Contacts of the helix formed by residues 44 - 60 (chain A) in PDB entry 2POZ
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A HIS* 5.1 0.2 + - - -
39A ILE* 3.7 12.8 - - - +
42A GLY 3.9 1.6 + - - -
43A VAL* 1.3 74.9 - - - +
45A GLY* 1.3 68.8 + - - +
46A THR 3.2 0.2 - - - -
47A ALA* 3.0 6.8 + - - +
48A ALA* 2.9 23.2 + - - +
88A ILE* 4.0 5.0 - - - +
51F MSE 3.8 14.8 - - - -
54F ASP* 3.1 18.1 + - - +
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Residues in contact with GLY 45 (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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12A LEU* 3.9 8.9 - - - +
19A HIS* 3.7 33.0 + - - -
21A VAL* 3.5 12.1 - - - +
39A ILE* 3.9 9.0 - - - -
44A GLY* 1.3 76.8 - - - +
46A THR* 1.3 55.8 + - - +
48A ALA* 3.2 4.3 + - - +
49A ALA* 3.0 24.8 + - - +
54F ASP* 3.1 2.8 + - - -
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Residues in contact with THR 46 (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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12A LEU* 4.0 17.3 - - + +
45A GLY* 1.3 72.2 - - - +
47A ALA* 1.3 60.2 + - - +
49A ALA* 3.3 2.3 + - - +
50A GLY* 2.9 25.6 + - - -
380A TRP* 3.8 28.4 - - + +
50F GLY* 3.8 21.6 - - - -
53F LYS* 4.4 16.4 + - + +
54F ASP* 2.6 29.5 + - - -
380F TRP* 4.0 7.4 - - + -
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Residues in contact with ALA 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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44A GLY* 3.0 15.4 + - - +
46A THR* 1.3 79.1 - - - +
48A ALA* 1.3 57.0 + - - +
50A GLY 3.2 0.9 + - - -
51A MSE 2.9 25.8 + - - +
88A ILE* 4.1 14.4 - - + -
47F ALA* 3.3 36.7 - - - +
50F GLY 4.0 1.2 - - - -
51F MSE 3.8 20.6 - - + +
54F ASP* 3.5 2.2 + - - -
88F ILE* 4.2 6.1 - - + -
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Residues in contact with ALA 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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21A VAL* 4.1 14.6 - - + -
37A ALA* 4.5 7.9 - - + -
39A ILE* 3.9 29.4 - - + -
44A GLY 2.9 11.4 + - - +
45A GLY 3.5 8.5 - - - +
47A ALA* 1.3 77.2 - - - +
49A ALA* 1.3 63.0 + - - +
51A MSE 3.2 3.9 + - - +
52A ILE* 3.1 27.5 + - - +
88A ILE* 4.3 12.0 - - + +
91A ALA* 5.1 2.5 - - + -
92A GLY* 5.1 0.8 - - - +
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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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10A ILE* 3.8 13.7 - - + +
12A LEU* 4.4 8.7 - - + -
21A VAL* 3.9 14.9 - - + +
45A GLY 3.0 12.9 + - - +
46A THR* 3.6 10.1 - - - +
47A ALA 3.3 0.2 - - - -
48A ALA* 1.3 75.9 - - - +
50A GLY* 1.3 62.9 + - - +
52A ILE* 3.4 3.3 + - - +
53A LYS* 3.2 17.7 + - - +
380A TRP* 3.4 38.5 - - + -
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Residues in contact with GLY 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 THR 2.9 14.0 + - - -
47A ALA 3.2 3.8 + - - -
49A ALA* 1.3 78.2 - - - +
51A MSE 1.3 55.8 + - - +
53A LYS* 3.3 3.3 + - - +
54A ASP* 3.0 33.1 + - - +
380A TRP* 3.6 18.8 - - - -
46F THR* 3.8 13.0 - - - -
47F ALA 4.0 10.5 - - - -
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Residues in contact with MSE 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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47A ALA 2.9 16.3 + - - +
48A ALA 3.2 5.4 + - - +
50A GLY* 1.3 75.2 - - - +
52A ILE* 1.3 65.1 + - - +
54A ASP* 3.2 8.7 + - + -
55A LEU* 2.9 40.2 + - + +
88A ILE* 3.7 27.1 - - + +
89A ILE* 3.5 27.1 - - - +
92A GLY* 4.3 2.9 - - - -
43F VAL* 3.2 37.9 - - + +
44F GLY* 4.0 7.9 - - - -
47F ALA* 3.7 11.4 - - + +
88F ILE* 5.5 2.9 - - - -
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Residues in contact with ILE 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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10A ILE* 3.6 24.2 - - + -
21A VAL* 3.8 28.5 - - + -
22A LEU 4.7 2.0 - - - +
23A VAL* 3.7 27.4 - - + -
37A ALA* 4.2 6.1 - - + -
48A ALA 3.1 10.1 + - - +
