Contacts of the helix formed by residues 45 - 60 (chain E) in PDB entry 2R6C
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 ARG 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17E GLU* 3.4 14.1 + - - +
18E GLN* 5.0 4.6 - - - +
43E PHE 4.0 2.8 - - - +
44E TYR* 1.3 89.5 - - + +
46E ALA* 1.3 67.4 + - - +
47E ALA* 4.4 8.3 - - + +
48E HIS* 3.2 25.9 + - + +
49E GLN* 3.0 19.6 + - - +
88E TYR* 3.8 23.6 + - - -
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Residues in contact with ALA 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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44E TYR 3.7 3.4 + - - -
45E ARG* 1.3 69.4 - - - +
47E ALA* 1.3 60.4 + - - +
49E GLN* 2.6 37.8 + - + +
50E LYS* 2.8 33.7 + - - +
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Residues in contact with ALA 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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45E ARG* 3.3 8.9 - - + +
46E ALA* 1.3 77.9 - - - +
48E HIS* 1.3 69.4 + - + +
50E LYS* 3.6 10.6 + - - +
51E ILE* 3.2 27.0 + - - +
82E GLU 4.6 4.9 - - - +
83E ILE* 3.7 36.1 - - + +
88E TYR* 5.1 2.9 - - + -
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Residues in contact with HIS 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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17E GLU* 3.0 33.5 + - + +
18E GLN* 3.9 20.2 - - + -
21E LEU* 3.6 21.4 - - + +
43E PHE* 3.5 19.5 - - + -
45E ARG* 3.2 27.8 + - + +
46E ALA 3.0 0.8 - - - -
47E ALA* 1.3 79.2 - - + +
49E GLN* 1.3 68.9 + - - +
51E ILE* 3.0 2.5 + - - +
52E PHE* 2.8 25.8 + - - +
88E TYR* 2.4 44.8 + + - -
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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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40E PRO* 3.0 35.9 - - + +
41E GLU* 3.6 28.6 + - - +
43E PHE* 3.3 20.7 - - - +
44E TYR 4.5 2.8 - - - +
45E ARG 3.0 7.4 + - - +
46E ALA* 2.6 31.1 + - - +
48E HIS* 1.3 70.8 - - - +
50E LYS* 1.3 63.6 + - + +
52E PHE* 3.3 0.7 + - - -
53E HIS* 2.9 26.6 + - - +
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Residues in contact with LYS 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 ALA* 2.8 48.3 + - + +
47E ALA* 3.7 10.3 - - - +
49E GLN* 1.3 75.5 - - + +
51E ILE* 1.3 55.7 + - - +
53E HIS* 3.4 5.9 + - - +
54E ALA* 2.8 30.8 + - - +
74E LEU* 3.9 3.2 - - + +
79E GLN* 3.2 39.0 - - + +
82E GLU* 2.6 42.4 + - - +
83E ILE* 4.4 9.2 - - + -
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Residues in contact with ILE 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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21E LEU* 4.0 17.5 - - + -
25E PHE* 4.6 4.3 - - + -
47E ALA 3.2 11.6 + - - +
48E HIS* 3.0 7.0 + - - +
50E LYS* 1.3 75.5 - - - +
52E PHE* 1.3 52.0 + - - +
54E ALA* 2.8 7.2 + - - +
55E MET* 2.6 55.2 + - - +
70E VAL* 4.7 4.4 - - + +
74E LEU* 4.2 7.2 - - + -
83E ILE* 3.5 38.8 - - + -
88E TYR* 4.5 4.9 - - + -
89E LEU* 3.7 29.6 - - + -
92E LEU* 4.0 16.6 - - + -
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Residues in contact with PHE 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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20E VAL* 3.9 20.2 - - + -
21E LEU* 3.8 2.5 - - + -
31E LEU* 4.3 7.6 - - + -
34E ALA* 4.0 31.6 - - + -
35E SER* 4.1 4.0 - - - -
38E LEU* 3.8 22.9 - - + -
40E PRO* 4.1 13.2 - - + -
43E PHE* 3.4 34.5 - + + -
48E HIS 2.8 18.6 + - - +
49E GLN 3.9 2.0 - - - +
51E ILE* 1.3 73.5 - - - +
