Contacts of the helix formed by residues 15 - 25 (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 GLU 15 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16E ALA* 1.3 67.8 + - - +
17E GLU* 3.2 11.6 - - - +
18E GLN* 3.6 23.4 + - - +
19E ALA 3.3 14.9 + - - -
68F VAL* 3.3 32.5 - - + +
71F THR* 3.4 22.9 + - - +
80F LEU* 4.2 10.4 - - - +
86F VAL* 3.3 36.6 - - - +
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Residues in contact with ALA 16 (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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15E GLU* 1.3 76.4 - - - +
17E GLU* 1.3 69.0 + - - +
19E ALA* 3.1 13.1 + - - +
20E VAL* 3.1 16.3 + - - +
105E TYR* 4.1 7.6 - - + +
108E ILE* 3.5 35.9 - - + -
109E VAL* 3.9 11.9 - - + -
68F VAL* 3.5 17.8 - - + +
72F ALA* 5.7 1.8 - - + -
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Residues in contact with GLU 17 (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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15E GLU 3.8 6.7 - - - +
16E ALA* 1.3 81.8 - - - +
18E GLN* 1.3 65.5 + - - +
20E VAL* 3.2 10.1 + - - +
21E LEU* 3.4 14.7 + - - +
42E ASP 4.4 0.2 - - - +
43E PHE* 3.4 24.8 - - + -
44E TYR* 2.5 38.1 + - - +
45E ARG* 3.4 17.4 + - - +
48E HIS* 3.0 31.6 + - + +
109E VAL* 3.7 22.2 - - + +
116E ARG* 5.3 0.7 + - - -
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Residues in contact with GLN 18 (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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15E GLU* 3.6 23.1 + - - +
16E ALA 3.3 0.4 - - - -
17E GLU* 1.3 80.2 - - + +
19E ALA* 1.3 64.3 + - - +
21E LEU* 3.3 2.4 + - - +
22E GLY* 2.9 22.5 + - - -
45E ARG* 5.0 5.5 - - - +
48E HIS* 3.9 7.2 - - + -
88E TYR* 3.3 32.8 + - - +
91E GLU* 5.2 4.0 + - - -
92E LEU* 3.6 27.7 - - + +
96E VAL* 4.7 4.3 - - + +
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Residues in contact with ALA 19 (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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15E GLU 3.3 11.1 + - - +
16E ALA 3.1 10.7 + - - +
18E GLN* 1.3 77.9 - - - +
20E VAL* 1.3 63.1 + - - +
22E GLY* 3.4 0.5 + - - -
23E ALA* 2.9 26.6 + - - +
96E VAL* 3.8 22.8 - - + +
105E TYR* 3.6 42.0 - - + -
68F VAL* 4.5 2.9 - - + -
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Residues in contact with VAL 20 (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 ALA 3.1 8.5 + - - +
17E GLU 3.2 6.0 + - - +
19E ALA* 1.3 78.8 - - - +
21E LEU* 1.3 65.8 + - - +
23E ALA* 3.0 13.0 + - - +
24E VAL* 3.1 14.7 + - + +
34E ALA* 3.9 17.0 - - + -
38E LEU* 4.1 6.3 - - + -
43E PHE* 4.1 11.0 - - + -
52E PHE* 3.9 27.1 - - + -
102E VAL* 3.7 13.8 - - + +
105E TYR* 3.8 8.7 - - + +
106E ALA* 3.5 33.0 - - + +
109E VAL* 4.8 2.9 - - + -
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Residues in contact with LEU 21 (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 3.4 9.2 + - - +
18E GLN 3.3 4.8 + - - +
20E VAL* 1.3 74.5 - - - +
22E GLY* 1.3 64.9 + - - +
24E VAL* 3.0 14.2 + - - +
25E PHE* 3.2 17.0 + - + -
43E PHE* 3.9 9.4 - - + -
48E HIS* 3.6 44.2 - - + +
51E ILE* 4.0 17.9 - - + -
52E PHE* 3.8 19.3 - - + +
55E MET* 3.5 29.7 - - + +
92E LEU* 3.8 27.6 - - + -
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Residues in contact with GLY 22 (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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18E GLN 2.9 18.6 + - - -
19E ALA 3.8 1.1 - - - -
21E LEU* 1.3 71.9 - - - +
23E ALA* 1.3 61.2 + - - +
25E PHE* 3.1 17.5 + - - +
26E LEU* 3.3 13.5 + - - +
92E LEU* 3.8 32.1 - - - +
93E ALA* 4.3 3.6 - - - -
96E VAL* 4.5 10.1 - - - -
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Residues in contact with ALA 23 (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 ALA 2.9 19.2 + - - +
20E VAL* 3.4 5.2 - - - +
22E GLY* 1.3 72.1 - - - +
24E VAL* 1.3 65.0 + - - +
26E LEU* 3.1 9.7 + - - +
27E ASP 3.0 20.1 + - - -
30E ALA* 3.3 9.5 - - + +
96E VAL* 4.3 5.4 - - + +
98E THR 4.3 4.9 - - - +
99E ALA* 3.8 14.8 - - + +
102E VAL* 3.6 30.5 - - + +
105E TYR* 6.1 0.7 - - + -
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Residues in contact with VAL 24 (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* 3.1 14.9 + - + +
21E LEU 3.0 9.4 + - - +
23E ALA* 1.3 74.2 - - - +
25E PHE* 1.3 56.9 + - + +
26E LEU 2.7 15.2 + - - -
28E PRO* 3.0 31.9 - - + +
30E ALA* 4.0 7.4 - - + +
31E LEU* 3.9 36.1 - - + +
34E ALA* 4.8 6.3 - - + -
55E MET* 3.4 48.0 - - + -
65E VAL* 4.4 12.6 - - + +
102E VAL* 5.5 0.2 - - + -
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Residues in contact with PHE 25 (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 3.2 19.9 + - - -
22E GLY* 3.1 7.4 + - - +
24E VAL* 1.3 76.8 - - + +
26E LEU* 1.3 62.4 + - - +
28E PRO* 5.2 1.6 - - - -
51E ILE* 4.6 7.9 - - + -
55E MET* 4.6 5.8 - - - -
66E ASP* 4.0 9.2 - - - +
67E LEU* 3.6 44.1 + - + +
70E VAL* 4.0 26.5 - - + -
89E LEU* 3.4 51.4 - - + -
92E LEU* 4.1 11.9 - - + -
93E ALA* 4.1 20.6 - - + -
588I ILE* 4.5 13.9 - - + +
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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