Contacts of the helix formed by residues 43 - 58 (chain E) in PDB entry 2ONK
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 LEU 43 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E HIS* 3.9 9.9 - - + +
40E ALA* 3.4 13.5 + - + +
41E GLY 3.3 0.8 - - - -
42E SER* 1.3 78.4 + - - +
44E THR* 1.3 57.9 + - - +
46E PRO* 3.7 15.5 - - + -
47E MET* 2.8 40.9 + - + +
50E PHE* 5.2 1.3 - - + -
88E ALA* 3.3 38.6 - - + +
89E THR 4.7 0.2 - - - +
110E PHE* 3.5 24.7 - - + -
285E TYR* 3.4 35.2 - - + -
315E LEU* 4.5 1.8 - - + -
320E GLN* 3.7 17.3 - - - +
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Residues in contact with THR 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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223D SER* 3.9 24.8 - - - +
224D GLU* 4.3 8.7 - - + -
39E HIS* 3.5 18.2 - - + -
41E GLY* 2.5 28.5 + - - -
42E SER 2.9 4.4 + - - -
43E LEU* 1.3 74.9 - - - +
45E GLU* 1.3 82.1 + - - +
47E MET* 3.3 4.2 + - - +
48E LYS* 3.1 21.9 + - + +
67E ALA* 3.9 7.2 - - + +
219E MET* 4.1 7.8 - - - +
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Residues in contact with GLU 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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223D SER 4.8 0.9 - - - +
224D GLU* 3.4 21.0 - - - +
42E SER 4.2 0.4 + - - -
44E THR* 1.3 77.2 - - - +
46E PRO* 1.3 66.8 - - + +
48E LYS* 2.6 63.9 + - - +
49E ALA 3.3 2.6 + - - -
219E MET* 4.9 1.0 - - + +
242E GLN* 3.0 41.7 - - + +
243E HIS* 3.7 20.4 - - + -
318E LEU* 3.5 16.9 - - + +
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Residues in contact with PRO 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 SER 3.7 6.3 - - - +
43E LEU* 3.7 18.2 - - + +
44E THR 3.5 2.0 - - - -
45E GLU* 1.3 94.5 - - + +
47E MET* 1.3 62.7 + - - +
49E ALA* 2.9 17.0 + - - +
50E PHE* 2.9 34.8 + - + -
242E GLN* 3.8 9.6 - - - +
314E ILE* 4.6 1.8 - - + -
315E LEU* 4.0 12.6 - - + -
318E LEU* 3.2 21.5 - - + -
320E GLN* 3.7 21.1 - - - +
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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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37E VAL* 3.9 24.9 - - + -
39E HIS* 3.7 29.4 - - + +
43E LEU* 2.8 45.1 + - + +
44E THR 3.5 4.9 - - - +
45E GLU 3.2 0.2 - - - -
46E PRO* 1.3 73.8 - - - +
48E LYS* 1.3 63.7 + - - +
50E PHE* 3.5 29.8 - - + +
51E LYS* 2.8 24.3 + - - +
63E VAL* 6.2 0.7 - - - -
65E THR* 4.7 14.4 - - + +
88E ALA* 4.8 7.2 - - + -
110E PHE* 5.8 1.8 - - + -
287E ILE* 5.6 1.8 - - + -
302E PHE* 3.7 28.3 - - + -
306E VAL* 5.0 4.0 - - + -
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Residues in contact with LYS 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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224D GLU* 2.4 34.8 + - - +
44E THR* 3.1 13.0 + - + +
45E GLU* 2.6 52.6 + - - +
47E MET* 1.3 70.7 - - - +
49E ALA* 1.3 59.1 + - - +
51E LYS* 3.1 24.7 + - + +
52E ARG* 3.1 24.3 + - - +
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Residues in contact with ALA 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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45E GLU 3.3 3.0 + - - +
46E PRO* 2.9 11.4 + - + +
48E LYS* 1.3 76.2 - - - +
50E PHE* 1.3 67.2 + - - +
51E LYS 2.9 2.6 + - - -
52E ARG* 3.3 21.8 + - - +
53E ALA* 3.0 24.4 + - - +
314E ILE* 3.5 31.4 - - + -
318E LEU* 4.8 6.1 - - + -
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Residues in contact with PHE 50 (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 LEU* 5.2 1.8 - - + -
46E PRO* 2.9 45.4 + - + -
47E MET* 3.5 28.5 - - + +
