Contacts of the helix formed by residues 41 - 55 (chain E) in PDB entry 4OA5
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 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E HIS* 4.4 6.5 - - - -
39E GLN 3.7 1.0 + - - -
40E LEU* 1.3 74.8 - - - +
42E THR* 1.3 61.2 + - - -
43E VAL 3.3 2.2 - - - -
44E GLU* 3.1 19.6 + - - -
45E GLY 2.9 23.2 + - - -
69E PHE* 3.6 8.9 - - - -
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Residues in contact with THR 42 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E ASN* 3.0 25.0 + - - -
18E ALA* 3.5 8.3 - - - +
19E VAL* 3.0 48.8 + - + +
25E LEU* 3.6 23.3 - - + -
28E HIS* 5.6 3.4 - - + -
41E GLY* 1.3 69.0 - - - -
43E VAL* 1.3 62.9 + - - +
46E GLN 3.2 12.1 + - - -
69E PHE* 4.1 19.3 - - + -
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Residues in contact with VAL 43 (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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13E LEU* 3.6 51.1 - - + +
14E ASN* 3.7 24.8 + - - +
17E PHE* 3.8 14.4 - - + +
18E ALA* 3.9 3.8 - - + +
41E GLY 3.3 0.8 - - - -
42E THR* 1.3 75.3 + - - +
44E GLU* 1.3 77.5 + - + +
46E GLN* 3.2 5.0 + - - +
47E MET* 3.0 20.5 + - + +
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Residues in contact with GLU 44 (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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40E LEU* 4.2 25.4 - - + -
41E GLY* 3.1 29.0 + - - +
43E VAL* 1.3 88.0 + - + +
45E GLY* 1.3 62.7 + - - +
47E MET* 3.2 15.2 + - + +
48E LEU* 3.1 25.3 + - - +
162E ASP* 5.8 0.9 - - - +
207E THR* 4.4 26.3 - - + +
209E GLU* 4.6 11.3 - - - +
211E MET* 4.6 7.6 - - + -
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Residues in contact with GLY 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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19E VAL* 3.7 6.5 - - - -
40E LEU* 4.3 11.2 - - - +
41E GLY 2.9 16.9 + - - -
42E THR 3.4 2.7 + - - -
43E VAL 3.2 0.4 - - - -
44E GLU* 1.3 77.4 - - - +
46E GLN* 1.3 60.1 + - - +
48E LEU* 3.4 6.3 + - - +
49E GLN* 3.2 24.3 + - - +
69E PHE* 4.9 0.4 - - - -
73E CYS* 4.0 23.8 - - - +
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Residues in contact with GLN 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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16E LEU 4.7 1.6 + - - -
17E PHE* 3.4 47.7 + - - +
18E ALA 3.2 21.3 + - - +
19E VAL* 3.5 8.5 + - + +
42E THR 3.2 11.6 + - - +
43E VAL 3.2 2.2 + - - +
45E GLY* 1.3 73.2 - - - +
47E MET* 1.3 60.3 + - - +
49E GLN* 3.1 20.0 + - + +
50E LEU* 3.0 28.8 + - + +
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Residues in contact with MET 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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43E VAL* 3.0 14.2 + - + +
44E GLU* 3.2 15.2 + - + +
46E GLN* 1.3 76.5 - - - +
48E LEU* 1.3 63.7 + - + +
50E LEU* 3.2 16.3 + - + +
51E LEU* 3.0 29.5 + - + +
205E ILE* 3.3 47.8 - - + -
207E THR* 4.4 10.3 - - + -
211E MET* 3.8 35.2 - - + -
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Residues in contact with LEU 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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40E LEU* 3.4 27.4 - - + -
44E GLU 3.1 17.3 + - - +
45E GLY* 3.7 7.9 - - - +
46E GLN 3.3 0.2 - - - -
47E MET* 1.3 77.4 - - + +
49E GLN* 1.3 58.2 + - - +
51E LEU* 3.2 13.8 + - + +
52E ILE* 2.9 35.0 + - + +
70E SER* 4.7 3.4 - - - +
73E CYS* 6.0 0.4 - - + -
74E MET* 3.9 35.4 - - + -
132E MET* 4.8 6.0 - - + +
134E PHE* 4.1 17.7 - - + -
160E VAL* 3.9 27.8 - - + -
211E MET* 4.5 10.5 - - + -
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Residues in contact with GLN 49 (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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19E VAL* 3.7 25.6 - - - +
21E THR* 6.2 1.2 - - - +
45E GLY 3.2 8.7 + - - +
46E GLN* 3.1 26.2 + - + +
48E LEU* 1.3 77.8 - - - +
50E LEU* 1.3 57.2 + - - +
52E ILE* 3.2 3.4 + - - +
53E ARG* 2.9 35.3 + - + +
73E CYS* 2.9 35.9 + - - +
76E HIS* 3.9 17.8 + - - +
77E ALA* 3.7 18.1 - - + +
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Residues in contact with LEU 50 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46E GLN* 3.0 14.3 + - + +
47E MET* 3.4 19.1 - - + +
49E GLN* 1.3 76.1 - - - +
51E LEU* 1.3 62.2 + - + +
53E ARG* 3.3 6.4 + - + +
54E MET* 2.8 58.3 + - + +
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Residues in contact with LEU 51 (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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47E MET* 3.0 27.4 + - + +
48E LEU* 3.5 25.6 - - + +
50E LEU* 1.3 79.4 - - + +
52E ILE* 1.3 63.8 + - + +
54E MET* 3.3 15.9 + - + +
55E ALA* 3.0 28.6 + - - +
132E MET* 5.7 1.8 - - + -
158E LEU* 4.2 14.3 - - + +
160E VAL* 4.4 9.9 - - + -
205E ILE* 5.0 5.6 - - + -
213E VAL* 3.7 44.0 - - + -
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Residues in contact with ILE 52 (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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48E LEU 2.9 22.0 + - - +
49E GLN* 3.6 4.7 - - - +
51E LEU* 1.3 76.3 - - - +
53E ARG* 1.3 62.9 + - - +
56E GLY* 3.1 3.5 + - - -
57E ILE* 3.1 39.2 + - + +
60E ILE* 3.6 12.3 - - + -
74E MET* 3.5 48.2 - - + +
77E ALA* 3.8 22.2 - - + +
78E LEU* 3.8 22.7 - - + -
132E MET* 3.9 22.2 - - + -
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Residues in contact with ARG 53 (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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49E GLN* 2.9 21.9 + - + +
50E LEU* 3.8 6.7 - - + +
52E ILE* 1.3 75.9 - - - +
54E MET* 1.3 65.8 + - + +
56E GLY* 3.3 10.8 + - - -
76E HIS 3.7 20.2 + - - -
77E ALA* 3.2 29.1 + - + +
78E LEU 4.7 6.9 + - - -
79E PRO* 5.2 4.8 - - - +
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Residues in contact with MET 54 (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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50E LEU* 2.8 51.7 + - + +
51E LEU* 3.7 15.3 - - + +
53E ARG* 1.3 76.5 - - - +
55E ALA* 1.3 60.8 + - + +
56E GLY 3.5 0.3 + - - -
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Residues in contact with ALA 55 (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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91D TYR* 5.4 4.0 + - - -
51E LEU 3.0 17.4 + - - +
54E MET* 1.3 76.7 - - + +
56E GLY* 1.3 63.8 + - - +
57E ILE* 3.3 22.8 + - + +
154E ARG* 4.4 9.4 + - - +
156E GLY 5.8 2.7 - - - +
158E LEU* 3.9 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
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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