Contacts of the helix formed by residues 42 - 49 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F SER* 2.8 22.6 + - - -
15F GLY* 3.5 8.3 - - - -
16F PRO* 3.7 4.2 - - - +
41F LEU* 1.3 74.7 - - - +
43F GLY* 1.3 66.4 + - - +
46F LEU* 3.3 30.4 + - - +
47F ASN* 3.6 1.3 - - - -
103F ILE* 3.5 19.6 - - - +
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Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER 3.6 2.2 + - - -
15F GLY* 3.7 8.1 - - - -
38F ASN* 5.5 3.4 - - - -
40F THR 5.0 0.8 + - - -
41F LEU 3.4 1.0 - - - -
42F GLY* 1.3 77.8 - - - +
44F THR* 1.3 62.9 + - - -
47F ASN* 3.0 34.0 + - - +
48F VAL* 5.0 0.4 - - - +
480F FAD 3.0 32.7 + - - -
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Residues in contact with THR 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F GLY* 1.3 70.3 - - - -
45F CYS* 1.3 61.1 + - - +
48F VAL* 3.0 23.5 + - + +
49F GLY 2.8 24.9 + - - -
150F SER* 4.1 3.2 + - - -
280F ARG* 3.2 36.7 + - - +
480F FAD 2.5 71.0 + - + +
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Residues in contact with CYS 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E HIS* 3.5 25.1 - - - -
16F PRO* 3.3 25.6 - - + -
42F GLY 3.9 0.4 + - - -
43F GLY 3.4 0.4 - - - -
44F THR* 1.3 80.7 - - - +
46F LEU* 1.3 65.0 + - + +
49F GLY 3.4 1.9 - - - -
50F CYS* 2.0 68.6 + - - +
51F ILE* 3.1 11.6 + - - -
328F ALA* 3.6 5.6 - - - -
480F FAD 3.3 14.0 + - - +
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392E SER* 5.4 3.4 - - - +
452E HIS* 5.5 3.4 - - + +
16F PRO* 4.8 3.4 - - + -
19F TYR* 4.6 11.9 - - + +
42F GLY* 3.3 36.5 + - - +
45F CYS* 1.3 89.7 - - + +
47F ASN* 1.3 67.1 + - - +
51F ILE* 3.7 21.2 - - + +
52F PRO* 3.5 14.3 - - - +
96F VAL* 3.5 15.6 - - - +
99F LEU* 3.4 43.1 - - + +
100F THR* 4.0 7.6 - - + +
103F ILE* 4.0 12.6 - - + -
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Residues in contact with ASN 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ASN* 6.0 3.2 - - - +
40F THR* 2.6 27.3 + - - +
41F LEU 3.0 24.0 + - - -
42F GLY* 3.6 1.4 - - - -
43F GLY* 3.0 31.2 + - - +
46F LEU* 1.3 80.9 - - - +
48F VAL* 1.3 72.4 + - + +
49F GLY 3.7 0.7 - - - -
52F PRO* 3.8 9.8 - - - +
96F VAL* 4.3 12.8 - - - +
100F THR* 3.4 13.0 - - - +
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Residues in contact with VAL 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F THR* 3.0 26.5 + - + +
47F ASN* 1.3 88.1 - - + +
49F GLY* 1.3 58.3 + - - +
52F PRO* 3.9 3.8 - - - -
168F SER* 4.4 3.7 + - - +
169F THR* 3.5 37.4 + - + +
172F LEU* 3.2 22.5 - - + +
280F ARG* 5.7 3.1 - - - +
480F FAD 3.5 13.0 - - + +
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Residues in contact with GLY 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F THR 2.8 12.7 + - - -
45F CYS 3.4 2.6 + - - -
48F VAL* 1.3 82.6 - - - +
50F CYS* 1.3 58.3 + - - -
51F ILE 3.3 0.6 + - - -
52F PRO* 3.4 5.3 - - - +
53F SER* 2.7 33.8 + - - -
172F LEU* 4.3 0.2 - - - +
480F FAD 3.3 25.7 - - - +
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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