Contacts of the helix formed by residues 34 - 49 (chain E) in PDB entry 1O9I
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 34 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU 3.8 10.4 + - - -
28E SER* 3.5 15.0 - - - -
29E LEU 4.9 0.2 - - - -
31E GLY 3.1 16.6 + - - -
32E GLN 3.5 0.4 + - - -
33E TRP* 1.3 79.0 - - - +
35E GLU* 1.3 66.6 + - - -
36E THR 3.2 2.9 - - - -
37E THR 3.1 12.7 + - - -
38E GLY 3.1 4.5 + - - -
147E ARG* 3.0 14.7 + - - -
151E ALA* 5.5 0.4 - - - -
154E GLN* 5.3 1.1 - - - -
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Residues in contact with GLU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E SER* 2.8 24.4 + - - +
29E LEU* 5.3 0.9 - - - +
34E GLY* 1.3 73.4 - - - -
36E THR* 1.3 58.7 + - - +
38E GLY* 3.7 0.7 - - - -
39E MET* 2.8 29.8 + - - +
66E GLU* 3.1 13.7 - - - +
69E HIS* 3.1 39.8 + - + +
70E VAL* 3.7 23.6 - - + +
73E ILE* 4.2 15.3 - - + -
147E ARG* 3.1 29.1 + - - +
151E ALA* 4.4 2.4 - - - +
174E LEU* 4.5 6.6 - - - +
178E GLU* 4.1 18.5 - - - +
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Residues in contact with THR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 4.4 15.9 - - + +
126C TRP* 5.9 1.1 - - + -
29E LEU* 2.8 31.1 + - - +
34E GLY 3.2 0.6 - - - -
35E GLU* 1.3 74.8 - - - +
37E THR* 1.3 66.9 + - - +
39E MET* 3.6 17.2 - - + +
40E MET* 2.9 29.9 + - + +
70E VAL* 3.8 18.4 - - - +
118E LEU* 5.0 2.2 - - + +
126E TRP* 3.6 36.3 - - + -
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Residues in contact with THR 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E GLY 3.4 4.2 + - - -
32E GLN 2.8 29.4 + - - +
33E TRP* 4.3 1.8 - - + -
34E GLY 3.1 11.7 + - - -
36E THR* 1.3 80.0 - - - +
38E GLY* 1.3 57.0 + - - +
41E SER* 2.8 42.3 + - - +
126E TRP* 2.9 25.1 + - - +
130E TYR* 3.4 27.1 - - - +
131E VAL* 4.4 1.0 - - + +
143E PHE* 4.7 2.2 - - + -
147E ARG* 4.1 16.8 - - + -
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Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E GLY 3.1 10.3 + - - -
35E GLU 3.2 3.3 + - - -
37E THR* 1.3 76.0 - - - +
39E MET* 1.3 65.0 + - - +
42E PHE* 2.9 43.4 + - - -
66E GLU* 4.0 2.0 - - - -
147E ARG* 3.6 29.8 - - - +
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Residues in contact with MET 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 5.3 1.1 - - - +
40C MET* 4.1 21.3 - - + +
43C LEU* 6.4 0.4 - - - -
67C MET* 3.9 12.6 - - + -
35E GLU 2.8 15.9 + - - +
36E THR* 3.6 26.5 - - + +
38E GLY* 1.3 75.9 - - - +
40E MET* 1.3 73.2 + - - +
42E PHE* 4.2 0.2 - - - -
43E LEU* 3.0 43.9 + - + +
63E GLY* 3.9 5.3 - - - +
66E GLU* 3.6 18.1 - - + +
67E MET* 3.5 42.2 - - + +
70E VAL* 4.1 12.3 - - + -
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Residues in contact with MET 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR* 4.5 21.3 - - + +
39C MET* 4.5 12.3 - - + -
40C MET* 5.9 0.2 - - - +
67C MET* 4.6 5.6 - - - +
70C VAL* 4.7 12.8 - - + -
118C LEU* 3.9 30.7 - - + -
36E THR* 2.9 25.6 + - + +
39E MET* 1.3 93.7 - - + +
41E SER* 1.3 61.8 + - - +
43E LEU* 4.8 4.0 - - - -
44E SER* 2.8 34.4 + - - -
47E TRP* 5.5 6.1 - - + -
126E TRP* 3.9 15.3 - - + -
131E VAL* 3.9 20.0 - - + +
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Residues in contact with SER 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E THR* 2.8 26.2 + - - +
38E GLY* 3.9 1.8 - - - -
40E MET* 1.3 78.9 - - - +
42E PHE* 1.3 68.1 + - - +
44E SER* 3.2 1.1 + - - -
45E GLN* 3.0 36.2 + - - +
131E VAL* 3.5 26.4 - - - +
132E THR 4.1 6.5 - - - -
