Contacts of the helix formed by residues 54 - 69 (chain B) in PDB entry 2Z43
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 PRO 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B SER* 3.5 1.9 + - - -
52B GLY 4.6 1.6 - - - +
53B ILE* 1.3 93.9 - - + +
55B LEU* 1.3 60.7 + - - +
56B SER* 4.3 10.5 - - - +
57B THR* 3.0 30.0 + - - +
58B ALA* 2.8 25.1 + - - +
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Residues in contact with LEU 55 (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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44B PRO* 3.8 18.4 - - + +
45B GLN* 4.7 6.3 - - + +
48B SER* 2.8 22.0 + - - +
53B ILE 3.8 0.2 + - - -
54B PRO* 1.3 71.2 - - - +
56B SER* 1.3 53.5 + - - +
58B ALA* 3.1 1.4 + - - +
59B GLN* 2.7 68.2 + - + +
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Residues in contact with SER 56 (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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54B PRO* 4.3 10.6 - - - +
55B LEU* 1.3 77.7 - - - +
57B THR* 1.3 60.4 + - - +
59B GLN* 3.2 10.7 - - - +
60B LYS* 2.8 30.2 + - - +
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Residues in contact with THR 57 (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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24B VAL* 5.1 7.4 - - + -
53B ILE* 4.3 17.0 - - + -
54B PRO* 3.0 32.1 + - + +
56B SER* 1.3 78.1 + - - +
58B ALA* 1.3 61.5 + - - +
60B LYS* 3.2 6.3 + - + +
61B ILE* 2.8 50.4 + - + +
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Residues in contact with ALA 58 (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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44B PRO* 3.6 13.9 - - + +
47B LEU* 3.8 24.4 - - + +
48B SER* 3.4 31.6 - - - +
53B ILE* 4.3 7.8 - - + +
54B PRO 2.8 8.0 + - - +
55B LEU 3.5 2.7 - - - +
57B THR* 1.3 75.9 - - - +
59B GLN* 1.3 66.5 + - - +
61B ILE* 3.3 2.6 + - - +
62B ILE* 3.1 27.8 + - - +
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Residues in contact with GLN 59 (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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44B PRO* 2.9 35.2 - - - +
55B LEU* 2.7 42.7 + - + +
56B SER* 3.2 12.6 - - - +
58B ALA* 1.3 75.6 - - - +
60B LYS* 1.3 63.4 + - - +
62B ILE* 3.1 5.3 + - - +
63B LYS* 3.1 22.3 + - - +
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Residues in contact with LYS 60 (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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56B SER 2.8 19.0 + - - +
57B THR* 3.8 7.0 - - - +
59B GLN* 1.3 73.8 - - - +
61B ILE* 1.3 58.7 + - + +
63B LYS* 3.3 40.2 + - + +
64B GLU* 2.9 50.6 + - - +
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Residues in contact with ILE 61 (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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17B LEU* 4.1 12.8 - - + +
20B ILE* 5.0 5.6 - - + -
24B VAL* 3.8 30.1 - - + -
28B LEU* 4.2 10.3 - - + -
39B LEU* 3.6 35.7 - - + -
47B LEU* 5.0 1.6 - - + -
53B ILE* 4.1 13.0 - - + -
57B THR* 2.8 37.9 + - + +
58B ALA* 3.7 5.2 - - - +
60B LYS* 1.3 74.3 - - + +
62B ILE* 1.3 59.9 + - - +
64B GLU* 3.4 10.2 + - - +
65B ALA* 2.9 25.1 + - - +
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Residues in contact with ILE 62 (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 LEU* 3.1 26.9 - - + +
40B ALA* 4.2 0.2 - - - -
42B ALA* 3.4 32.5 - - + +
43B SER 4.0 0.2 - - - -
44B PRO* 4.0 18.8 - - + -
47B LEU* 4.0 20.4 - - + -
58B ALA 3.1 12.0 + - - +
59B GLN* 3.7 8.1 - - - +
61B ILE* 1.3 73.3 - - - +
63B LYS* 1.3 68.4 + - - +
65B ALA* 3.1 4.8 + - - +
66B ARG* 3.0 60.6 + - - +
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Residues in contact with LYS 63 (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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59B GLN 3.1 12.8 + - - +
60B LYS* 3.3 43.8 - - + +
62B ILE* 1.3 78.3 - - - +
64B GLU* 1.3 71.4 + - + +
66B ARG* 2.9 13.5 + - - +
67B ASP* 2.4 57.4 + - - +
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Residues in contact with GLU 64 (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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17B LEU* 4.1 14.9 - - + +
18B PRO* 3.0 55.2 - - + +
20B ILE* 5.8 0.2 - - - +
60B LYS* 2.9 44.8 + - + +
61B ILE* 3.6 9.5 - - - +
63B LYS* 1.3 85.8 + - + +
65B ALA* 1.3 56.5 + - - +
67B ASP* 3.1 10.3 + - + +
68B ALA* 2.8 30.3 + - - +
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Residues in contact with ALA 65 (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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17B LEU* 4.1 9.1 - - + +
36B LEU* 3.8 18.5 - - + +
39B LEU* 3.6 32.8 - - + -
40B ALA* 3.9 4.5 - - - +
61B ILE 2.9 17.6 + - - +
62B ILE 3.1 5.6 + - - +
64B GLU* 1.3 75.5 - - - +
66B ARG* 1.3 58.1 + - - +
68B ALA* 3.6 4.5 + - - +
69B LEU* 3.2 32.2 + - - +
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Residues in contact with ARG 66 (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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40B ALA* 2.8 44.1 + - + -
42B ALA 3.6 14.8 + - - +
44B PRO* 6.1 0.4 - - - +
62B ILE* 3.0 35.4 + - - +
63B LYS* 2.9 11.9 + - - +
65B ALA* 1.3 75.9 - - - +
67B ASP* 1.3 63.0 + - - +
68B ALA 3.1 0.2 - - - -
69B LEU 3.1 2.3 + - - +
70B ASP 3.0 4.9 + - - -
71B ILE* 2.8 59.4 + - + +
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Residues in contact with ASP 67 (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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63B LYS* 2.4 57.8 + - - +
64B GLU* 3.1 8.1 - - + +
66B ARG* 1.3 76.6 - - - +
68B ALA* 1.3 61.6 + - - +
70B ASP* 3.1 14.0 + - - +
71B ILE 4.7 8.0 - - - +
72B ARG* 5.7 5.2 - - - +
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Residues in contact with ALA 68 (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 LYS 5.6 3.4 + - - +
16B ASP* 6.2 2.7 - - + -
17B LEU* 4.9 7.0 - - + -
18B PRO* 6.3 1.1 - - + -
36B LEU* 4.2 18.6 - - + +
64B GLU 2.8 17.5 + - - +
65B ALA* 3.7 8.7 - - - +
67B ASP* 1.3 77.4 - - - +
69B LEU* 1.3 62.5 + - - +
70B ASP* 3.3 1.4 + - - +
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Residues in contact with LEU 69 (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 LYS* 5.6 3.1 - - - -
36B LEU* 4.2 18.8 - - + +
37B GLU* 3.9 44.9 - - + +
40B ALA* 4.6 7.2 - - + -
65B ALA 3.2 17.8 + - - +
66B ARG 3.1 5.7 + - - +
68B ALA* 1.3 81.5 - - - +
70B ASP* 1.3 71.4 + - - +
71B ILE* 3.3 18.8 + - + +
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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