Contacts of the helix formed by residues 42 - 49 (chain G) in PDB entry 1ZMC
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G SER* 2.9 23.7 + - - -
15G GLY* 3.5 8.6 - - - -
16G PRO* 3.7 8.5 - - - +
19G TYR* 5.3 1.0 - - - -
41G LEU* 1.3 76.1 - - - +
43G GLY* 1.3 66.8 + - - +
46G LEU* 3.6 21.2 + - - +
47G ASN* 3.6 2.5 - - - -
103G ILE* 3.7 18.6 - - - +
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Residues in contact with GLY 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G SER* 3.6 2.8 + - - -
15G GLY* 3.6 4.3 - - - -
36G GLU* 4.7 0.2 + - - -
38G ASN* 5.6 3.1 - - - -
40G THR 5.1 0.6 + - - -
41G LEU 3.6 0.6 - - - -
42G GLY* 1.3 76.1 - - - +
44G THR* 1.3 70.0 + - - +
47G ASN* 2.8 35.1 + - - +
480G FAD 2.9 36.1 + - - -
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Residues in contact with THR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G GLY* 1.3 70.3 - - - +
45G CYS* 1.3 56.0 + - - +
48G VAL* 2.7 45.2 + - + +
49G GLY 2.8 10.0 + - - -
150G SER 3.9 4.0 + - - -
280G ARG* 3.2 36.6 + - - +
480G FAD 2.5 65.7 + - + +
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Residues in contact with CYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G PRO* 3.6 22.4 - - + -
43G GLY 3.4 0.4 - - - -
44G THR* 1.3 77.7 - - - +
46G LEU* 1.3 63.8 + - - +
49G GLY 3.2 5.2 + - - -
50G CYS* 2.1 54.7 + - - +
51G ILE* 3.1 25.6 + - - -
52G PRO* 3.6 0.2 - - - +
328G ALA* 3.7 4.7 - - - -
480G FAD 3.4 15.1 + - - +
452H HIS* 3.6 26.0 - - - -
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU 4.6 0.2 - - - +
42G GLY* 3.6 21.4 + - - +
44G THR 3.4 0.4 - - - -
45G CYS* 1.3 82.9 - - - +
47G ASN* 1.3 61.0 + - - +
51G ILE* 3.6 25.7 - - + +
52G PRO* 3.5 9.4 - - - +
96G VAL* 3.3 19.0 - - - +
99G LEU* 3.5 27.1 - - + +
100G THR* 3.6 36.6 - - + +
103G ILE* 3.5 30.3 - - + -
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Residues in contact with ASN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ASN* 5.7 5.4 - - - +
40G THR* 2.5 27.4 + - - +
41G LEU 3.2 22.4 + - - -
42G GLY* 3.6 1.4 - - - -
43G GLY 2.8 33.5 + - - +
46G LEU* 1.3 80.6 - - - +
48G VAL* 1.3 71.4 + - + +
49G GLY 3.8 0.2 - - - -
52G PRO* 4.0 8.9 - - - +
96G VAL* 4.3 11.9 - - - +
100G THR* 3.5 15.3 - - - +
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G THR* 2.7 30.6 + - + +
47G ASN* 1.3 85.3 - - + +
49G GLY* 1.3 58.1 + - - +
52G PRO* 3.8 5.6 - - - -
168G SER* 4.7 2.3 + - - -
169G THR* 3.9 40.2 + - + +
172G LEU* 3.4 21.5 - - + +
280G ARG* 5.8 2.0 - - - +
480G FAD 3.6 14.4 - - + +
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Residues in contact with GLY 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G THR 2.8 10.1 + - - -
45G CYS* 3.2 10.8 + - - -
48G VAL* 1.3 80.2 - - - +
50G CYS* 1.3 58.2 + - - -
51G ILE 3.3 0.4 + - - -
52G PRO* 3.3 3.7 - - - +
53G SER* 2.6 32.9 + - - -
172G LEU* 4.4 0.2 - - - +
480G FAD 3.3 26.0 - - - +
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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