Contacts of the helix formed by residues 35 - 47 (chain A) in PDB entry 2DZJ
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A HIS 3.4 6.5 + - - +
34A ALA* 1.3 75.1 - - - +
36A ILE* 1.3 68.8 + - - +
37A ALA* 3.9 5.5 - - - +
38A GLU* 2.7 28.3 + - - +
39A ILE* 3.3 9.1 + - - +
68A ASP* 3.0 40.8 + - - +
69A GLU* 4.8 1.1 - - - +
70A ASP 3.6 4.5 - - - -
71A VAL* 4.0 17.9 - - + +
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Residues in contact with ILE 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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34A ALA 4.1 0.6 + - - -
35A THR* 1.3 72.6 - - - +
37A ALA* 1.3 63.5 + - - +
39A ILE* 2.9 25.1 + - + +
40A LYS* 2.9 42.7 - - - +
57A LEU* 3.8 13.9 - - + -
59A LEU* 6.2 0.2 - - + -
66A LEU* 4.1 35.7 - - + -
67A LYS 3.5 20.4 - - - +
68A ASP* 3.9 0.2 - - - -
70A ASP* 3.2 27.9 + - + +
71A VAL* 4.9 6.3 - - - +
72A LEU* 5.4 4.7 - - + +
75A LEU* 5.7 7.2 - - + -
83A LEU* 4.8 10.5 - - + -
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Residues in contact with ALA 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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35A THR* 2.9 3.2 + - - +
36A ILE* 1.3 79.7 - - - +
38A GLU* 1.3 63.0 + - + +
40A LYS* 3.2 29.6 + - - +
41A ASN* 3.5 12.4 + - - +
68A ASP* 3.2 34.4 - - + +
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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 ALA* 4.3 14.4 - - + -
35A THR* 2.7 32.5 + - - +
37A ALA* 1.3 73.4 - - + +
39A ILE* 1.3 66.7 + - - +
41A ASN* 2.9 36.1 + - - +
42A LEU* 3.2 11.7 + - + +
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Residues in contact with ILE 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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13A VAL* 4.8 4.7 - - + -
15A ILE* 4.6 12.3 - - + -
27A LEU* 4.4 7.0 - - + +
30A VAL* 3.4 36.3 - - + -
34A ALA* 4.8 3.8 - - + -
35A THR 3.7 9.9 - - - +
36A ILE* 2.9 28.8 + - + +
38A GLU* 1.3 76.5 - - - +
40A LYS* 1.3 61.8 + - - +
42A LEU* 3.1 26.7 + - + +
43A PHE* 3.4 5.4 + - - +
57A LEU* 4.1 8.7 - - + -
72A LEU* 3.7 18.2 - - + -
83A LEU* 3.7 26.5 - - + -
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 2.9 54.4 - - - +
37A ALA* 3.4 16.5 - - - +
38A GLU 3.2 0.6 - - - -
39A ILE* 1.3 79.0 - - - +
41A ASN* 1.3 66.0 + - - +
43A PHE* 3.1 18.0 + - - +
44A THR* 2.9 15.0 + - - -
52A PRO* 4.1 26.9 - - + +
55A GLN* 3.8 27.6 + - + +
57A LEU* 3.8 21.8 - - + +
66A LEU 4.8 6.9 + - - -
68A ASP* 4.4 8.5 - - - +
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Residues in contact with ASN 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 ALA* 3.5 15.4 + - - +
38A GLU* 2.9 26.9 + - - +
40A LYS* 1.3 78.2 - - - +
42A LEU* 1.3 65.8 + - - +
44A THR* 2.9 26.0 + - - -
45A LYS* 3.1 9.7 + - - +
52A PRO* 5.5 4.2 - - - +
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Residues in contact with LEU 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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27A LEU* 3.6 27.9 - - + +
29A LYS 5.2 8.3 - - - +
30A VAL* 4.0 34.5 - - + -
34A ALA* 6.2 0.9 - - + -
38A GLU* 3.2 7.9 + - + +
39A ILE* 3.1 24.3 + - + +
41A ASN* 1.3 77.7 - - + +
43A PHE* 1.3 56.0 + - - +
45A LYS* 2.6 63.7 + - + +
46A THR* 3.9 2.3 + - - -
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Residues in contact with PHE 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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15A ILE* 3.7 33.7 - - + -
24A LEU* 4.6 16.6 - - + -
25A CYS* 3.6 34.5 - - + -
27A LEU* 4.3 3.6 - - - +
39A ILE 3.4 6.3 + - - +
40A LYS* 3.1 8.5 + - - +
42A LEU* 1.3 76.3 - - - +
44A THR* 1.3 60.8 + - - +
46A THR* 3.8 3.9 + - - -
47A HIS* 3.5 34.7 + + + +
50A TRP* 3.3 44.0 - + + -
55A GLN* 2.7 32.3 - - + +
85A PHE* 5.6 4.5 - + - -
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Residues in contact with THR 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 LYS 2.9 16.4 + - - -
41A ASN* 2.9 17.7 + - - -
42A LEU 2.7 1.6 + - - -
43A PHE* 1.3 77.0 - - - +
45A LYS* 1.3 66.3 + - - +
47A HIS 2.7 27.7 - - - +
48A PRO* 3.0 17.4 - - + +
50A TRP 3.3 20.6 + - - +
51A TYR* 5.0 3.6 - - - -
52A PRO* 4.7 9.2 - - + +
55A GLN* 3.8 6.8 + - - -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN* 3.9 7.9 - - - +
42A LEU* 2.6 49.1 + - + +
44A THR* 1.3 75.2 - - - +
46A THR* 1.3 65.8 + - - +
48A PRO* 3.9 7.1 - - - +
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Residues in contact with THR 46 (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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25A CYS* 4.9 11.5 - - - -
27A LEU* 6.1 0.9 - - - +
42A LEU 3.9 1.2 + - - -
43A PHE* 3.8 4.3 + - - -
44A THR 3.3 0.2 - - - -
45A LYS* 1.3 80.0 - - - +
47A HIS* 1.3 86.4 + - + +
48A PRO* 3.0 12.6 - - - +
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Residues in contact with HIS 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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24A LEU 5.0 8.7 + - - -
25A CYS* 5.2 5.5 - - - -
43A PHE* 3.5 29.6 + + + +
44A THR* 2.7 20.0 + - - +
46A THR* 1.3 101.3 + - + +
48A PRO* 1.3 65.7 - - - +
49A GLN* 3.4 1.8 - - + +
50A TRP* 3.4 42.3 + + + +
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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