Contacts of the helix formed by residues 44 - 62 (chain E) in PDB entry 5B6N
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 THR 44 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E PRO* 6.3 0.7 - - + -
41E ARG* 3.2 36.7 + - + +
42E ASP 3.1 3.2 + - - -
43E PHE* 1.3 79.2 + - - +
45E PRO* 1.3 71.4 - - + +
46E VAL* 3.2 4.2 + - + +
47E CSD 3.4 17.8 + - - +
48E THR* 2.8 27.4 + - - -
82E TRP* 4.4 0.2 - - - -
132E ARG* 5.8 0.9 - - - +
191F PRO* 3.7 20.4 - - + +
217F TYR* 3.9 0.4 - - - -
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Residues in contact with PRO 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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44E THR* 1.3 92.7 - - + +
46E VAL* 1.3 61.4 + - + +
48E THR* 3.5 3.9 - - - +
49E THR* 3.3 20.6 - - - +
188F MET* 3.6 21.0 - - + +
189F VAL 4.2 8.3 - - - +
191F PRO* 3.7 28.5 - - + -
217F TYR* 3.3 32.1 - - + +
218F LEU* 3.5 26.8 - - + +
219F ARG 4.5 0.4 - - - +
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Residues in contact with VAL 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E THR* 3.4 3.2 - - + +
45E PRO* 1.3 77.2 - - + +
47E CSD 1.3 62.2 + - - +
48E THR 3.0 4.5 - - - -
49E THR* 2.3 28.1 + - - -
50E GLU* 3.2 9.4 + - + +
132E ARG* 3.3 34.5 - - - +
151E ALA 4.8 0.7 - - - +
152E THR 5.3 0.4 - - - +
154E GLY* 4.5 6.3 - - - +
176F ALA* 3.6 33.7 - - + +
177F THR 4.1 12.8 - - - +
178F PRO* 4.1 13.5 - - + -
188F MET* 3.8 19.1 - - + -
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Residues in contact with CSD 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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39E HIS* 3.7 27.6 - - + -
40E PRO* 3.4 10.0 - - - +
41E ARG 2.8 36.7 + - - +
44E THR* 3.5 24.6 - - - +
46E VAL* 1.3 74.5 + - - +
48E THR* 1.3 60.6 + - - +
50E GLU* 3.8 5.8 - - - -
51E LEU* 3.3 25.8 + - - +
82E TRP* 3.7 6.6 - - + -
132E ARG* 2.3 49.4 + - - -
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Residues in contact with THR 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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44E THR 2.8 18.6 + - - -
45E PRO 3.5 11.2 - - - -
47E CSD 1.3 79.6 + - - +
49E THR* 1.3 61.3 - - - +
51E LEU 3.7 0.2 + - - -
52E GLY* 3.2 21.0 + - - -
82E TRP* 3.3 19.0 + - - -
85E ASP 5.3 1.3 - - - +
86E ILE* 3.9 19.8 - - + +
89E TYR* 4.3 20.9 - - + -
211F LEU* 6.2 0.7 - - + -
217F TYR* 3.4 21.5 - - - +
218F LEU* 3.9 17.7 - - + -
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Residues in contact with THR 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 PRO 3.3 15.9 - - - +
46E VAL* 2.3 29.5 + - - -
48E THR* 1.3 73.7 - - - +
50E GLU* 1.3 65.2 + - - +
52E GLY* 4.1 0.7 - - - -
53E ARG* 3.3 13.2 + - - +
89E TYR* 3.7 32.7 + - + +
178F PRO* 3.9 4.6 - - + +
179F VAL* 3.3 40.7 + - - +
188F MET* 3.6 22.2 - - + -
218F LEU* 4.7 2.5 - - + -
220F TYR* 4.6 2.0 - - + +
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Residues in contact with GLU 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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46E VAL* 3.2 16.5 + - + +
47E CSD 3.8 7.3 - - - +
48E THR 3.2 0.4 - - - -
49E THR* 1.3 83.9 + - - +
51E LEU* 1.3 63.6 + - + +
53E ARG* 3.0 24.6 + - - +
54E ALA 3.2 4.7 + - - -
132E ARG* 3.4 19.7 + - - -
154E GLY* 3.5 5.4 - - - -
155E ARG* 2.5 78.1 + - - +
157E PHE* 4.0 16.5 - - + -
179F VAL* 4.1 17.9 - - + -
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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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37E PHE* 3.4 29.6 - - + -
39E HIS* 3.9 33.9 - - + -
47E CSD 3.3 16.5 + - - +
48E THR 4.5 1.8 - - - +
50E GLU* 1.3 82.9 - - + +
52E GLY* 1.3 59.8 + - - +
53E ARG 3.1 0.2 - - - -
54E ALA* 3.4 9.5 + - - +
55E ALA* 3.1 24.4 + - - +
70E ALA* 4.3 6.3 - - + -
82E TRP* 3.5 29.8 - - + -
86E ILE* 4.3 8.5 - - + +
98E LEU* 5.5 2.1 - - + +
100E PHE* 3.9 14.6 - - + -
102E ILE* 3.9 16.8 - - + -
155E ARG* 4.6 0.7 - - - +
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Residues in contact with GLY 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 THR 3.2 14.3 + - - -
49E THR 3.6 2.2 + - - -
50E GLU 3.1 1.0 - - - -
51E LEU* 1.3 78.1 - - - +
53E ARG* 1.3 61.7 + - - +
55E ALA* 3.5 8.7 - - - +
56E LYS 3.7 0.9 + - - -
86E ILE* 3.7 14.1 - - - +
89E TYR* 4.1 7.9 - - - -
