Contacts of the helix formed by residues 48 - 55 (chain A) in PDB entry 1ZD4
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 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LYS 4.0 3.1 - - - -
44A GLY* 3.6 15.3 - - - -
45A GLY 3.0 17.3 + - - -
46A PRO 3.0 1.6 + - - -
47A GLU* 1.3 79.5 - - - +
49A ALA* 1.3 66.6 + - - -
50A THR* 3.3 3.1 - - - -
51A THR* 3.1 3.9 + - - -
52A ARG* 2.9 26.3 + - - +
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS 4.4 5.6 + - - +
48A GLY* 1.3 71.1 - - - -
50A THR* 1.3 58.2 + - - +
52A ARG* 3.0 14.3 + - - +
53A LEU* 2.8 29.1 + - - +
58A ILE* 4.2 1.8 - - - +
63A TRP* 3.7 17.1 - - + +
66A LEU* 4.1 30.1 - - + +
70A ASN* 4.8 13.5 - - - +
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ALA 5.3 0.2 + - - -
41A PHE* 2.7 54.6 + - + +
42A GLN* 5.2 3.4 - - + -
48A GLY 3.3 0.4 - - - -
49A ALA* 1.3 78.6 - - - +
51A THR* 1.3 56.5 + - - +
53A LEU* 3.6 5.2 + - + +
54A MET* 3.0 41.4 + - + +
63A TRP* 2.8 33.5 + - + +
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 2.7 23.4 + - - -
46A PRO* 3.0 28.8 - - + +
48A GLY 3.1 6.7 + - - -
50A THR* 1.3 77.2 - - - +
52A ARG* 1.3 67.0 + - + +
54A MET* 2.9 16.0 + - - +
55A LYS* 3.0 37.2 + - + +
57A GLU* 6.0 0.2 - - - +
159A VAL* 4.5 9.6 - - + -
162A GLU* 5.1 1.6 - - - +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO 5.8 0.9 - - - +
47A GLU* 5.4 3.6 - - - -
48A GLY 2.9 21.9 + - - +
49A ALA* 3.3 12.1 - - - +
51A THR* 1.3 75.8 - - - +
53A LEU* 1.3 55.9 + - - +
55A LYS* 2.8 22.3 + - - -
57A GLU* 2.6 65.3 + - + +
58A ILE* 3.9 34.6 - - + +
66A LEU* 5.6 5.9 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 2.8 15.5 + - - +
50A THR* 3.6 11.0 - - + +
52A ARG* 1.3 76.1 - - - +
54A MET* 1.3 74.6 + - + +
55A LYS 3.6 0.3 + - - -
56A GLY* 3.6 7.0 + - - -
58A ILE* 3.2 28.6 - - + +
59A THR* 3.6 1.8 - - - +
60A LEU* 3.6 29.4 - - + +
63A TRP* 3.7 30.3 - - + -
126A TRP* 3.2 45.3 - - + +
127A LEU 4.6 1.4 + - - +
154A CYS* 4.1 0.7 - - - +
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Residues in contact with MET 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.9 9.2 - - + -
50A THR* 3.0 38.3 + - + +
51A THR* 2.9 10.9 + - - +
53A LEU* 1.3 87.2 - - + +
55A LYS* 1.3 57.3 + - - +
56A GLY 3.4 1.6 - - - -
124A ASN* 3.1 46.9 - - + +
125A THR 3.4 12.6 - - - +
126A TRP* 4.2 9.4 - - + -
153A SER* 2.8 27.1 + - - +
154A CYS* 2.9 10.0 + - - -
159A VAL* 3.2 14.2 - - + +
900A PO4 5.4 0.2 - - - +
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Residues in contact with LYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PRO 5.7 0.2 + - - -
51A THR* 3.0 23.5 + - + +
52A ARG 2.8 7.8 + - - +
54A MET* 1.3 76.0 - - - +
56A GLY* 1.3 63.0 + - - +
57A GLU* 3.2 25.5 + - + +
153A SER 4.3 3.6 - - - -
154A CYS* 3.6 10.4 - - - +
157A GLY* 3.6 34.5 + - - +
159A VAL* 3.3 26.0 - - + -
162A GLU* 2.6 38.7 + - - -
164A GLN* 4.8 3.4 - - - +
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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