Contacts of the helix formed by residues 36 - 51 (chain A) in PDB entry 2DIZ
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 GLY 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TRP 4.0 1.2 + - - -
35A CYS* 1.3 73.7 - - - +
37A HIS* 1.3 57.2 + - - +
38A CYS 3.0 1.6 - - - -
39A LYS* 2.7 52.6 + - - +
40A THR* 3.9 1.6 + - - -
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Residues in contact with HIS 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 CYS* 4.2 7.7 - - - -
36A GLY* 1.3 75.3 - - - +
38A CYS* 1.3 57.6 + - - +
40A THR* 2.9 38.9 + - + -
41A LEU* 3.8 2.6 + - - +
81A TYR 4.8 3.1 - - - +
82A PRO* 3.7 26.3 - - + +
100A ARG* 5.2 9.4 - - + -
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Residues in contact with CYS 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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29A LYS* 4.8 2.2 + - - +
31A TYR* 4.0 23.8 - - + -
32A ALA 4.1 8.3 - - - +
35A CYS* 3.4 33.4 - - + +
36A GLY 2.9 0.8 + - - -
37A HIS* 1.3 79.2 - - - +
39A LYS* 1.3 57.5 + - - +
41A LEU* 2.9 7.3 + - - +
42A ALA* 2.9 25.3 + - - +
81A TYR* 3.5 25.4 - - - -
82A PRO* 3.6 24.9 - - + -
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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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33A PRO 5.4 6.3 - - - -
34A TRP 5.7 1.7 + - - -
35A CYS 3.5 19.7 - - - +
36A GLY* 2.7 29.9 + - - +
38A CYS* 1.3 73.1 - - + +
40A THR* 1.3 57.5 + - - +
42A ALA* 3.3 23.9 - - - +
43A PRO* 3.3 6.2 - - - +
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Residues in contact with THR 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 GLY 4.6 0.9 + - - -
37A HIS* 2.9 32.5 + - + -
39A LYS* 1.3 79.4 - - - +
41A LEU* 1.3 56.8 + - - +
43A PRO* 3.5 11.3 - - - +
44A THR* 3.4 14.0 + - - +
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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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29A LYS* 3.5 24.2 - - + +
37A HIS* 4.9 0.9 - - - +
38A CYS* 2.9 10.7 + - - +
40A THR* 1.3 75.0 - - - +
42A ALA* 1.3 68.3 + - - +
43A PRO* 3.2 3.4 - - - -
44A THR* 2.8 30.2 + - + +
45A TRP* 2.7 31.1 + - + +
82A PRO* 3.9 23.8 - - + -
84A LEU* 3.8 28.7 - - + -
100A ARG* 3.9 24.2 - - + +
105A LEU* 4.3 9.2 - - + -
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Residues in contact with ALA 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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29A LYS* 4.3 7.4 - - - +
38A CYS 2.9 9.5 + - - +
39A LYS* 3.3 17.3 - - + +
41A LEU* 1.3 77.5 - - - +
43A PRO* 1.3 70.7 - - + +
45A TRP* 3.8 4.5 + - - +
46A GLU* 3.8 20.0 + - - +
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Residues in contact with PRO 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 3.3 11.2 - - - +
40A THR* 3.5 10.3 - - - +
41A LEU 3.3 2.5 - - - -
42A ALA* 1.3 97.0 - - + +
44A THR* 1.3 72.2 + - - +
46A GLU* 2.9 26.3 + - - +
47A GLU* 3.1 16.5 + - + +
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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 THR* 3.4 14.7 + - - +
41A LEU* 2.8 26.1 + - + +
43A PRO* 1.3 74.2 - - - +
45A TRP* 1.3 66.2 + - - +
47A GLU* 2.8 27.4 + - - +
48A LEU* 3.2 5.0 + - - +
100A ARG 4.4 1.1 + - - +
101A ASP* 4.0 3.6 - - - -
102A LEU* 3.4 34.0 - - + +
105A LEU* 3.5 17.9 - - + -
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Residues in contact with TRP 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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9A VAL* 3.6 27.8 - - + +
27A PHE* 3.0 58.1 - + - -
28A ILE 3.6 5.8 - - - -
29A LYS* 3.2 53.2 - - + +
41A LEU* 2.7 23.3 + - + +
42A ALA 3.9 5.2 - - - +
44A THR* 1.3 74.1 - - - +
46A GLU* 1.3 65.2 + - - +
48A LEU* 3.3 25.0 + - + +
49A SER 3.5 3.1 + - - -
61A ILE* 3.5 16.0 - - + +
62A ALA 2.8 35.7 + - - -
63A GLU* 3.8 5.3 - - + +
84A LEU* 3.8 11.0 - - + -
105A LEU* 4.9 8.3 - - + -
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Residues in contact with GLU 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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8A THR* 3.6 36.5 + - + +
9A VAL* 3.6 20.0 - - + -
42A ALA 3.8 14.2 + - - +
43A PRO* 2.9 17.4 + - - +
45A TRP* 1.3 75.9 - - - +
47A GLU* 1.3 68.3 + - + +
49A SER* 2.5 28.1 + - - -
50A LYS* 3.4 9.1 + - - +
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Residues in contact with GLU 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 PRO* 3.1 13.0 + - + +
44A THR* 2.8 18.8 + - - +
46A GLU* 1.3 75.9 - - - +
48A LEU* 1.3 63.7 + - - +
50A LYS* 2.9 46.3 + - - +
51A LYS* 3.2 12.3 + - - +
102A LEU* 3.2 36.1 - - + +
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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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27A PHE* 3.7 22.7 - - + -
44A THR 3.2 4.2 + - - +
45A TRP* 3.3 23.6 - - + +
46A GLU 3.1 0.2 - - - -
47A GLU* 1.3 78.2 - - - +
49A SER* 1.3 56.3 + - - +
51A LYS* 2.6 41.2 + - + +
53A PHE* 4.7 11.4 - - + -
61A ILE* 3.5 29.2 - - + +
102A LEU* 3.7 10.1 - - + +
105A LEU* 3.6 34.1 - - + +
106A HIS* 3.6 22.9 - - + +
109A VAL* 5.6 0.9 - - + -
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Residues in contact with SER 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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7A GLY 3.4 7.8 + - - +
8A THR* 2.5 43.3 + - - -
9A VAL* 4.7 0.4 - - - -
10A LEU* 6.2 1.8 - - - -
45A TRP 3.5 2.0 + - - -
46A GLU 2.5 22.6 + - - -
48A LEU* 1.3 75.7 - - - +
50A LYS* 1.3 60.8 + - - +
51A LYS 3.4 6.2 - - - +
53A PHE* 5.8 0.3 - - - -
61A ILE* 3.7 27.7 - - - +
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Residues in contact with LYS 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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7A GLY 4.1 9.4 - - - +
8A THR* 4.6 18.8 - - - -
46A GLU* 4.6 10.4 - - - +
47A GLU* 2.9 41.2 + - - +
49A SER* 1.3 83.4 + - - +
51A LYS* 1.3 70.7 + - + +
52A GLU* 3.7 11.4 - - - +
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Residues in contact with LYS 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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47A GLU 3.2 10.7 + - - +
48A LEU* 2.6 34.2 + - + +
49A SER 3.4 8.8 - - - +
50A LYS* 1.3 79.3 - - + +
52A GLU* 1.3 62.5 + - - +
53A PHE* 4.2 10.1 - - + -
102A LEU* 3.8 24.7 - - + -
103A ASP* 5.9 0.9 - - - +
106A HIS* 3.4 50.3 + - + -
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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