Contacts of the helix formed by residues 45 - 56 (chain A) in PDB entry 1POZ
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 SER 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A SER 4.1 1.8 + - - -
44A ILE* 1.3 76.2 - - - +
46A ARG* 1.3 66.2 + - - +
47A THR* 3.2 18.1 + - - -
48A GLU* 3.7 15.0 + - - -
49A ALA* 3.0 29.5 + - - +
81A PHE* 4.7 2.5 - - - -
113A GLN* 4.0 17.1 + - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER* 1.3 75.7 + - - +
47A THR* 1.3 60.8 + - - +
49A ALA* 4.3 4.3 - - - -
50A ALA* 2.7 48.0 + - + +
60A LEU* 5.2 21.4 - - + +
81A PHE* 4.3 30.6 - - + -
84A GLY* 6.1 6.1 - - - -
116A THR* 5.5 2.7 - - - +
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Residues in contact with THR 47 (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 SER* 3.6 18.4 + - - -
46A ARG* 1.3 78.6 - - - +
48A GLU* 1.3 67.3 + - - +
50A ALA* 4.2 1.1 - - - +
51A ASP* 2.9 30.6 + - - +
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Residues in contact with GLU 48 (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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38A LYS* 3.1 41.9 - - + +
43A SER 5.5 1.2 - - - +
44A ILE* 4.8 1.5 - - + -
45A SER* 3.7 26.3 + - - +
47A THR* 1.3 82.2 + - - +
49A ALA* 1.3 70.3 + - - +
51A ASP* 3.0 21.1 - - - +
162A ARG* 3.1 51.3 + - + -
164A ASN* 5.5 4.3 - - - +
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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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36A VAL* 3.8 9.2 - - + +
38A LYS* 4.5 2.0 - - - -
44A ILE* 3.9 17.1 - - + +
45A SER 3.0 20.9 + - - +
46A ARG* 4.0 2.7 - - - +
48A GLU* 1.3 76.6 - - - +
50A ALA* 1.3 65.8 + - - +
52A LEU* 2.7 18.2 + - - +
53A CYS 3.0 9.5 + - - -
81A PHE* 5.5 0.9 - - + -
115A ASP 5.3 0.2 - - - -
116A THR* 3.3 37.0 - - + +
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Residues in contact with ALA 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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46A ARG* 2.7 40.8 + - + +
47A THR 4.2 1.1 - - - +
49A ALA* 1.3 73.8 - - - +
51A ASP* 1.3 61.7 + - - +
53A CYS* 3.4 14.9 + - - +
54A LYS* 3.0 25.3 + - - +
60A LEU* 6.2 5.6 - - + -
116A THR* 4.4 3.4 + - - +
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Residues in contact with ASP 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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38A LYS* 4.7 3.1 - - - -
47A THR* 2.9 23.7 + - - +
48A GLU* 3.0 17.4 + - - +
49A ALA 2.8 0.6 + - - -
50A ALA* 1.3 76.5 - - - +
52A LEU* 1.3 54.8 + - - +
54A LYS* 2.9 19.7 - - - +
55A ALA* 2.9 22.7 + - - +
139A PHE* 5.9 0.5 - - - -
161A TYR* 3.1 37.8 - - + +
162A ARG* 4.5 6.7 - - - +
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Residues in contact with LEU 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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24A LEU* 3.1 46.2 - - + -
26A ILE* 4.6 0.9 - - + -
34A PHE* 3.2 35.0 - - + -
36A VAL* 3.3 26.0 - - + -
37A GLU 3.9 6.5 - - - +
38A LYS* 3.8 12.0 - - + +
48A GLU 3.2 0.6 + - - -
49A ALA 2.7 8.9 + - - +
51A ASP* 1.3 71.6 - - - +
53A CYS* 1.3 53.1 + - - +
54A LYS 2.6 7.2 + - - -
55A ALA* 2.4 34.8 + - - +
56A PHE* 3.1 11.5 - - + -
135A LEU* 3.8 15.5 - - + -
147A ILE* 4.5 1.3 - - + -
161A TYR* 3.9 7.2 - - + -
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Residues in contact with CYS 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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36A VAL* 3.4 21.6 - - + +
49A ALA 3.0 8.8 + - - +
50A ALA* 3.7 19.5 - - - +
52A LEU* 1.3 76.6 - - - +
54A LYS* 1.3 57.9 + - - +
56A PHE* 3.5 5.1 - - - -
58A SER* 2.5 41.0 + - - -
59A THR 4.3 4.3 - - - -
60A LEU* 4.4 8.1 - - - -
61A PRO* 5.2 0.7 - - - -
116A THR* 4.5 2.5 - - + -
117A TYR 4.2 5.6 - - - +
118A CYS* 2.0 49.1 - - + -
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Residues in contact with LYS 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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50A ALA 3.0 11.7 + - - +
51A ASP* 2.9 28.3 - - - +
52A LEU 2.6 4.2 + - - -
53A CYS* 1.3 76.0 - - - +
55A ALA* 1.3 64.7 + - - +
56A PHE 3.0 3.1 - - - -
57A ASN* 2.9 15.8 + - - -
58A SER 4.2 12.8 - - - +
137A ASN* 3.0 35.3 + - - +
138A ALA* 5.7 1.1 - - - +
139A PHE* 6.3 3.6 - - - -
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Residues in contact with ALA 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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51A ASP 2.9 10.0 + - - +
52A LEU* 2.4 38.9 + - - +
54A LYS* 1.3 69.9 - - - +
56A PHE* 1.3 51.6 + - - +
135A LEU* 2.8 38.8 - - + +
137A ASN* 2.7 40.3 + - - +
138A ALA* 4.8 4.5 - - + -
161A TYR* 4.0 9.9 - - + -
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Residues in contact with PHE 56 (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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29A ARG* 3.7 2.2 - - - +
34A PHE* 2.8 73.4 - + + -
52A LEU* 3.1 22.2 - - + -
53A CYS* 3.5 17.0 - - - -
54A LYS 2.9 0.2 + - - -
55A ALA* 1.3 76.2 - - - +
57A ASN* 1.3 83.6 + - - +
58A SER* 2.8 12.4 + - - -
118A CYS 3.8 5.8 - - - -
120A ASN* 2.9 44.2 - - + +
122A SER* 5.6 1.6 - - - -
132A VAL* 4.8 2.5 - - + -
134A ASP* 5.8 0.7 - - + -
135A LEU* 3.6 22.9 - - + +
136A PRO* 5.0 1.1 - - + -
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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