Contacts of the helix formed by residues 43 - 52 (chain H) in PDB entry 2ZNZ
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 43 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39H ASP* 5.4 1.3 - - - +
41H LYS 3.0 9.1 - - - +
42H ALA* 1.3 86.3 - - - +
44H LEU* 1.3 66.8 + - - +
45H ARG* 3.9 39.0 - - + +
46H GLU* 3.0 33.3 + - + -
47H ILE* 3.1 11.0 + - - +
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H ALA 3.8 1.6 + - - +
43H PRO* 1.3 72.3 - - - +
45H ARG* 1.3 59.0 + - - +
47H ILE* 3.3 7.5 + - + +
48H SER* 2.8 34.4 + - - -
55H GLU* 3.6 34.8 - - + +
58H ILE* 3.7 28.2 - - + +
59H HIS* 3.9 36.6 - - + +
62H ILE* 4.3 9.9 - - + -
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Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H PRO* 3.9 29.4 - - + +
44H LEU* 1.3 79.2 - - - +
46H GLU* 1.3 61.9 + - + +
48H SER* 3.4 5.6 + - - -
49H LYS* 3.1 25.5 + - - +
55H GLU* 3.3 27.8 + - - +
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ILE* 6.0 0.7 - - + -
42H ALA* 5.2 6.1 - - + -
43H PRO* 3.0 29.8 + - + +
45H ARG* 1.3 80.6 - - + +
47H ILE* 1.3 64.3 + - + +
49H LYS* 3.0 36.0 + - - +
50H ILE* 3.2 41.9 + - + +
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Residues in contact with ILE 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ILE* 4.2 12.1 - - + -
35H ILE* 3.9 32.8 - - + -
36H LEU* 4.0 23.1 - - + -
42H ALA* 3.8 21.3 - - + +
43H PRO 3.1 12.4 + - - +
44H LEU* 3.8 7.6 - - + +
46H GLU* 1.3 75.5 - - - +
48H SER* 1.3 57.3 + - - +
50H ILE* 3.5 1.6 + - - -
51H THR* 2.7 47.2 + - - +
58H ILE* 3.8 36.8 - - + -
62H ILE* 4.4 6.3 - - + -
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Residues in contact with SER 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H LEU 2.8 21.7 + - - -
45H ARG* 3.5 7.0 - - - -
46H GLU 3.2 0.2 - - - -
47H ILE* 1.3 73.7 - - - +
49H LYS* 1.3 59.3 + - - +
52H GLY* 2.7 33.2 + - - +
53H LEU 3.2 20.0 + - - +
55H GLU* 3.2 24.3 - - - +
58H ILE* 3.3 13.3 - - - +
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Residues in contact with LYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H ARG 3.1 12.7 + - - +
46H GLU* 3.0 50.4 + - - +
48H SER* 1.3 78.9 - - - +
50H ILE* 1.3 73.3 + - + +
51H THR 3.6 0.2 + - - -
52H GLY* 4.0 3.6 + - - -
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Residues in contact with ILE 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ILE* 4.1 36.6 - - + -
46H GLU* 3.2 38.0 + - + +
47H ILE* 4.0 3.1 - - - +
49H LYS* 1.3 90.9 - - + +
51H THR* 1.3 60.7 + - - +
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Residues in contact with THR 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ILE* 5.0 0.2 - - + -
31H LYS* 3.5 50.7 + - + +
32H ILE* 5.1 2.3 - - + +
35H ILE* 4.0 10.6 - - - +
47H ILE* 2.7 31.4 + - - +
50H ILE* 1.3 77.5 - - - +
52H GLY* 1.3 59.1 + - - +
53H LEU* 3.2 34.8 + - + +
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Residues in contact with GLY 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H SER 2.7 20.0 + - - -
49H LYS 4.0 3.3 + - - -
50H ILE 3.6 1.4 - - - -
51H THR* 1.3 71.6 - - - +
53H LEU* 1.3 63.9 + - - +
54H ALA 4.0 0.2 + - - -
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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