Contacts of the helix formed by residues 44 - 60 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C MSE 4.0 13.9 - - - -
54C ASP* 3.2 16.0 + - - +
19G HIS* 4.8 0.6 + - - -
39G ILE* 3.4 18.0 - - - +
42G GLY 4.0 1.6 + - - -
43G VAL* 1.3 75.6 - - - +
45G GLY* 1.3 67.5 + - - +
46G THR 3.2 2.9 - - - -
47G ALA* 3.1 5.6 + - - +
48G ALA 2.9 19.6 + - - -
88G ILE* 4.1 3.7 - - - +
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Residues in contact with GLY 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ASP* 3.3 2.4 + - - -
12G LEU* 3.8 11.0 - - - +
19G HIS* 3.6 33.0 + - - -
21G VAL* 3.5 11.2 - - - +
39G ILE* 3.9 7.9 - - - -
44G GLY* 1.3 77.2 - - - +
46G THR* 1.3 62.3 + - - +
48G ALA* 3.2 5.4 + - - +
49G ALA 3.0 17.2 + - - -
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Residues in contact with THR 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLY* 3.7 19.7 - - - -
53C LYS* 4.2 17.8 + - + +
54C ASP* 2.5 30.0 + - - -
380C TRP* 4.1 6.3 - - + -
12G LEU* 4.0 18.0 - - + +
45G GLY* 1.3 72.5 - - - +
47G ALA* 1.3 61.8 + - - +
49G ALA* 3.1 3.8 + - - +
50G GLY* 2.8 26.9 + - - -
380G TRP* 4.0 28.3 - - + +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ALA* 3.3 35.5 - - - +
50C GLY* 3.9 1.4 - - - -
51C MSE 3.7 22.9 - - + +
54C ASP* 3.5 2.0 + - - -
88C ILE* 4.1 10.3 - - + -
44G GLY* 3.1 15.1 + - - +
46G THR* 1.3 79.1 - - - +
48G ALA* 1.3 56.7 + - - +
50G GLY 3.1 1.0 + - - -
51G MSE 2.9 25.3 + - - +
88G ILE* 4.1 9.6 - - + -
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Residues in contact with ALA 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G VAL* 4.2 13.0 - - + -
37G ALA* 4.6 6.3 - - + -
39G ILE* 3.7 30.7 - - + -
44G GLY 2.9 12.5 + - - +
45G GLY 3.3 9.0 - - - +
47G ALA* 1.3 76.7 - - - +
49G ALA* 1.3 62.7 + - - +
51G MSE 3.1 4.8 + - - +
52G ILE* 3.1 27.5 + - - +
88G ILE* 4.3 12.3 - - + +
91G ALA* 5.2 2.5 - - + -
92G GLY* 5.0 1.2 - - - +
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 3.7 23.4 - - + +
12G LEU* 4.6 8.3 - - + -
21G VAL* 4.1 10.0 - - + +
45G GLY 3.0 11.2 + - - +
46G THR* 3.5 9.6 - - - +
48G ALA* 1.3 76.9 - - - +
50G GLY* 1.3 62.9 + - - +
52G ILE* 3.3 2.1 + - - +
53G LYS* 3.1 23.0 + - - +
380G TRP* 3.7 31.1 - - + -
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Residues in contact with GLY 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.7 14.7 - - - -
47C ALA 3.9 10.5 - - - -
46G THR 2.8 13.8 + - - -
47G ALA 3.1 4.0 + - - -
49G ALA* 1.3 78.4 - - - +
51G MSE 1.3 60.3 + - - +
53G LYS* 3.5 2.4 + - - +
54G ASP* 3.1 28.6 + - - +
380G TRP* 3.8 17.2 - - - -
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Residues in contact with MSE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.2 38.8 - - + +
44C GLY* 4.0 7.2 - - - -
47C ALA* 3.7 11.6 - - + +
88C ILE* 5.4 3.1 - - - -
47G ALA 2.9 13.3 + - - +
48G ALA 3.1 8.5 + - - +
50G GLY* 1.3 73.7 - - - +
52G ILE* 1.3 61.3 + - - +
54G ASP* 3.2 8.2 + - + -
55G LEU* 2.9 46.2 + - + +
81G TRP* 6.4 0.2 - - - -
88G ILE* 3.7 26.5 - - + +
89G ILE* 3.6 29.2 - - - +
92G GLY* 4.3 3.4 - - - -
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ILE* 3.4 27.1 - - + -
21G VAL* 4.0 27.1 - - + -
22G LEU 4.7 1.1 - - - +
23G VAL* 3.7 25.4 - - + -
37G ALA* 4.2 4.7 - - + -
48G ALA 3.1 11.4 + - - +
49G ALA 3.8 2.2 - - - +
51G MSE 1.3 75.4 - - - +
53G LYS* 1.3 55.7 + - - +
