Contacts of the helix formed by residues 42 - 49 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C SER* 2.8 23.3 + - - -
15C GLY* 3.7 7.0 - - - -
16C PRO* 3.8 5.2 - - - +
41C LEU* 1.3 75.8 - - - +
43C GLY* 1.3 67.9 + - - +
46C LEU* 3.2 28.5 + - - +
47C ASN* 3.7 1.8 - - - -
103C ILE* 3.5 18.8 - - - +
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Residues in contact with GLY 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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14C SER* 3.6 2.8 + - - -
15C GLY* 3.7 2.7 - - - -
36C GLU* 4.7 0.2 + - - -
38C ASN* 5.5 3.1 - - - -
40C THR 5.0 0.4 + - - -
41C LEU 3.6 0.8 - - - -
42C GLY* 1.3 80.1 - - - +
44C THR* 1.3 62.7 + - - -
47C ASN* 2.9 34.8 + - - +
480C FAD 3.0 38.3 + - - -
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Residues in contact with THR 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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43C GLY* 1.3 70.1 - - - -
45C CYS* 1.3 56.9 + - - +
48C VAL* 2.9 26.2 + - + +
49C GLY 2.6 29.6 + - - -
150C SER* 4.1 2.1 + - - -
280C ARG* 3.4 34.9 + - - +
480C FAD 2.5 70.5 + - + +
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Residues in contact with CYS 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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16C PRO* 3.7 16.6 - - + -
42C GLY 4.2 0.2 - - - +
43C GLY 3.4 0.6 - - - -
44C THR* 1.3 79.1 - - - +
46C LEU* 1.3 65.7 + - + +
49C GLY 3.4 1.0 - - - -
50C CYS* 2.0 67.3 + - - +
51C ILE* 3.1 11.8 + - - -
328C ALA* 3.4 18.6 - - - -
480C FAD 3.3 22.1 + - - +
452D HIS* 3.5 15.5 - - - -
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Residues in contact with LEU 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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16C PRO* 5.2 2.0 - - + -
19C TYR* 4.9 10.5 - - + +
42C GLY* 3.2 28.0 + - - +
45C CYS* 1.3 88.7 - - + +
47C ASN* 1.3 66.7 + - - +
51C ILE* 3.6 20.9 - - + +
52C PRO* 3.4 14.6 - - - +
96C VAL* 3.5 17.2 - - - +
99C LEU* 3.4 40.2 - - + +
100C THR* 3.7 14.1 - - + -
103C ILE* 3.4 25.1 - - + -
392D SER* 5.8 2.7 - - - +
452D HIS* 5.6 3.4 - - + +
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Residues in contact with ASN 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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38C ASN* 5.9 3.4 - - - +
40C THR* 2.7 27.5 + - - +
41C LEU 3.2 21.8 + - - -
42C GLY 3.7 1.0 - - - -
43C GLY 2.9 30.3 + - - +
46C LEU* 1.3 80.4 - - - +
48C VAL* 1.3 71.3 + - + +
49C GLY 3.7 0.2 - - - -
52C PRO* 3.9 10.3 - - - +
96C VAL* 4.1 14.7 - - + +
100C THR* 3.3 15.3 - - - +
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Residues in contact with VAL 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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43C GLY 5.0 0.4 - - - +
44C THR* 2.9 30.8 + - + +
47C ASN* 1.3 83.8 - - + +
49C GLY* 1.3 57.8 + - - +
52C PRO* 3.8 3.4 - - - -
168C SER* 4.7 1.9 + - - -
169C THR* 3.5 42.7 + - + +
172C LEU* 3.2 22.9 - - + +
280C ARG* 5.7 2.9 - - - +
480C FAD 3.6 12.2 - - + +
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Residues in contact with GLY 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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44C THR 2.6 18.9 + - - -
45C CYS 3.4 2.3 + - - -
48C VAL* 1.3 78.4 - - - +
50C CYS* 1.3 59.8 + - - -
51C ILE 3.5 0.7 - - - -
52C PRO* 3.2 5.3 - - - +
53C SER* 2.7 34.0 + - - -
480C FAD 3.3 25.9 - - - +
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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