLN 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 ILE* 2.9 25.1 + - + +
42B GLN* 3.5 24.0 + - - +
43B GLU 3.2 0.4 - - - -
44B ILE* 1.3 77.6 - - - +
46B ARG* 1.3 60.4 + - + +
47B LYS* 3.5 10.9 + - - +
80B VAL* 3.3 26.2 + - - +
81B VAL* 3.6 27.1 - - - +
84B HIS* 3.5 57.1 + - + +
115B ALA* 4.8 10.4 - - + +
119B ILE* 4.8 9.5 - - + +
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Residues in contact with ARG 46 (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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42B GLN* 3.1 42.3 + - - +
43B GLU* 3.0 28.0 + - - +
45B GLN* 1.3 78.3 - - + +
47B LYS* 1.3 73.6 + - - +
48B ASN* 3.1 8.0 + - + +
84B HIS* 5.6 5.1 - - + +
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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
------------------------------------------------------------
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