55G LEU* 3.8 7.9 - - - +
56G SER* 2.8 44.6 + - - +
92G GLY* 3.7 17.5 - - - +
95G ALA* 3.8 23.8 - - + -
96G ILE* 4.3 9.0 - - + -
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 4.5 17.7 + - + +
10G ILE* 3.0 21.6 - - + +
49G ALA 3.1 6.3 + - - +
50G GLY 3.6 8.3 - - - +
52G ILE* 1.3 77.4 - - - +
54G ASP* 1.3 65.5 + - - +
56G SER* 3.8 0.9 - - - -
57G GLU* 2.6 71.9 + - - +
380G TRP* 3.8 20.6 - - + -
381G ALA* 3.9 18.8 - - + -
382G SER 5.9 1.8 - - - +
383G CYS* 4.3 6.5 - - - -
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Residues in contact with ASP 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL* 3.6 11.1 - - + +
44C GLY* 3.2 17.4 - - - +
45C GLY 4.2 0.7 - - - -
46C THR* 2.6 48.4 + - - -
47C ALA 3.5 0.3 + - - -
50G GLY 3.1 9.9 + - - +
51G MSE 3.4 17.5 - - + -
53G LYS* 1.3 86.0 + - - +
55G LEU* 1.3 61.7 + - - +
57G GLU* 3.7 6.0 + - - +
58G ARG* 3.3 24.4 + - - +
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 3.9 3.8 - - + -
51G MSE 2.9 47.3 + - + +
52G ILE 3.8 0.2 - - - +
54G ASP* 1.3 74.9 - - - +
56G SER* 1.3 57.1 + - - +
58G ARG 3.1 0.9 + - - -
59G PHE* 2.7 67.7 + - + +
60G LEU* 4.8 0.2 - - - -
75G MSE 4.2 13.5 - - + -
79G SER* 4.4 2.7 - - - -
89G ILE* 4.3 11.2 - - + +
92G GLY* 3.9 7.6 - - - -
93G ILE* 3.7 37.0 - - + +
96G ILE* 3.8 18.6 - - + -
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Residues in contact with SER 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G VAL* 3.3 40.0 - - - +
52G ILE* 2.8 31.6 + - - +
53G LYS 3.8 2.7 - - - -
55G LEU* 1.3 73.2 - - - +
57G GLU* 1.3 60.4 + - - +
60G LEU* 3.1 40.8 + - - +
61G ILE* 3.6 15.3 + - - +
96G ILE* 4.0 0.9 - - - +
383G CYS* 4.2 9.6 - - - -
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Residues in contact with GLU 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LYS* 2.6 63.4 + - - +
54G ASP* 4.2 6.7 - - - +
56G SER* 1.3 76.1 - - - +
58G ARG* 1.3 59.0 + - - +
61G ILE* 4.2 13.3 - - + +
382G SER 5.4 0.5 - - - +
383G CYS* 3.8 23.4 - - + -
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Residues in contact with ARG 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 4.1 12.4 - - + +
170C GLN* 4.4 15.4 + - - +
54G ASP 3.3 16.6 + - - +
55G LEU 3.1 2.7 + - - +
57G GLU* 1.3 80.5 - - - +
59G PHE* 1.3 95.7 + - + +
63G LYS* 4.7 5.8 + - - +
74G THR* 5.7 0.2 - - - +
78G HIS* 4.8 10.5 + - - +
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Residues in contact with PHE 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 3.8 9.4 - - + -
55G LEU* 2.7 50.3 + - + +
58G ARG* 1.3 117.0 - - + +
60G LEU* 1.3 65.7 + - + +
61G ILE 5.5 0.2 - - - -
63G LYS* 2.8 37.4 + - - +
71G LEU* 4.8 3.3 - - + +
74G THR* 3.6 36.3 - - + -
75G MSE 3.6 29.2 - - + -
78G HIS* 3.7 32.3 - - + -
79G SER* 4.0 2.2 - - - -
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ILE* 3.4 27.1 - - + +
8G VAL* 4.0 16.2 - - + -
25G ILE* 4.1 11.4 - - + -
55G LEU 4.5 1.6 - - - +
56G SER* 3.1 39.9 + - - +
59G PHE* 1.3 89.0 - - + +
61G ILE* 1.3 67.8 + - - +
62G GLY 3.1 0.7 + - - -
63G LYS* 3.0 21.6 + - - +
71G LEU* 4.4 18.6 - - + -
75G MSE 4.8 4.9 - - + -
96G ILE* 3.7 39.7 - - + -
100G LEU* 5.2 0.2 - - + -
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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
------------------------------------------------------------
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