Contacts of the helix formed by residues 42 - 49 (chain E) in PDB entry 1ZMD
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 42 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E SER* 2.9 22.3 + - - -
15E GLY* 3.7 6.1 - - - -
16E PRO* 3.9 1.7 - - - +
19E TYR* 4.9 0.7 - - - -
41E LEU* 1.3 75.5 - - - +
43E GLY* 1.3 68.7 + - - +
45E CYS 3.9 1.9 + - - -
46E LEU* 3.2 45.9 + - - +
47E ASN* 3.8 1.3 - - - -
103E ILE* 4.7 4.1 - - - +
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Residues in contact with GLY 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E SER 3.6 2.8 + - - -
15E GLY* 3.7 2.9 - - - -
38E ASN* 5.8 2.0 - - - -
40E THR 5.1 0.8 + - - -
41E LEU 3.5 2.8 - - - -
42E GLY* 1.3 80.5 - - - +
44E THR* 1.3 66.1 + - - +
47E ASN* 3.2 25.1 + - - +
48E VAL* 5.0 0.2 - - - +
480E FAD 3.0 40.1 + - - -
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Residues in contact with THR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E GLY* 1.3 70.7 - - - -
45E CYS* 1.3 54.3 + - - +
48E VAL* 3.0 25.7 + - + +
49E GLY 2.7 29.3 + - - -
150E SER* 4.1 2.1 + - - -
280E ARG* 3.2 37.6 + - - +
480E FAD 2.4 71.2 + - + +
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Residues in contact with CYS 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PRO* 3.4 25.6 - - + -
42E GLY 4.2 0.4 - - - +
43E GLY 3.4 0.4 - - - -
44E THR* 1.3 78.0 - - - +
46E LEU* 1.3 62.6 + - + +
49E GLY 3.3 2.1 - - - -
50E CYS* 2.0 69.6 + - - +
51E ILE* 3.0 13.3 + - - -
328E ALA* 3.3 18.8 - - - -
480E FAD 3.3 14.9 + - - +
452F HIS* 3.6 15.3 - - - -
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E PRO* 4.8 3.4 - - + -
19E TYR* 4.5 16.6 - - + -
42E GLY* 3.2 39.2 + - - +
45E CYS* 1.3 89.2 - - + +
47E ASN* 1.3 61.9 + - - +
51E ILE* 3.6 21.6 - - + +
52E PRO* 3.4 17.2 - - - +
96E VAL* 3.4 16.5 - - - +
99E LEU* 3.7 40.2 - - + +
100E THR* 4.0 8.5 - - + +
103E ILE* 3.8 18.4 - - + -
392F SER* 6.1 0.7 - - - +
452F HIS* 5.6 2.2 - - + +
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Residues in contact with ASN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ASN* 6.0 3.0 - - - +
40E THR* 2.7 26.8 + - - +
41E LEU 3.2 22.8 + - - -
42E GLY* 3.8 0.8 - - - -
43E GLY 3.2 28.2 + - - +
46E LEU* 1.3 78.4 - - - +
48E VAL* 1.3 72.2 + - + +
49E GLY 3.7 0.4 - - - -
52E PRO* 3.9 9.5 - - - +
96E VAL* 4.0 14.5 - - + +
100E THR* 3.2 15.6 - - - +
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Residues in contact with VAL 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR* 3.0 28.7 + - + +
47E ASN* 1.3 84.4 - - + +
49E GLY* 1.3 59.3 + - - +
52E PRO* 3.7 9.4 - - - -
168E SER* 4.6 3.1 + - - -
169E THR* 3.7 41.0 + - + +
172E LEU* 3.4 15.2 - - + +
280E ARG* 5.8 2.5 - - - +
480E FAD 3.6 13.4 - - + +
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Residues in contact with GLY 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E THR 2.7 13.1 + - - -
45E CYS* 3.3 4.7 + - - -
48E VAL* 1.3 82.5 - - - +
50E CYS* 1.3 59.0 + - - -
51E ILE 3.4 0.4 - - - -
52E PRO* 3.2 5.4 - - - +
53E SER* 2.8 34.1 + - - -
480E FAD 3.3 25.0 - - - +
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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