Contacts of the helix formed by residues 44 - 60 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A MSE 4.0 15.0 - - - -
54A ASP* 3.2 16.3 + - - +
19F HIS* 4.9 0.2 + - - -
39F ILE* 3.6 16.5 - - - +
42F GLY 3.9 1.6 + - - -
43F VAL* 1.3 78.7 - - - +
45F GLY* 1.3 67.9 + - - +
47F ALA* 3.1 7.0 + - - +
48F ALA 2.9 18.5 + - - -
88F ILE* 4.1 3.9 - - - +
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Residues in contact with GLY 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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54A ASP* 3.2 2.8 + - - -
12F LEU* 3.8 9.1 - - - +
19F HIS* 3.6 34.3 + - - -
21F VAL* 3.6 11.7 - - - +
39F ILE* 3.8 7.9 - - - -
44F GLY* 1.3 77.4 - - - +
46F THR* 1.3 62.3 + - - +
48F ALA* 3.2 5.0 + - - +
49F ALA* 3.1 18.9 + - - +
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Residues in contact with THR 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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50A GLY* 3.8 19.5 - - - -
53A LYS* 4.4 15.6 + - + +
54A ASP* 2.7 29.5 + - - -
380A TRP* 4.1 7.2 - - + -
12F LEU* 3.9 16.7 - - + +
45F GLY* 1.3 72.3 - - - +
47F ALA* 1.3 60.3 + - - +
49F ALA* 3.3 2.3 + - - +
50F GLY* 2.9 26.2 + - - -
380F TRP* 3.8 29.1 - - + +
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Residues in contact with ALA 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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47A ALA* 3.3 35.9 - - - +
50A GLY* 4.0 1.4 - - - -
51A MSE 3.7 22.9 - - + +
54A ASP* 3.6 2.2 + - - -
88A ILE* 4.1 2.9 - - + -
44F GLY* 3.1 14.0 + - - +
46F THR* 1.3 79.8 - - - +
48F ALA* 1.3 56.6 + - - +
50F GLY 3.3 0.7 + - - -
51F MSE 2.9 24.4 + - - +
88F ILE* 3.6 17.4 - - + +
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Residues in contact with ALA 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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21F VAL* 4.2 13.7 - - + -
37F ALA* 4.4 8.3 - - + -
39F ILE* 3.8 29.6 - - + -
44F GLY 2.9 11.9 + - - +
45F GLY 3.5 8.7 - - - +
46F THR 3.2 0.2 - - - -
47F ALA* 1.3 76.3 - - - +
49F ALA* 1.3 62.2 + - - +
51F MSE 3.1 4.0 + - - +
52F ILE* 3.0 26.9 + - - +
88F ILE* 4.1 12.3 - - + +
91F ALA* 5.0 2.2 - - + -
92F GLY* 5.0 0.9 - - - +
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Residues in contact with ALA 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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10F ILE* 3.8 14.6 - - + +
12F LEU* 4.6 8.5 - - + -
21F VAL* 3.9 15.3 - - + +
45F GLY 3.1 14.0 + - - +
46F THR* 3.6 9.0 - - - +
47F ALA 3.3 0.2 - - - -
48F ALA* 1.3 74.1 - - - +
50F GLY* 1.3 64.1 + - - +
52F ILE* 3.3 4.6 + - - +
53F LYS* 3.0 18.0 + - - +
380F TRP* 3.6 36.6 - - + -
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Residues in contact with GLY 50 (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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46A THR* 3.8 13.8 - - - -
47A ALA 4.0 9.2 - - - -
46F THR 2.9 13.2 + - - -
47F ALA 3.3 4.0 + - - -
49F ALA* 1.3 76.2 - - - +
51F MSE 1.3 56.3 + - - +
53F LYS* 3.3 2.6 + - - +
54F ASP* 2.9 33.8 + - - +
380F TRP* 3.6 21.0 - - - -
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Residues in contact with MSE 51 (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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43A VAL* 3.2 35.7 - - + +
44A GLY* 3.8 8.3 - - - -
47A ALA* 3.8 10.1 - - + +
88A ILE* 5.5 3.4 - - - -
47F ALA 2.9 14.5 + - - +
48F ALA 3.1 8.3 + - - +
50F GLY* 1.3 75.0 - - - +
52F ILE* 1.3 66.1 + - - +
54F ASP* 3.2 27.3 + - + -
55F LEU* 2.9 29.5 + - + +
81F TRP* 6.4 0.2 - - - -
88F ILE* 3.7 26.2 - - + +
89F ILE* 3.7 24.9 - - - -
92F GLY* 4.3 2.5 - - - -
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Residues in contact with ILE 52 (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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10F ILE* 3.6 24.5 - - + -
21F VAL* 3.9 26.5 - - + -
22F LEU 4.8 1.6 - - - +
23F VAL* 3.8 25.8 - - + -
37F ALA* 4.1 5.2 - - + -
48F ALA 3.0 11.2 + - - +
49F ALA 3.3 6.7 + - - +
51F MSE 1.3 74.3 - - - +
53F LYS* 1.3 54.5 + - - +
