Contacts of the helix formed by residues 44 - 60 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B HIS* 4.9 0.2 + - - -
39B ILE* 3.7 15.9 - - - +
42B GLY 3.9 1.8 + - - -
43B VAL* 1.3 76.4 - - - +
45B GLY* 1.3 69.0 + - - +
47B ALA* 2.9 15.9 + - - +
48B ALA 3.0 10.0 + - - -
88B ILE* 4.1 4.6 - - - +
51H MSE 3.9 14.6 - - - -
54H ASP* 3.2 17.6 + - - +
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.6 12.3 - - - +
19B HIS* 3.6 34.1 + - - -
21B VAL* 3.6 14.9 - - - +
39B ILE* 3.9 7.9 - - - -
44B GLY* 1.3 76.7 - - - +
46B THR* 1.3 55.3 + - - +
48B ALA 3.4 0.9 + - - -
49B ALA 3.1 21.0 + - - -
54H ASP* 3.3 3.2 + - - -
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.8 17.0 - - + +
45B GLY* 1.3 74.1 - - - +
47B ALA* 1.3 59.4 + - - +
49B ALA* 3.5 1.5 + - - +
50B GLY* 2.9 24.8 + - - -
380B TRP* 3.9 28.6 - - + +
50H GLY* 3.7 20.9 - - - +
53H LYS* 4.5 15.8 + - + -
54H ASP* 2.7 30.3 + - - -
380H TRP* 4.0 7.2 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLY* 2.9 11.8 + - - +
46B THR* 1.3 77.2 - - - +
48B ALA* 1.3 59.2 + - - +
50B GLY 3.2 0.3 + - - -
51B MSE 2.8 26.5 + - - +
88B ILE* 3.9 21.1 - - + -
47H ALA* 3.2 36.3 - - - +
50H GLY 3.9 0.8 - - - -
51H MSE 3.7 22.7 - - + +
54H ASP* 3.6 2.2 + - - -
88H ILE* 4.1 1.3 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.2 11.7 - - + -
37B ALA* 4.4 11.0 - - + -
39B ILE* 3.8 30.1 - - + -
44B GLY 3.0 11.6 + - - +
45B GLY 3.6 8.1 - - - +
47B ALA* 1.3 77.8 - - - +
49B ALA* 1.3 61.5 + - - +
51B MSE 3.2 3.0 + - - +
52B ILE* 3.0 28.1 + - - +
88B ILE* 4.1 12.5 - - + +
91B ALA* 5.1 2.2 - - + -
92B GLY* 5.0 1.0 - - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.7 17.2 - - + +
12B LEU* 4.5 7.6 - - + -
21B VAL* 3.8 14.7 - - + +
45B GLY 3.1 13.0 + - - +
46B THR* 3.8 6.7 - - - +
48B ALA* 1.3 78.1 - - - +
50B GLY* 1.3 64.0 + - - +
52B ILE* 3.3 5.1 + - - +
53B LYS* 3.1 17.3 + - - +
380B TRP* 3.5 36.3 - - + -
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B THR 2.9 14.2 + - - -
47B ALA 3.6 3.1 - - - -
48B ALA 3.2 0.2 - - - -
49B ALA* 1.3 78.4 - - - +
51B MSE 1.3 55.8 + - - +
53B LYS* 3.2 3.8 + - - +
54B ASP* 3.0 32.4 + - - +
380B TRP* 3.6 20.1 - - - -
46H THR* 3.7 12.0 - - - -
47H ALA 3.9 10.1 - - - -
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Residues in contact with MSE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ALA 2.8 16.1 + - - +
48B ALA 3.2 4.9 + - - +
50B GLY* 1.3 74.4 - - - +
52B ILE* 1.3 61.0 + - - +
54B ASP* 3.3 24.7 - - + -
55B LEU* 2.9 44.6 + - + +
81B TRP* 6.3 0.2 - - - -
88B ILE* 3.7 26.0 - - + +
89B ILE* 3.7 26.7 - - - -
92B GLY* 4.3 2.9 - - - -
43H VAL* 3.3 22.4 - - + +
44H GLY* 3.8 10.8 - - - -
47H ALA* 3.6 11.6 - - + +
88H ILE* 5.4 3.8 - - - -
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Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.6 22.0 - - + -
21B VAL* 3.8 23.6 - - + +
22B LEU 4.9 2.0 - - - +
23B VAL* 3.8 26.7 - - + -
37B ALA* 4.2 7.0 - - + -
48B ALA 3.0 16.3 + - - +
49B ALA* 3.7 6.1 - - - +
51B MSE 1.3 75.0 - - - +
53B LYS* 1.3 55.4 + - - +
55B LEU* 3.9 7.0 - - - +
56B SER* 2.7 43.5 + - - +