49A ALA 3.8 5.8 - - - +
51A MSE 1.3 75.0 - - - +
53A LYS* 1.3 57.3 + - - +
55A LEU* 3.8 7.0 - - - +
56A SER* 2.8 41.2 + - - +
92A GLY* 3.8 20.0 - - - +
95A ALA* 3.9 22.2 - - + -
96A ILE* 4.4 8.3 - - + -
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Residues in contact with LYS 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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10A ILE* 3.2 18.5 - - + +
49A ALA 3.2 10.6 + - - +
50A GLY 3.4 9.2 - - - +
51A MSE 3.1 0.6 - - - -
52A ILE* 1.3 78.0 - - - +
54A ASP* 1.3 62.8 + - - +
56A SER* 3.3 0.9 + - - -
57A GLU* 3.0 64.4 + - - +
380A TRP* 4.0 12.3 - - + -
381A ALA* 3.9 25.6 - - + -
382A SER 5.8 1.3 - - - -
383A CYS* 4.3 4.9 - - - -
46F THR* 4.4 18.9 + - + +
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Residues in contact with ASP 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 GLY 3.0 14.4 + - - +
51A MSE 3.4 15.9 - - + -
53A LYS* 1.3 79.1 + - - +
55A LEU* 1.3 64.6 + - - +
57A GLU* 4.0 10.0 - - - +
58A ARG* 3.1 26.2 + - - +
43F VAL* 3.6 11.3 - - + +
44F GLY* 3.2 17.9 - - - +
45F GLY 4.2 1.1 - - - -
46F THR* 2.7 47.2 + - - -
47F ALA 3.6 0.7 + - - -
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Residues in contact with LEU 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 MSE 2.9 47.5 + - + +
52A ILE 3.8 3.1 - - - +
54A ASP* 1.3 75.5 - - - +
56A SER* 1.3 57.5 + - - +
58A ARG 3.3 0.5 + - - -
59A PHE* 2.8 59.7 + - + +
60A LEU* 4.0 1.1 + - - +
75A MSE 4.1 16.8 - - + -
79A SER* 4.5 3.4 - - - -
89A ILE* 4.3 11.7 - - + +
92A GLY* 3.7 8.7 - - - -
93A ILE* 3.6 35.2 - - + +
96A ILE* 3.8 17.0 - - + -
43F VAL* 4.0 5.6 - - + -
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Residues in contact with SER 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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8A VAL* 3.2 41.1 - - - +
52A ILE* 2.8 33.0 + - - +
53A LYS* 3.7 3.1 - - - -
55A LEU* 1.3 75.1 - - - +
57A GLU* 1.3 59.1 + - - +
60A LEU* 3.0 37.8 + - - +
61A ILE* 3.1 14.5 - - - +
96A ILE* 4.1 1.4 - - - +
383A CYS* 4.1 10.3 - - - -
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Residues in contact with GLU 57 (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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53A LYS* 3.0 53.4 + - - +
54A ASP* 4.1 8.6 - - - +
56A SER* 1.3 76.0 - - - +
58A ARG* 1.3 59.8 + - - +
60A LEU 5.2 0.2 + - - -
61A ILE* 4.2 10.7 + - - +
382A SER 4.8 4.2 - - - +
383A CYS* 3.5 24.5 - - + +
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Residues in contact with ARG 58 (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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54A ASP 3.1 18.3 + - - +
57A GLU* 1.3 80.6 - - - +
59A PHE* 1.3 101.4 + - + +
63A LYS* 5.2 1.1 + - - +
78A HIS* 4.7 13.7 + - - +
43F VAL* 4.0 14.1 - - + +
170F GLN* 5.3 9.9 + - - +
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Residues in contact with PHE 59 (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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55A LEU* 2.8 38.6 + - + +
58A ARG* 1.3 113.7 - - + +
60A LEU* 1.3 63.2 + - + +
61A ILE 5.4 0.7 - - - -
63A LYS* 2.8 41.5 + - - +
71A LEU* 3.9 1.5 - - + +
74A THR* 3.6 26.2 - - + -
75A MSE 3.8 29.2 - - + -
78A HIS* 3.7 44.9 - + + -
79A SER* 4.0 1.8 - - - -
43F VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 60 (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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5A ILE* 3.5 24.4 - - + +
8A VAL* 3.9 20.0 - - + -
25A ILE* 4.4 9.0 - - + -
55A LEU 4.3 1.8 - - - +
56A SER* 3.0 40.0 + - - +
58A ARG 4.0 0.2 - - - -
59A PHE* 1.3 86.9 - - + +
61A ILE* 1.3 66.4 + - - +
62A GLY 3.3 0.7 + - - -
63A LYS* 3.1 19.0 + - - +
71A LEU* 4.1 20.2 - - + -
75A MSE 4.7 6.5 - - + -
96A ILE* 3.8 39.9 - - + -
100A LEU* 5.4 1.6 - - + -
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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