Contacts of the helix formed by residues 44 - 60 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C HIS* 4.9 0.4 + - - -
39C ILE* 3.5 17.3 - - - +
42C GLY 4.0 1.4 + - - -
43C VAL* 1.3 78.0 - - - +
45C GLY* 1.3 67.6 + - - +
46C THR 3.2 2.9 - - - -
47C ALA* 3.0 6.2 + - - +
48C ALA 3.0 19.2 + - - -
88C ILE* 4.3 3.7 - - - +
51G MSE 4.0 14.6 - - - -
54G ASP* 3.2 14.2 + - - +
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Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.6 10.8 - - - +
19C HIS* 3.7 33.0 + - - -
21C VAL* 3.4 15.6 - - - +
39C ILE* 3.7 10.1 - - - -
44C GLY* 1.3 78.1 - - - +
46C THR* 1.3 60.3 + - - +
48C ALA* 3.4 1.1 + - - -
49C ALA 3.2 16.3 + - - -
54G ASP* 3.3 3.2 + - - -
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Residues in contact with THR 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.0 17.9 - - + +
45C GLY* 1.3 75.1 - - - +
47C ALA* 1.3 59.9 + - - +
49C ALA* 3.3 2.3 + - - +
50C GLY* 2.9 25.5 + - - -
380C TRP* 3.9 28.0 - - + +
50G GLY* 3.7 20.4 - - - +
53G LYS* 4.5 15.6 + - + +
54G ASP* 2.6 31.8 + - - -
380G TRP* 4.0 7.6 - - + -
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Residues in contact with ALA 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY* 3.0 15.6 + - - +
46C THR* 1.3 80.0 - - - +
48C ALA* 1.3 56.9 + - - +
50C GLY 3.3 0.5 + - - -
51C MSE 3.0 24.4 + - - +
88C ILE* 4.0 15.7 - - + -
47G ALA* 3.3 36.2 - - - +
50G GLY 3.9 0.8 - - - -
51G MSE 3.7 22.7 - - + +
54G ASP* 3.5 1.8 + - - -
88G ILE* 4.2 4.9 - - + -
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 4.2 14.4 - - + -
37C ALA* 4.3 8.5 - - + -
39C ILE* 3.8 28.9 - - + -
44C GLY 3.0 11.3 + - - +
45C GLY 3.6 8.7 - - - +
47C ALA* 1.3 75.7 - - - +
49C ALA* 1.3 66.3 + - - +
51C MSE 3.1 4.4 + - - +
52C ILE* 3.0 26.7 + - - +
88C ILE* 4.2 10.7 - - + +
91C ALA* 5.2 2.0 - - + -
92C GLY* 5.0 1.4 - - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.7 18.4 - - + +
12C LEU* 4.5 7.6 - - + -
21C VAL* 3.9 14.9 - - + +
45C GLY 3.2 12.1 + - - +
46C THR* 3.7 9.2 - - - +
48C ALA* 1.3 79.3 - - - +
50C GLY* 1.3 63.4 + - - +
52C ILE* 3.3 1.1 + - - +
53C LYS* 3.1 16.8 + - - +
380C TRP* 3.5 36.6 - - + -
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Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR 2.9 13.4 + - - -
47C ALA 3.3 3.6 + - - -
49C ALA* 1.3 77.1 - - - +
51C MSE 1.3 58.2 + - - +
53C LYS* 3.2 4.2 + - - +
54C ASP* 2.9 31.7 + - - +
380C TRP* 3.6 21.2 - - - -
46G THR* 3.7 12.5 - - - -
47G ALA* 3.9 9.0 - - - -
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Residues in contact with MSE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ALA 3.0 14.3 + - - +
48C ALA 3.1 8.3 + - - +
50C GLY* 1.3 74.5 - - - +
52C ILE* 1.3 60.3 + - - +
54C ASP* 3.5 9.4 - - + -
55C LEU* 2.8 47.0 + - + +
81C TRP* 6.3 0.2 - - - -
88C ILE* 3.8 25.6 - - + +
89C ILE* 3.8 22.9 - - - +
92C GLY* 4.4 3.1 - - - -
43G VAL* 3.2 43.5 - - + +
44G GLY* 4.0 7.4 - - - -
47G ALA* 3.7 11.4 - - + +
88G ILE* 5.4 3.4 - - - -
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Residues in contact with ILE 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.7 16.2 - - + -
21C VAL* 3.9 27.4 - - + -
22C LEU 4.7 1.6 - - - +
23C VAL* 3.6 34.3 - - + -
37C ALA* 4.2 5.2 - - + -
