Contacts of the helix formed by residues 34 - 51 (chain A) in PDB entry 2Y4U
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 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLN* 3.1 26.7 + - + +
33A SER* 1.3 69.7 - - - +
35A ALA* 1.3 62.2 + - - +
36A ASP* 3.3 3.6 - - - +
37A VAL* 3.4 30.8 + - + +
38A GLU* 3.1 21.0 + - + +
66A GLY 6.0 0.2 - - - +
67A ASP* 3.2 29.6 - - - +
70A ASN* 5.6 5.6 - - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 3.0 17.7 - - - +
34A MSE 1.3 75.0 - - - +
36A ASP* 1.3 59.3 + - - +
38A GLU* 2.7 12.8 + - - -
39A LYS* 2.5 58.9 + - + +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 5.2 7.3 + - - +
34A MSE 3.3 1.5 - - - +
35A ALA* 1.3 79.1 - - - +
37A VAL* 1.3 59.5 + - + +
39A LYS* 3.5 6.1 + - - +
40A HIS* 3.0 44.9 + - - +
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MSE 3.4 33.3 + - + -
35A ALA 3.2 0.4 - - - -
36A ASP* 1.3 78.6 - - + +
38A GLU* 1.3 59.0 + - - +
40A HIS* 3.8 13.9 - - + +
41A LEU* 3.0 34.3 - - + +
63A ALA* 4.1 13.4 - - + +
66A GLY* 3.9 27.1 - - - +
67A ASP* 3.7 24.0 - - + -
70A ASN* 5.4 3.8 - - + +
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Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MSE 3.1 16.4 + - + +
35A ALA* 2.7 19.8 + - - +
37A VAL* 1.3 71.5 - - - +
39A LYS* 1.3 80.8 + - - +
41A LEU* 3.0 28.3 + - - +
42A GLU* 3.1 13.3 + - + +
70A ASN* 5.9 0.3 + - - -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 2.5 50.8 + - + +
36A ASP* 4.0 6.1 - - - +
38A GLU* 1.3 92.3 - - - +
40A HIS* 1.3 65.0 + - - +
42A GLU* 2.7 35.5 + - - +
43A LEU* 2.8 32.4 + - + +
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Residues in contact with HIS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 3.0 36.6 + - + +
37A VAL* 3.8 13.5 - - + +
38A GLU 3.3 0.2 - - - -
39A LYS* 1.3 74.9 - - - +
41A LEU* 1.3 56.4 + - - +
43A LEU* 4.0 4.8 - - + +
44A GLY* 2.8 26.3 + - - -
59A GLN* 2.9 39.1 + - - +
60A PHE* 4.4 0.9 - - - -
62A ALA* 3.3 39.1 + - + +
63A ALA* 3.9 14.1 - - + -
66A GLY* 5.7 0.9 - - - -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.0 30.3 - - + +
38A GLU* 3.0 23.9 + - - +
39A LYS 3.0 0.6 - - - -
40A HIS* 1.3 74.8 - - - +
42A GLU* 1.3 56.3 + - - +
44A GLY* 3.4 0.2 - - - -
45A LYS* 2.7 53.3 + - - +
60A PHE* 3.8 16.7 - - + -
63A ALA* 4.0 14.6 - - + -
70A ASN* 4.6 13.5 - - - +
72A ILE* 4.7 7.0 - - + -
73A ALA* 3.9 31.0 - - + +
76A ARG* 4.5 8.3 - - + -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 3.1 9.9 + - - +
39A LYS* 2.7 32.4 + - + +
41A LEU* 1.3 71.7 - - - +
43A LEU* 1.3 58.2 + - + +
45A LYS* 2.8 28.7 + - - +
46A LYS* 2.9 47.7 + - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 2.8 42.6 + - + +
40A HIS* 3.9 9.0 - - - +
42A GLU* 1.3 76.0 + - + +
44A GLY* 1.3 61.4 + - - +
46A LYS* 3.6 10.6 + - - +
47A LEU* 3.1 33.4 + - + +
59A GLN* 4.6 15.9 - - + +
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Residues in contact with GLY 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS 2.8 24.0 + - - -
41A LEU 3.4 1.6 - - - -
42A GLU 3.1 0.2 - - - -
43A LEU* 1.3 74.4 - - - +
45A LYS* 1.3 60.7 + - - +
47A LEU* 3.3 5.3 + - - +
48A LEU* 3.1 18.4 + - - +
56A ALA* 3.9 1.8 - - - +
59A GLN* 3.8 15.2 - - - +
60A PHE* 3.1 26.8 - - - -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 2.7 36.9 + - - +
42A GLU* 2.8 6.6 + - - +
44A GLY* 1.3 68.6 - - - -
46A LYS* 1.3 61.8 + - + +
48A LEU* 3.4 8.2 + - - +
49A ALA* 2.9 29.4 + - - +
60A PHE* 3.8 11.7 - - + -
72A ILE* 3.9 14.0 - - - +
76A ARG* 3.2 56.0 - - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 2.9 49.7 + - + +
43A LEU* 3.9 8.3 - - + +
45A LYS* 1.3 78.1 - - + +
47A LEU* 1.3 56.6 + - + +
49A ALA* 3.1 10.0 + - - +
50A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 47 (chain A).
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* 3.1 22.4 + - + +
44A GLY 3.5 6.3 - - - +
46A LYS* 1.3 72.8 - - + +
48A LEU* 1.3 68.7 - - - +
50A ALA* 2.8 16.9 + - + +
51A GLY 3.1 0.2 + - - -
52A GLN* 3.0 43.4 + - + +
55A ASP* 3.6 37.5 - - + +
56A ALA* 3.7 9.4 - - - +
59A GLN* 3.7 17.0 - - + +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLY 3.1 10.5 + - - +
45A LYS* 3.6 11.0 - - - +
47A LEU* 1.3 77.2 - - - +
49A ALA* 1.3 60.9 + - + +
51A GLY* 2.7 26.7 + - - -
52A GLN 4.5 2.5 - - - +
53A LEU* 4.6 11.2 - - + +
56A ALA* 3.6 12.6 - - + +
60A PHE* 4.4 7.2 - - + -
76A ARG* 5.8 5.6 - - - +
79A THR* 4.0 19.1 - - - +
80A VAL* 3.7 28.7 - - + +
83A ALA* 6.1 1.1 - - + -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LYS 2.9 14.9 + - - +
46A LYS* 3.2 13.7 - - - +
47A LEU 3.1 0.2 - - - -
48A LEU* 1.3 83.1 - - + +
50A ALA* 1.3 60.0 + - - +
51A GLY* 3.4 0.7 + - - -
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS 2.9 11.9 + - - +
47A LEU* 2.8 12.7 + - + +
49A ALA* 1.3 77.1 - - - +
51A GLY* 1.3 57.0 + - - +
52A GLN* 3.0 27.1 + - + +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU 2.7 13.9 + - - -
49A ALA 3.2 2.0 + - - -
50A ALA* 1.3 78.2 - - - +
52A GLN* 1.3 68.1 + - - +
53A LEU* 3.3 19.9 - - - +
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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