53E HIS* 1.3 63.5 + - - +
55E MET* 3.3 31.7 - - + +
56E LEU* 3.0 44.3 + - + +
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Residues in contact with HIS 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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40E PRO* 3.8 27.2 - - + +
49E GLN 2.9 18.5 + - - +
50E LYS* 3.6 6.3 - - - +
52E PHE* 1.3 77.9 - - - +
54E ALA* 1.3 58.2 + - - +
56E LEU* 2.8 26.6 + - + +
57E ARG* 2.8 63.5 + - - +
79E GLN* 5.9 1.4 + - - -
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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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50E LYS 2.8 13.9 + - - +
51E ILE 2.8 12.1 + - - +
53E HIS* 1.3 73.8 + - - +
55E MET* 1.3 62.1 + - - +
57E ARG* 3.1 6.7 + - - +
58E VAL* 3.0 28.6 + - - +
70E VAL* 4.5 4.0 - - + -
73E GLU* 3.9 21.0 - - + +
74E LEU* 3.6 29.6 - - + +
77E SER* 5.9 1.6 - - - +
79E GLN* 5.9 0.7 - - - +
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Residues in contact with MET 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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21E LEU* 3.5 20.9 - - + +
24E VAL* 3.4 49.1 - - + -
25E PHE* 4.6 10.1 - - - -
31E LEU* 4.3 8.1 - - + -
51E ILE* 2.6 29.6 + - + +
52E PHE* 3.3 39.9 - - + +
54E ALA* 1.3 74.4 - - - +
56E LEU* 1.3 60.6 + - - +
58E VAL* 3.3 4.7 + - - +
59E ALA* 3.2 17.2 + - - +
65E VAL* 3.6 23.4 - - + +
70E VAL* 4.4 10.9 - - + +
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Residues in contact with LEU 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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31E LEU* 4.7 11.9 - - + -
35E SER* 3.7 26.9 - - - +
38E LEU 5.1 1.6 - - - +
39E ILE* 5.4 0.4 - - + -
40E PRO* 4.2 17.7 - - + -
52E PHE* 3.0 44.1 + - + +
53E HIS* 2.8 13.9 + - + +
55E MET* 1.3 69.5 - - - +
57E ARG* 1.3 62.4 + - - +
58E VAL 3.0 1.8 - - - -
59E ALA* 2.9 24.0 + - + +
60E ASP* 3.0 24.1 + - - +
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Residues in contact with ARG 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 HIS* 2.8 53.3 + - - +
54E ALA* 3.1 11.4 + - - +
56E LEU* 1.3 76.7 - - - +
58E VAL* 1.3 61.2 + - - +
60E ASP* 3.7 16.5 + - + +
61E ARG* 3.7 19.9 + - - +
73E GLU* 4.0 21.3 + - - +
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Residues in contact with VAL 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 3.0 17.3 + - - +
55E MET 3.5 8.7 - - - +
57E ARG* 1.3 75.3 - - - +
59E ALA* 1.3 65.5 + - - +
60E ASP 3.0 2.8 + - - -
61E ARG* 3.2 19.0 + - - +
62E GLY* 3.2 12.6 - - - +
63E GLU* 3.7 13.9 - - + +
64E PRO 3.3 30.1 - - - +
65E VAL* 4.1 6.1 - - + -
69E THR* 3.8 22.0 - - + +
70E VAL* 4.6 3.6 - - + -
73E GLU* 3.6 30.7 - - + +
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Residues in contact with ALA 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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31E LEU* 3.7 29.4 - - + -
55E MET 3.2 5.2 + - - +
56E LEU* 2.9 15.2 + - + +
58E VAL* 1.3 77.0 - - - +
60E ASP* 1.3 58.4 + - - +
61E ARG 2.8 9.6 + - - -
62E GLY 2.9 16.7 - - - +
65E VAL* 4.0 7.6 - - + -
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Residues in contact with ASP 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 LEU* 3.0 25.0 + - - +
57E ARG* 3.9 12.2 - - + +
58E VAL 3.0 2.0 - - - -
59E ALA* 1.3 76.6 - - - +
61E ARG* 1.3 64.0 + - - +
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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