143E PHE* 3.6 29.2 - - - -
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Residues in contact with PHE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLY* 2.9 24.1 + - - +
41E SER* 1.3 82.7 - - - +
43E LEU* 1.3 57.1 + - - +
45E GLN* 4.6 0.4 - - - -
46E GLY* 2.8 27.0 + - - -
59E LEU* 3.6 35.1 - - + +
62E THR* 3.7 23.1 - - + -
63E GLY* 3.7 4.5 - - - -
66E GLU* 3.5 18.4 - - + -
143E PHE* 5.4 0.2 - + - -
144E ASN* 3.2 49.8 - - + -
147E ARG* 4.2 17.0 - - + -
148E GLU* 3.3 31.6 - - + -
181E HIS* 5.8 0.2 - - + -
185E PHE* 5.7 2.9 - + - -
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 5.8 0.2 - - + -
67C MET* 3.8 28.9 - - + -
2E PHE* 4.1 16.6 - - + -
39E MET* 3.0 29.5 + - + +
40E MET* 4.4 5.2 - - - +
42E PHE* 1.3 76.8 - - - +
44E SER* 1.3 58.0 + - - +
46E GLY* 3.2 0.5 + - - -
47E TRP* 2.9 59.2 + - + -
60E LEU* 4.0 21.9 - - + +
63E GLY* 3.8 22.4 - - - +
64E THR* 3.9 13.2 - - - +
67E MET* 4.3 6.3 - - - -
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Residues in contact with SER 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C SER* 6.0 0.4 - - - -
116C ALA 5.7 4.3 - - - -
118C LEU* 4.6 19.3 - - - -
40E MET* 2.8 26.2 + - - -
41E SER* 3.2 7.6 + - - -
43E LEU* 1.3 75.1 - - - +
45E GLN* 1.3 59.7 + - - +
47E TRP* 3.4 15.8 + - - +
48E ALA* 3.0 29.5 + - - +
131E VAL* 3.9 5.9 - - - +
133E SER* 3.5 20.4 + - - -
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Residues in contact with GLN 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E SER* 3.0 27.0 + - - +
42E PHE 3.9 1.1 - - - +
44E SER* 1.3 74.1 + - - +
46E GLY* 1.3 65.8 + - - +
48E ALA* 3.2 3.1 + - - +
49E SER* 3.0 24.6 + - - -
59E LEU* 3.3 20.5 - - + +
132E THR 2.9 27.3 + - - +
133E SER* 3.5 15.0 - - - +
137E LEU* 4.3 6.8 - - + +
140E ASP* 3.7 27.9 - - - +
143E PHE* 4.0 6.3 - - - -
144E ASN* 2.8 43.5 + - - -
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E PHE 2.8 19.2 + - - -
43E LEU 3.6 1.3 - - - -
45E GLN* 1.3 79.8 - - - +
47E TRP* 1.3 50.2 + - - +
49E SER* 3.4 2.5 + - - -
56E LYS* 2.7 41.9 + - - +
59E LEU* 3.7 19.3 - - - +
60E LEU* 3.8 16.8 - - - -
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Residues in contact with TRP 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 5.3 9.7 - - - +
4C HIS* 4.3 1.8 + + - -
67C MET* 4.2 5.4 - - - -
70C VAL* 3.8 24.9 - - + -
71C GLU* 3.0 49.9 + - + +
74C SER* 3.6 36.6 - - - -
75C THR* 5.0 10.7 + - - +
118C LEU* 6.1 1.6 - - + -
2E PHE* 4.0 19.5 - + - -
40E MET* 5.5 5.6 - - + -
43E LEU* 2.9 47.6 + - + +
44E SER* 3.8 12.1 - - - +
46E GLY* 1.3 76.9 - - - +
48E ALA* 1.3 61.4 + - - +
49E SER 4.1 0.3 - - - +
56E LYS* 3.3 12.8 + - - +
60E LEU* 3.7 21.2 - - + +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ILE* 5.6 1.3 - - - +
265B GLN* 4.1 6.4 + - - +
115C ASN* 3.3 44.6 - - + +
44E SER 3.0 17.4 + - - +
45E GLN* 3.2 5.6 + - - +
47E TRP* 1.3 76.8 - - - +
49E SER* 1.3 64.1 + - - +
50E THR* 3.4 11.4 + - - +
133E SER* 4.1 11.7 - - - +
135E GLY* 5.7 3.1 - - - -
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Residues in contact with SER 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 5.8 0.9 + - - +
265B GLN* 3.8 15.9 + - - +
45E GLN 3.0 15.4 + - - -
46E GLY* 3.4 6.7 + - - -
47E TRP 3.3 2.7 - - - +
48E ALA* 1.3 77.9 - - - +
50E THR* 1.3 61.8 + - - +
51E GLY* 3.0 17.4 + - - -
52E ALA 4.7 0.7 + - - -
56E LYS* 2.8 49.9 + - - +
59E LEU* 5.2 0.4 - - - -
137E LEU* 4.1 17.5 - - - +
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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