49E ALA* 1.3 76.4 - - - +
51E LYS* 1.3 55.9 + - - +
53E ALA* 4.5 1.1 - - - -
54E PHE* 2.9 33.1 + - - +
110E PHE* 5.1 4.3 - + - -
302E PHE* 3.9 21.4 - + + -
305E LEU* 3.6 9.3 - - + +
306E VAL* 4.0 30.3 - - + -
311E GLY* 3.8 24.9 - - - -
314E ILE* 3.9 18.8 - - + +
315E LEU* 3.7 30.5 - - + -
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Residues in contact with LYS 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 2.8 13.9 + - - +
48E LYS* 3.1 13.9 - - + +
49E ALA 2.9 1.4 + - - -
50E PHE* 1.3 75.0 - - - +
52E ARG* 1.3 69.4 + - - +
54E PHE* 3.2 4.2 + - - +
55E GLU* 2.8 59.2 + - - +
62E GLU* 4.2 6.7 - - - +
63E VAL* 2.6 49.8 + - + +
65E THR* 4.5 11.4 - - + -
302E PHE* 5.1 0.2 - - - -
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Residues in contact with ARG 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 LYS* 3.1 19.3 + - - +
49E ALA* 3.3 32.0 - - - +
51E LYS* 1.3 81.1 - - - +
53E ALA* 1.3 66.9 + - + +
55E GLU* 3.5 7.4 - - - +
56E GLU* 2.7 52.1 + - - +
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Residues in contact with ALA 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 ALA 3.0 13.4 + - - +
50E PHE 3.8 3.4 - - - +
52E ARG* 1.3 83.3 - - + +
54E PHE* 1.3 56.3 + - - +
56E GLU* 2.7 37.0 + - - +
57E LYS* 3.2 5.7 + - - +
305E LEU* 4.2 11.2 - - + -
310E GLU* 4.4 19.3 - - - +
314E ILE* 4.3 13.2 - - + -
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Residues in contact with PHE 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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35E LEU* 4.2 9.9 - - + -
50E PHE 2.9 23.2 + - - +
51E LYS 3.7 2.5 - - - +
53E ALA* 1.3 73.6 - - - +
55E GLU* 1.3 59.5 + - + +
57E LYS* 3.1 25.1 + - + +
58E HIS* 3.2 34.9 + + + -
61E VAL* 4.5 15.7 - - + -
63E VAL* 3.5 25.6 - - + -
298E LEU* 3.8 20.2 - - + -
301E GLU* 3.7 14.8 - - + -
302E PHE* 3.3 48.9 - + + -
305E LEU* 3.5 17.2 - - + +
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Residues in contact with GLU 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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49D LYS* 5.6 1.0 + - - -
51E LYS* 2.8 51.3 + - - +
52E ARG* 3.7 6.1 - - - +
54E PHE* 1.3 70.4 - - + +
56E GLU* 1.3 55.9 + - - +
57E LYS 2.8 5.7 + - - -
58E HIS 4.1 6.1 - - - +
59E PRO* 2.8 37.6 - - + +
61E VAL 3.0 11.3 - - - +
62E GLU* 2.9 16.5 - - - +
63E VAL* 2.8 35.1 + - + -
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Residues in contact with GLU 56 (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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52E ARG* 2.7 29.4 + - - +
53E ALA* 2.7 17.5 + - - +
55E GLU* 1.3 76.5 - - - +
57E LYS* 1.3 56.3 + - - +
59E PRO* 4.0 11.7 - - - +
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Residues in contact with LYS 57 (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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53E ALA 3.2 4.2 + - - +
54E PHE* 3.1 18.1 + - + +
56E GLU* 1.3 79.2 - - - +
58E HIS* 1.3 82.3 + - + +
59E PRO* 3.2 10.0 - - - +
301E GLU* 5.9 2.0 - - - -
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Residues in contact with HIS 58 (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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54E PHE* 3.2 41.3 + + + +
55E GLU* 3.1 6.3 + - - +
57E LYS* 1.3 109.1 - - + +
59E PRO* 1.3 50.8 - - - +
60E ASN* 2.4 33.2 + - - +
61E VAL* 2.7 30.4 + - + +
298E LEU* 4.5 14.6 - - + -
301E GLU* 4.1 24.6 + - + +
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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