55F LEU* 3.5 7.6 + - - +
56F SER* 2.7 42.1 + - - +
92F GLY* 3.7 18.2 - - - +
95F ALA* 3.8 25.6 - - + -
96F ILE* 4.4 9.2 - - + -
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Residues in contact with LYS 53 (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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46A THR* 4.4 18.5 + - + +
10F ILE* 3.2 15.0 - - + +
49F ALA 3.0 13.4 + - - +
50F GLY 3.4 8.5 - - - +
51F MSE 3.1 0.2 - - - -
52F ILE* 1.3 76.9 - - - +
54F ASP* 1.3 64.4 + - - +
56F SER* 3.3 1.7 + - - -
57F GLU* 2.9 66.1 + - - +
380F TRP* 4.0 13.0 - - + -
381F ALA* 3.9 25.6 - - + -
382F SER 6.0 1.3 - - - -
383F CYS* 4.3 6.5 - - - -
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Residues in contact with ASP 54 (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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43A VAL* 3.5 12.3 - - + +
44A GLY* 3.1 8.9 - - - +
45A GLY 3.1 10.2 + - - -
46A THR* 2.6 48.9 + - - -
47A ALA 3.5 0.5 + - - -
50F GLY 2.9 13.0 + - - +
51F MSE 3.2 16.6 - - + -
53F LYS* 1.3 77.2 + - - +
55F LEU* 1.3 61.7 + - - +
57F GLU* 4.1 12.2 - - - +
58F ARG* 3.2 26.0 + - - +
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Residues in contact with LEU 55 (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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43A VAL* 4.0 10.3 - - + -
51F MSE 2.9 43.7 + - + +
52F ILE 3.9 0.2 - - - +
54F ASP* 1.3 77.3 - - - +
56F SER* 1.3 58.3 + - - +
59F PHE* 2.8 60.5 + - + +
60F LEU* 3.9 1.5 + - - +
75F MSE 4.2 15.0 - - + -
79F SER* 4.4 2.7 - - - -
89F ILE* 4.3 14.6 - - + +
92F GLY* 3.7 27.6 - - - +
93F ILE* 3.8 10.5 - - + +
96F ILE* 3.8 17.3 - - + -
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Residues in contact with SER 56 (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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8F VAL* 3.3 36.2 - - - +
10F ILE* 4.5 0.2 - - - +
52F ILE* 2.7 27.4 + - - +
53F LYS 3.7 3.1 - - - -
55F LEU* 1.3 74.5 - - - +
57F GLU* 1.3 65.5 + - - +
60F LEU* 3.0 33.5 + - - +
61F ILE* 3.0 19.0 + - - +
96F ILE* 4.2 1.0 - - - +
383F CYS* 3.9 12.3 - - - -
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Residues in contact with GLU 57 (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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53F LYS* 2.9 55.0 + - - +
54F ASP* 4.1 9.6 - - - +
56F SER* 1.3 75.3 - - - +
58F ARG* 1.3 59.7 + - - +
61F ILE* 4.1 12.1 + - - +
382F SER 5.2 2.4 - - - +
383F CYS* 3.7 21.6 - - + +
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Residues in contact with ARG 58 (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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43A VAL* 4.1 14.1 - - + +
170A GLN* 5.4 8.9 + - - +
54F ASP 3.2 17.7 + - - +
55F LEU 4.0 1.6 - - - +
56F SER 3.1 1.0 - - - -
57F GLU* 1.3 80.4 - - - +
59F PHE* 1.3 98.2 + - + +
60F LEU 4.0 0.2 - - - -
63F LYS* 5.2 1.8 + - - +
74F THR* 5.8 0.2 - - - +
78F HIS* 4.7 13.3 + - - +
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Residues in contact with PHE 59 (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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43A VAL* 3.9 9.9 - - + -
55F LEU* 2.8 47.8 + - + +
58F ARG* 1.3 114.1 - - + +
60F LEU* 1.3 64.5 + - + +
61F ILE 4.1 0.4 - - - -
63F LYS* 2.6 36.7 + - - +
71F LEU* 4.2 3.5 - - + +
74F THR* 3.6 27.4 - - + -
75F MSE 3.7 29.6 - - + -
78F HIS* 3.7 44.4 - - + -
79F SER* 3.9 2.9 - - - -
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Residues in contact with LEU 60 (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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5F ILE* 3.5 26.5 - - + +
8F VAL* 4.0 19.3 - - + -
25F ILE* 4.3 8.5 - - + -
55F LEU 4.4 2.5 - - - +
56F SER* 3.0 38.0 + - - +
58F ARG 4.0 0.2 - - - -
59F PHE* 1.3 87.5 - - + +
61F ILE* 1.3 66.4 + - - +
62F GLY 3.2 0.7 + - - -
63F LYS* 3.1 20.5 + - - +
71F LEU* 4.1 22.4 - - + -
75F MSE 5.0 4.3 - - - -
96F ILE* 3.7 41.1 - - + -
100F LEU* 5.2 0.9 - - + -
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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