92B GLY* 3.7 18.6 - - - +
95B ALA* 4.0 23.1 - - + -
96B ILE* 4.3 8.7 - - + -
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 4.0 12.7 - - + +
49B ALA 3.1 13.2 + - - +
50B GLY 3.3 9.4 - - - +
52B ILE* 1.3 78.5 - - - +
54B ASP* 1.3 58.0 + - - +
56B SER* 3.6 0.9 - - - -
57B GLU* 2.8 71.0 + - - +
380B TRP* 4.0 20.0 - - + -
381B ALA* 4.0 14.8 - - + -
382B SER 5.8 2.0 - - - -
383B CYS* 4.1 10.3 - - - -
46H THR* 4.4 19.9 + - + +
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Residues in contact with ASP 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B GLY 3.0 11.5 + - - +
51B MSE 3.2 17.2 + - + -
53B LYS* 1.3 78.3 - - - +
55B LEU* 1.3 62.3 + - - +
57B GLU* 4.1 12.9 - - - +
58B ARG* 3.2 26.2 + - - +
43H VAL* 3.7 10.4 - - + +
44H GLY* 3.1 17.8 - - - +
45H GLY* 4.2 1.3 - - - -
46H THR* 2.7 49.6 + - - -
47H ALA 3.5 2.4 + - - -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B MSE 2.9 47.9 + - + +
54B ASP* 1.3 72.2 - - - +
56B SER* 1.3 59.4 + - - +
58B ARG 3.4 0.2 + - - -
59B PHE* 2.8 52.2 + - + +
60B LEU* 3.9 0.7 + - - +
75B MSE 4.4 16.8 - - + -
79B SER* 4.5 2.7 - - - -
89B ILE* 4.1 15.3 - - + +
92B GLY* 3.7 10.1 - - - +
93B ILE* 3.7 33.9 - - + +
96B ILE* 3.8 18.2 - - + -
43H VAL* 3.9 11.7 - - + -
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B VAL* 3.3 37.7 - - - +
52B ILE* 2.7 28.2 + - - +
53B LYS 3.6 3.6 - - - -
54B ASP 3.3 0.2 - - - -
55B LEU* 1.3 77.3 - - - +
57B GLU* 1.3 62.1 + - - +
60B LEU* 3.0 34.5 + - - +
61B ILE* 2.9 19.1 - - - +
96B ILE* 4.1 1.4 - - - +
383B CYS* 4.2 9.6 - - - -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LYS* 2.8 55.5 + - - +
54B ASP* 4.1 11.7 - - - +
56B SER* 1.3 75.5 - - - +
58B ARG* 1.3 58.8 + - - +
61B ILE* 4.0 11.1 + - - +
382B SER 5.1 2.1 - - - +
383B CYS* 3.6 22.3 - - + +
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ASP 3.2 18.0 + - - +
57B GLU* 1.3 80.2 - - - +
59B PHE* 1.3 104.0 + - + +
60B LEU 4.0 0.2 - - - -
63B LYS* 4.9 4.5 + - - +
74B THR* 5.6 0.6 - - - +
78B HIS* 4.7 12.9 + - - +
43H VAL* 4.0 13.3 - - + +
165H VAL* 5.9 3.6 - - - +
170H GLN* 4.7 12.5 + - - +
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Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 2.8 45.8 + - + +
58B ARG* 1.3 115.3 - - + +
60B LEU* 1.3 64.6 + - + +
61B ILE 4.1 0.4 - - - -
63B LYS* 2.7 40.2 + - - +
71B LEU* 4.2 2.4 - - + +
74B THR* 3.6 30.7 - - + -
75B MSE 3.7 32.8 - - + -
78B HIS* 3.7 35.0 - - + -
79B SER* 4.0 2.2 - - - -
43H VAL* 3.8 14.4 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ILE* 3.4 33.4 - - + +
8B VAL* 4.1 13.7 - - + -
25B ILE* 4.3 8.5 - - + -
55B LEU 4.4 2.7 - - - +
56B SER* 3.0 39.4 + - - +
58B ARG 4.0 0.4 - - - -
59B PHE* 1.3 88.2 - - + +
61B ILE* 1.3 66.6 + - - +
62B GLY 3.2 0.5 + - - -
63B LYS* 3.1 16.8 + - - +
71B LEU* 4.1 22.4 - - + -
75B MSE 4.8 5.6 - - - -
96B ILE* 3.6 41.5 - - + -
100B LEU* 5.1 1.3 - - + -
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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
------------------------------------------------------------
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