Contacts of the helix formed by residues 42 - 49 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D SER* 2.8 23.6 + - - -
15D GLY* 3.5 7.8 - - - -
16D PRO* 3.8 7.3 - - - +
19D TYR* 5.0 1.0 - - - -
41D LEU* 1.3 77.0 - - - +
43D GLY* 1.3 68.7 + - - +
46D LEU* 3.5 20.4 + - - +
47D ASN* 3.5 3.6 - - - -
103D ILE* 3.6 18.1 - - - +
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D SER* 3.5 3.4 + - - -
15D GLY* 3.7 2.0 - - - -
38D ASN* 5.2 4.5 - - - -
40D THR 4.8 1.4 + - - -
41D LEU 3.6 0.8 - - - -
42D GLY* 1.3 79.1 - - - +
44D THR* 1.3 64.0 + - - -
47D ASN* 2.8 34.6 + - - +
48D VAL* 5.5 0.4 - - - -
480D FAD 2.8 37.0 + - - -
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY* 1.3 70.7 - - - -
45D CYS* 1.3 54.9 + - - +
48D VAL* 3.1 19.2 + - + +
49D GLY* 2.7 32.6 + - - -
150D SER 3.9 3.3 + - - -
280D ARG* 3.3 39.2 + - - +
480D FAD 2.4 66.7 + - + +
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Residues in contact with CYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C HIS* 3.6 26.0 - - - -
16D PRO* 3.5 23.6 - - + -
42D GLY 4.1 0.6 + - - +
43D GLY 3.4 0.4 - - - -
44D THR* 1.3 79.3 - - - +
46D LEU* 1.3 62.0 + - - +
49D GLY 3.2 3.8 - - - -
50D CYS* 2.1 66.9 + - - +
51D ILE* 3.0 14.4 + - - -
328D ALA* 3.9 3.6 - - - -
480D FAD 3.3 14.8 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU 3.7 5.6 - - - +
42D GLY 3.5 14.9 + - - +
44D THR 3.4 0.2 - - - -
45D CYS* 1.3 79.5 - - - +
47D ASN* 1.3 61.8 + - - +
51D ILE* 3.7 17.2 - - + +
52D PRO* 3.2 17.7 - - - +
96D VAL* 3.5 34.6 - - + +
99D LEU* 3.7 18.6 - - + -
100D THR* 3.4 37.2 - - + +
103D ILE* 3.7 24.2 - - + -
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Residues in contact with ASN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D ASN* 5.8 5.1 - - - +
40D THR* 2.9 34.2 + - - +
41D LEU 3.3 21.0 + - - -
42D GLY* 3.5 2.6 - - - -
43D GLY* 2.8 32.6 + - - +
46D LEU* 1.3 79.7 - - - +
48D VAL* 1.3 69.8 + - + +
49D GLY 3.8 0.7 - - - -
52D PRO* 3.7 10.8 - - - +
96D VAL* 4.3 11.8 - - - +
100D THR* 3.6 6.8 - - - +
172D LEU* 5.3 0.2 - - - +
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR* 3.1 26.4 + - + +
47D ASN* 1.3 86.0 - - + +
49D GLY* 1.3 57.4 + - - +
52D PRO* 3.8 3.6 - - - -
168D SER* 4.6 1.6 + - - +
169D THR* 3.5 41.1 + - + +
172D LEU* 3.3 22.0 - - + +
280D ARG* 5.4 4.0 - - - +
480D FAD 3.7 14.7 - - + +
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D THR 2.7 16.4 + - - -
45D CYS* 3.2 5.2 + - - -
48D VAL* 1.3 77.9 - - - +
50D CYS* 1.3 58.6 + - - -
51D ILE 3.2 0.7 + - - -
52D PRO* 3.3 6.3 - - - +
53D SER* 2.6 36.3 + - - -
172D LEU* 4.6 0.2 - - - +
480D FAD 3.4 21.7 - - - +
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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