Contacts of the helix formed by residues 7 - 21 (chain E) in PDB entry 7CR3
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 7 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E THR* 1.3 76.7 + - - +
8E GLU* 1.3 57.9 + - - +
9E GLN 3.4 0.2 - - - -
10E ILE* 3.7 25.4 - - - +
11E ALA* 2.9 34.8 + - + +
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Residues in contact with GLU 8 (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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6E THR* 3.2 16.2 + - + +
7E GLU* 1.3 79.1 - - - +
9E GLN* 1.3 84.8 + - - +
11E ALA* 3.7 4.0 - - - +
12E GLU* 2.9 36.0 + - - +
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Residues in contact with GLN 9 (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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351D LEU* 3.5 32.0 - - + +
541D ARG* 5.7 4.4 - - - +
6E THR* 3.5 18.7 + - + +
8E GLU* 1.3 96.1 + - - +
10E ILE* 1.3 60.8 + - + +
12E GLU* 3.4 20.0 - - - +
13E PHE* 2.9 59.6 + - + -
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Residues in contact with ILE 10 (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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6E THR 3.2 18.8 + - - +
7E GLU* 3.6 28.3 - - - +
8E GLU 3.2 0.2 - - - -
9E GLN* 1.3 78.5 - - + +
11E ALA* 1.3 59.0 + - - +
13E PHE* 3.3 6.8 + - + +
14E LYS* 2.9 24.9 + - + +
66E PHE* 3.8 11.2 - - + -
70E LEU* 3.6 30.1 - - + -
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Residues in contact with ALA 11 (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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7E GLU* 2.9 21.2 + - + +
8E GLU* 4.0 3.8 - - - +
10E ILE* 1.3 76.3 - - - +
12E GLU* 1.3 60.8 + - - +
14E LYS* 3.2 11.8 + - + +
15E GLU* 2.9 26.7 + - - +
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Residues in contact with GLU 12 (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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535D GLY* 3.2 27.4 + - - -
538D VAL* 3.1 36.0 - - - +
541D ARG* 6.3 0.2 - - - -
8E GLU* 2.9 28.0 + - - +
9E GLN* 3.4 22.4 - - - +
11E ALA* 1.3 77.2 - - - +
13E PHE* 1.3 61.1 + - - +
15E GLU* 3.2 10.2 + - + +
16E ALA* 3.0 21.7 + - - +
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Residues in contact with PHE 13 (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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351D LEU* 6.6 0.2 - - + -
538D VAL* 3.6 30.5 - - + -
9E GLN* 2.9 49.3 + - + +
10E ILE* 3.8 6.1 - - + +
12E GLU* 1.3 72.5 - - - +
14E LYS* 1.3 60.1 + - - +
16E ALA* 4.0 4.5 - - - -
17E PHE 2.8 22.7 + - - -
66E PHE* 3.4 4.4 - - - -
69E PHE* 3.2 19.3 - + + -
70E LEU* 3.8 28.0 - - + -
73E MET* 3.6 50.9 - - + -
74E ALA* 5.1 3.1 - - + -
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Residues in contact with LYS 14 (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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10E ILE* 2.9 15.1 + - + +
11E ALA* 3.3 15.7 - - + +
12E GLU 3.2 0.2 - - - -
13E PHE* 1.3 74.5 - - - +
15E GLU* 1.3 61.8 + - - +
17E PHE* 3.1 18.2 + - + +
18E SER* 2.9 34.1 + - - +
66E PHE* 3.6 29.1 - - + -
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Residues in contact with GLU 15 (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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535D GLY* 4.3 20.1 + - - -
538D VAL* 5.4 0.2 - - - +
11E ALA 2.9 13.7 + - - +
12E GLU* 3.2 13.0 + - - +
14E LYS* 1.3 72.5 - - - +
16E ALA* 1.3 63.5 + - - +
18E SER* 3.3 7.9 + - - +
19E LEU* 2.9 39.5 + - - +
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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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538D VAL* 3.6 32.3 - - + +
539D SER* 5.2 1.8 - - - +
12E GLU 3.0 9.5 + - - +
13E PHE* 3.5 10.8 - - - +
15E GLU* 1.3 77.8 + - - +
17E PHE* 1.3 57.0 + - - +
19E LEU* 3.8 6.2 - - - +
20E PHE* 2.9 41.1 + - + -
69E PHE* 3.6 21.3 - - + -
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Residues in contact with PHE 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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13E PHE 2.8 14.3 + - - +
14E LYS* 3.1 22.6 + - + +
16E ALA* 1.3 77.3 - - - +
18E SER* 1.3 55.0 + - - +
20E PHE* 3.4 2.5 + - - -
21E ASP* 2.7 40.8 + - - +
26E GLY* 3.2 41.1 - - - -
27E THR* 3.5 7.4 - - - -
28E ILE* 3.3 34.7 - - + +
64E ILE 3.6 0.2 - - - -
65E ASP 3.4 4.9 - - - -
66E PHE* 3.3 55.4 - + + -
69E PHE* 4.0 11.4 - + + -
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Residues in contact with SER 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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14E LYS* 2.9 25.6 + - - +
15E GLU* 3.7 9.0 - - - -
17E PHE* 1.3 77.3 - - - +
19E LEU* 1.3 58.6 + - - +
21E ASP* 2.9 29.0 + - - +
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Residues in contact with LEU 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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535D GLY* 4.4 7.4 - - - +
536D LEU* 5.3 0.7 - - - +
539D SER* 3.4 28.0 - - - +
15E GLU* 2.9 32.1 + - - +
16E ALA* 3.8 6.7 - - - +
17E PHE 3.2 0.2 - - - -
18E SER* 1.3 77.9 - - - +
20E PHE* 1.3 66.3 + - + +
21E ASP 3.4 1.0 + - - +
22E LYS* 3.3 25.9 - - - -
36E VAL* 4.3 5.8 - - + +
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Residues in contact with PHE 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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539D SER* 4.3 20.0 - - - -
542D ALA* 3.7 30.3 - - + -
543D VAL* 4.2 12.6 - - + -
546D MET* 3.8 23.1 - - + -
16E ALA* 2.9 29.9 + - + +
17E PHE* 4.3 1.1 - - - -
19E LEU* 1.3 79.9 - - + +
21E ASP* 1.3 59.3 + - - +
22E LYS* 3.8 4.2 - - - +
28E ILE* 3.6 36.1 - - + -
32E GLU* 2.9 30.2 - - - +
33E LEU* 3.7 15.5 - - + -
36E VAL* 4.6 24.0 - - + -
64E ILE* 5.7 2.5 - - + -
69E PHE* 5.0 10.8 - + - -
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Residues in contact with ASP 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 PHE* 2.7 27.8 + - + +
18E SER* 2.9 27.7 + - - +
19E LEU 3.2 0.9 - - - +
20E PHE* 1.3 72.6 - - - +
22E LYS* 1.3 67.7 + - - +
24E GLY* 3.2 31.8 + - - -
25E ASP* 3.6 6.5 + - - +
26E GLY* 3.9 7.1 + - - -
27E THR 2.9 22.7 + - - +
28E ILE* 3.6 2.9 - - + -
32E GLU* 2.8 17.2 - - - +
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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