90E ASN* 2.9 41.8 + - - +
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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 THR 3.3 8.3 + - - +
50E GLU 3.0 12.3 + - - +
52E GLY* 1.3 76.9 - - - +
54E ALA* 1.3 59.2 + - - +
55E ALA 3.1 0.2 - - - -
56E LYS* 3.1 17.3 + - - +
57E LEU* 2.8 61.1 + - - +
89E TYR* 4.9 0.4 - - + -
90E ASN* 5.1 1.3 - - - +
157E PHE* 4.5 9.4 - - + +
158E ASP* 3.1 28.1 + - - -
179F VAL* 4.0 20.2 - - + -
180F ASP* 3.7 23.0 + - - +
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Residues in contact with ALA 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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37E PHE* 4.3 2.9 - - + -
50E GLU 3.2 4.8 + - - +
51E LEU* 3.6 6.3 - - - +
53E ARG* 1.3 78.8 - - - +
55E ALA* 1.3 56.2 + - - +
57E LEU* 4.2 6.5 - - - -
58E ALA* 2.8 36.2 + - - +
68E LEU* 3.7 11.2 - - + +
100E PHE* 3.5 24.2 - - + -
157E PHE* 3.6 30.0 - - + -
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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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51E LEU 3.1 13.1 + - - +
52E GLY* 3.5 14.8 - - - +
53E ARG 3.1 0.4 - - - -
54E ALA* 1.3 77.4 - - - +
56E LYS* 1.3 70.4 + - + +
59E PRO* 3.8 6.4 - - - +
86E ILE* 5.0 2.2 - - + -
87E ASN* 6.0 1.6 - - - +
90E ASN* 4.4 7.4 - - - +
92E GLU* 4.7 5.6 - - - +
97E LYS 5.7 0.7 - - - +
98E LEU* 4.8 10.1 - - + -
99E PRO* 3.6 36.5 - - + +
100E PHE* 4.0 4.0 - - + -
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Residues in contact with LYS 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 GLY 3.7 0.4 + - - +
53E ARG* 3.1 20.8 + - - +
55E ALA* 1.3 84.6 + - - +
57E LEU* 1.3 65.1 + - - +
58E ALA 3.5 0.4 - - - -
59E PRO* 4.0 20.9 - - - +
60E GLU* 5.1 3.1 - - - +
90E ASN* 3.4 28.0 - - + +
92E GLU* 3.0 42.2 + - + +
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Residues in contact with LEU 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 ARG* 2.8 43.9 + - - +
54E ALA* 4.1 4.5 - - - +
56E LYS* 1.3 79.5 - - - +
58E ALA* 1.3 53.9 + - - +
59E PRO 3.2 2.9 - - - -
60E GLU* 2.6 51.1 + - + +
61E PHE* 3.3 21.1 + - + -
157E PHE* 3.6 42.6 - - + +
158E ASP* 3.7 14.6 - - - +
161E LEU* 4.4 13.0 - - + -
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Residues in contact with ALA 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 ALA 2.8 18.2 + - - +
57E LEU* 1.3 77.0 - - - +
59E PRO* 1.3 59.0 - - + +
61E PHE* 3.0 6.1 + - - +
62E ALA* 2.7 38.4 + - + +
66E VAL 5.2 0.2 - - - +
68E LEU* 3.6 22.7 - - + -
99E PRO* 3.7 27.4 - - + -
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Residues in contact with PRO 59 (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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55E ALA 3.8 14.4 - - - +
56E LYS* 4.0 21.1 - - - +
57E LEU 3.6 2.7 - - - -
58E ALA* 1.3 91.7 - - + +
60E GLU* 1.3 61.2 + - + +
62E ALA* 4.2 8.2 - - + +
63E LYS* 3.3 22.9 + - - +
99E PRO* 5.2 3.4 - - + -
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Residues in contact with GLU 60 (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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56E LYS 5.1 2.9 - - - +
57E LEU* 2.6 37.3 + - + +
59E PRO* 1.3 78.1 - - + +
61E PHE* 1.3 60.2 + - - +
62E ALA 3.4 0.2 - - - -
63E LYS* 3.8 12.3 + - - +
64E ARG* 3.0 57.7 + - - +
161E LEU* 4.0 25.4 - - + +
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Residues in contact with PHE 61 (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 ILE* 4.9 4.5 - - + -
57E LEU* 3.3 43.7 + - + -
58E ALA* 3.0 9.1 + - - +
60E GLU* 1.3 78.0 - - - +
62E ALA* 1.3 57.6 + - - +
63E LYS 3.3 0.2 - - - -
64E ARG* 3.0 13.7 + - + -
65E ASN 3.1 0.3 + - - -
66E VAL* 2.6 65.5 + - + +
68E LEU* 4.3 24.2 - - + -
157E PHE* 4.6 8.5 - + - -
160E ILE* 4.2 12.6 - - + -
161E LEU* 3.6 41.5 - - + -
164E VAL* 3.8 24.5 - - + -
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Residues in contact with ALA 62 (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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58E ALA 2.7 18.1 + - - +
59E PRO* 4.4 5.8 - - + -
61E PHE* 1.3 72.4 - - - +
63E LYS* 1.3 57.7 + - - +
64E ARG 2.9 9.7 + - - -
65E ASN* 3.2 11.3 + - - -
66E VAL 3.7 11.8 + - - +
67E LYS* 6.0 4.3 - - + -
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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