Contacts of the helix formed by residues 39 - 49 (chain C) in PDB entry 1Z83
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 39 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LEU 4.1 0.6 - - - -
38C SER* 1.3 72.7 - - - +
40C GLY* 1.3 55.7 + - - +
42C LEU* 3.6 9.4 - - + +
43C LEU* 2.9 36.8 + - - +
72C VAL* 3.6 26.5 - - + +
76C LEU* 4.1 26.5 - - + -
92C ILE* 5.6 0.7 - - + -
93C ASP 3.3 4.9 + - - +
94C GLY* 3.2 19.1 + - - -
95C TYR* 3.7 19.5 - - + -
633C AP5 3.0 25.2 + - - -
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Residues in contact with GLY 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C SER* 3.2 3.4 + - - -
39C THR* 1.3 79.8 + - - +
41C ASP* 1.3 56.2 + - - +
43C LEU* 3.3 2.9 + - - +
44C ARG* 2.9 43.6 + - - +
633C AP5 3.5 43.9 + - - -
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C HIS* 4.4 9.2 - - - -
38C SER* 3.1 32.1 + - - +
40C GLY* 1.3 74.6 - - - +
42C LEU* 1.3 60.4 + - + +
44C ARG* 2.8 25.7 + - - +
45C SER* 2.8 34.6 + - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 5.1 9.6 - - + -
38C SER 3.0 19.3 + - - +
39C THR* 3.6 16.2 - - + +
41C ASP* 1.3 76.8 - - + +
43C LEU* 1.3 64.3 + - - +
45C SER* 3.3 8.5 + - - +
46C GLU* 3.2 16.6 + - - +
75C MET* 3.7 32.3 - - + +
76C LEU* 3.9 36.8 - - + +
79C ALA* 4.2 19.3 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR 2.9 21.2 + - - +
40C GLY 3.8 0.4 - - - +
42C LEU* 1.3 77.2 - - - +
44C ARG* 1.3 63.1 + - - +
46C GLU* 3.1 7.4 + - - +
47C VAL* 3.0 26.3 + - - +
57C LEU* 3.7 29.9 - - + +
61C MET* 3.7 15.5 - - + -
67C VAL* 3.9 25.6 - - + -
71C THR* 5.1 1.1 - - + -
72C VAL* 4.4 9.6 - - + -
75C MET* 4.0 19.7 - - + -
633C AP5 3.4 45.3 - - + +
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C SER* 4.6 1.0 + - - -
40C GLY 2.9 19.3 + - - +
41C ASP* 2.8 34.8 + - - +
43C LEU* 1.3 75.2 - - - +
45C SER* 1.3 57.9 + - - +
47C VAL* 3.3 10.8 + - + +
48C SER* 2.9 30.7 + - - -
61C MET* 3.8 14.3 - - + +
138C ARG* 3.2 52.4 - - - +
139C VAL 6.3 0.4 - - - +
140C ASP* 4.8 1.9 + - - -
633C AP5 3.0 34.2 + - - -
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASP* 2.8 20.5 + - - +
42C LEU* 3.5 9.3 - - - +
44C ARG* 1.3 77.2 - - - +
46C GLU* 1.3 62.3 + - - +
48C SER* 3.2 17.3 + - - -
49C SER* 3.2 12.5 + - - -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU 3.2 8.9 + - - +
43C LEU* 3.1 10.8 + - - +
45C SER* 1.3 76.7 - - - +
47C VAL* 1.3 64.0 + - - +
49C SER* 2.6 33.1 + - - -
51C SER* 2.6 31.6 + - - +
53C ARG* 5.1 4.7 - - + +
54C GLY* 4.0 6.6 + - - +
57C LEU* 4.1 22.2 - - + -
75C MET* 4.8 12.3 - - + +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 3.0 16.6 + - - +
44C ARG* 3.5 13.7 - - + +
46C GLU* 1.3 73.8 - - - +
48C SER* 1.3 64.2 + - - +
50C GLY* 3.0 17.5 + - - -
54C GLY* 3.6 27.1 - - - +
55C LYS* 5.2 1.1 - - - +
57C LEU* 4.6 2.7 - - + -
58C SER* 3.8 35.4 - - - +
61C MET* 4.4 8.5 - - + -
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ARG 2.9 14.9 + - - -
45C SER* 3.2 14.5 + - - -
47C VAL* 1.3 77.5 - - - +
49C SER* 1.3 60.9 + - - +
50C GLY* 3.1 2.0 + - - -
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Residues in contact with SER 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER 3.2 10.0 + - - -
46C GLU* 2.6 27.8 + - - -
47C VAL 3.1 0.2 + - - -
48C SER* 1.3 76.0 - - - +
50C GLY* 1.3 58.8 + - - +
51C SER* 3.2 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