48C ALA 3.0 10.2 + - - +
49C ALA 3.8 6.1 - - - +
51C MSE 1.3 76.0 - - - +
53C LYS* 1.3 56.0 + - - +
55C LEU* 4.0 7.5 - - - +
56C SER* 2.6 43.4 + - - +
92C GLY* 3.8 18.2 - - - +
95C ALA* 3.9 24.0 - - + -
96C ILE* 4.3 9.0 - - + -
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.2 17.9 - - + +
49C ALA 3.1 10.3 + - - +
50C GLY 3.2 10.1 - - - +
51C MSE 3.1 0.4 - - - -
52C ILE* 1.3 77.1 - - - +
54C ASP* 1.3 58.7 + - - +
56C SER* 3.8 1.2 - - - -
57C GLU* 2.5 69.1 + - - +
380C TRP* 3.9 19.1 - - + -
381C ALA* 4.2 13.7 - - + -
382C SER 6.0 0.7 - - - -
383C CYS* 4.1 10.5 - - - -
46G THR* 4.2 21.2 + - + +
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Residues in contact with ASP 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLY 2.9 14.2 + - - +
51C MSE 3.5 7.1 - - + +
53C LYS* 1.3 79.5 + - - +
55C LEU* 1.3 64.7 + - - +
57C GLU* 4.0 6.3 - - - +
58C ARG* 3.1 26.3 + - - +
43G VAL* 3.4 21.1 - - + +
44G GLY* 3.2 18.0 - - - +
45G GLY 4.2 0.9 - - - -
46G THR* 2.5 47.1 + - - -
47G ALA 3.5 1.4 + - - -
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C MSE 2.8 48.1 + - + +
52C ILE 4.0 0.2 - - - +
54C ASP* 1.3 72.8 - - - +
56C SER* 1.3 62.2 + - - +
58C ARG 3.3 0.3 + - - -
59C PHE* 2.8 59.6 + - + +
60C LEU* 3.9 1.9 + - - +
75C MSE 4.1 17.0 - - + -
79C SER* 4.5 2.7 - - - -
89C ILE* 4.2 12.1 - - + +
92C GLY* 3.8 8.1 - - - -
93C ILE* 3.6 38.4 - - + +
96C ILE* 3.7 17.3 - - + -
43G VAL* 4.1 4.3 - - + -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.3 35.4 - - - +
52C ILE* 2.6 26.8 + - - +
53C LYS* 3.8 3.6 - - - -
55C LEU* 1.3 77.6 - - - +
57C GLU* 1.3 64.2 + - - +
60C LEU* 3.0 46.0 + - - +
61C ILE* 3.8 8.8 + - - +
96C ILE* 4.2 0.3 - - - +
383C CYS* 4.3 10.5 - - - -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS* 2.5 60.9 + - - +
54C ASP* 4.0 7.4 - - - +
56C SER* 1.3 77.9 - - - +
58C ARG* 1.3 59.6 + - - +
61C ILE* 5.2 8.6 + - - +
382C SER 5.5 0.2 - - - +
383C CYS* 3.6 22.1 - - + -
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Residues in contact with ARG 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ASP 3.1 18.6 + - - +
57C GLU* 1.3 78.8 - - - +
59C PHE* 1.3 98.6 + - + +
63C LYS* 5.2 5.9 + - - +
74C THR* 5.6 1.4 - - - +
78C HIS* 4.5 14.1 + - - +
43G VAL* 4.1 13.0 - - + +
170G GLN* 4.5 14.6 + - - +
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Residues in contact with PHE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 2.8 39.5 + - + +
58C ARG* 1.3 119.3 - - + +
60C LEU* 1.3 63.8 + - + +
61C ILE 4.0 0.2 - - - -
63C LYS* 2.9 33.2 - - - +
71C LEU* 5.2 2.9 - - + +
74C THR* 3.6 28.0 - - + -
75C MSE 3.8 29.6 - - + -
78C HIS* 3.6 41.5 - - + -
79C SER* 4.0 2.7 - - - -
43G VAL* 3.8 13.5 - - + -
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Residues in contact with LEU 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 3.5 20.9 - - + +
8C VAL* 4.0 18.8 - - + -
25C ILE* 4.3 8.5 - - + -
55C LEU 4.3 2.0 - - - +
56C SER* 3.0 41.7 + - - +
59C PHE* 1.3 87.2 - - + +
61C ILE* 1.3 66.7 + - - +
62C GLY 3.1 0.7 + - - -
63C LYS* 3.0 20.5 + - - +
71C LEU* 4.3 23.3 - - + -
75C MSE 4.8 6.7 - - + -
96C ILE* 3.7 39.5 - - + -
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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