Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 1Z3E
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 SER 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PRO 3.5 2.3 + - - -
37A LEU* 1.3 76.6 - - - +
39A ILE* 1.3 66.1 + - - +
40A ASP* 3.5 8.2 + - - +
41A GLU* 2.9 38.1 + - - +
42A ILE* 3.0 22.8 + - - +
84A ASN* 4.0 5.2 - - - -
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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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38A SER* 1.3 75.0 - - - +
40A ASP* 1.3 65.7 + - - +
42A ILE* 3.2 7.9 + - - +
43A LYS* 3.0 28.6 + - - +
77A GLN* 5.1 4.0 - - - +
80A TYR* 3.5 52.9 - - + +
81A ARG* 3.7 19.1 - - + +
84A ASN* 3.7 22.8 + - + +
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Residues in contact with ASP 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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38A SER* 3.2 7.4 + - - +
39A ILE* 1.3 80.9 - - - +
41A GLU* 1.3 66.0 + - + +
43A LYS* 2.6 38.3 + - - +
44A GLN* 3.0 37.7 + - - +
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Residues in contact with GLU 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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5A TYR* 4.4 10.6 + - - +
30A ARG* 2.8 46.2 + - - -
37A LEU* 3.4 12.8 - - + -
38A SER* 2.9 33.8 + - - +
40A ASP* 1.3 79.1 - - + +
42A ILE* 1.3 62.6 + - - +
44A GLN* 3.3 18.5 + - + +
45A ILE* 3.3 18.7 + - - +
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Residues in contact with ILE 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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37A LEU* 4.0 24.0 - - + +
38A SER 3.0 16.7 + - - +
39A ILE* 3.5 7.2 - - - +
40A ASP 3.2 0.2 - - - -
41A GLU* 1.3 72.5 - - - +
43A LYS* 1.3 65.8 + - - +
45A ILE* 3.1 20.4 + - + +
46A LEU* 3.1 12.7 + - + +
56A ILE* 5.3 3.3 - - + +
80A TYR* 3.7 28.9 - - + +
83A ILE* 3.8 34.3 - - + +
84A ASN* 3.5 39.0 - - + +
90A LEU* 5.1 4.0 - - + -
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Residues in contact with LYS 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 ILE* 3.0 20.0 + - - +
40A ASP* 2.6 43.0 + - - +
42A ILE* 1.3 78.4 - - - +
44A GLN* 1.3 65.3 + - - +
46A LEU* 3.2 2.8 + - - +
47A ARG* 2.9 30.5 + - + +
77A GLN* 5.3 2.6 + - - +
80A TYR* 3.9 23.2 - - + +
252B THR* 5.7 0.4 - - - +
254B GLU* 3.7 31.1 - - + +
255B GLU* 3.3 40.6 - - - +
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Residues in contact with GLN 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 ASP* 3.0 30.3 + - - +
41A GLU* 3.6 14.6 - - + +
42A ILE 3.2 0.4 - - - -
43A LYS* 1.3 84.5 - - - +
45A ILE* 1.3 62.5 + - + +
47A ARG* 2.8 44.7 + - - +
48A MET* 3.2 28.0 + - + +
96A ILE* 4.4 7.9 - - + -
98A GLU* 5.0 2.7 - - - +
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Residues in contact with ILE 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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5A TYR* 3.9 23.8 - - + -
37A LEU* 4.1 17.3 - - + -
41A GLU 3.4 14.4 - - - +
42A ILE* 3.1 12.2 + - + +
44A GLN* 1.3 76.9 - - - +
46A LEU* 1.3 63.0 + - - +
48A MET* 3.1 14.6 + - - +
49A THR* 3.5 10.9 + - - +
56A ILE* 3.8 31.4 - - + -
90A LEU* 4.4 6.7 - - + -
94A ILE* 3.9 26.7 - - + -
96A ILE* 3.8 18.8 - - + -
101A LEU* 3.9 12.8 - - + +
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Residues in contact with LEU 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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42A ILE* 3.1 9.2 + - + +
43A LYS 3.7 6.5 - - - +
45A ILE* 1.3 80.1 - - - +
47A ARG* 1.3 63.2 + - - +
49A THR* 2.7 28.0 + - + +
52A GLY 3.6 9.6 - - - +
53A THR* 3.6 33.4 - - + +
56A ILE* 3.8 22.2 - - + +
76A LEU* 3.6 23.8 - - + -
79A LEU* 5.4 1.3 - - + -
80A TYR* 3.7 19.7 - - + +
254B GLU* 3.6 3.5 - - + +
263B TYR* 3.0 40.6 + - + +
267B LYS* 3.9 0.3 - - - -
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Residues in contact with ARG 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 LYS* 2.9 18.4 + - + +
44A GLN* 2.8 40.2 + - - +
45A ILE 3.2 0.2 - - - -
46A LEU* 1.3 77.0 - - - +
48A MET* 1.3 73.3 + - - +
49A THR 3.6 1.6 - - - +
98A GLU* 2.8 43.8 + - - -
252B THR* 3.7 32.8 - - + -
254B GLU* 3.4 23.1 + - + +
267B LYS* 3.1 17.9 + - - +
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Residues in contact with MET 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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44A GLN* 3.2 13.2 + - + +
45A ILE 3.1 10.7 + - - +
47A ARG* 1.3 96.3 - - - +
49A THR* 1.3 64.5 + - - +
50A GLU* 5.1 2.8 - - - +
96A ILE* 4.0 11.0 - - + -
97A ASP 3.3 28.3 - - - +
98A GLU* 3.5 30.1 - - - +
99A LYS 3.7 4.0 - - - +
100A ARG* 3.7 20.2 - - - +
101A LEU* 3.9 24.5 + - + +
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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