Contacts of the helix formed by residues 20 - 31 (chain F) in PDB entry 5A0Q
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 HIS 20 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F ASP* 3.4 36.0 + - + +
9F ASP 5.3 0.4 + - - -
12F VAL 4.7 1.4 + - - -
14F SER* 3.2 31.2 + - - -
16F GLN* 5.7 6.4 - - + +
18F ARG 3.4 5.3 + - - -
19F ILE* 1.4 73.9 - - - +
21F GLN* 1.3 60.4 + - - +
22F ILE 3.3 0.2 - - - -
23F GLU* 3.1 27.7 + - - +
24F TYR* 3.0 56.3 + - + -
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Residues in contact with GLN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ASN 4.3 1.0 - - - +
14E THR* 3.5 14.7 - - - +
15E PHE* 2.9 43.4 + - + +
7F ASP 3.5 20.4 + - - -
8F ASN* 3.8 13.6 + - - +
9F ASP 3.9 4.5 - - - +
10F VAL* 3.8 37.2 - - + +
19F ILE* 3.4 3.0 - - + +
20F HIS* 1.3 74.6 - - - +
22F ILE* 1.3 58.6 + - - +
24F TYR* 3.4 17.5 + - - -
25F ALA* 2.9 27.2 + - - +
127F PRO* 4.2 21.7 - - + +
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Residues in contact with ILE 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 5.6 0.2 - - + -
19F ILE* 3.9 41.7 - - + +
20F HIS 3.3 0.4 - - - -
21F GLN* 1.3 74.8 - - - +
23F GLU* 1.4 62.1 + - + +
25F ALA* 3.2 10.4 + - - +
26F MET* 3.2 39.9 + - + +
120F THR* 3.7 36.8 - - + -
127F PRO* 4.4 8.7 - - + -
149F PRO 4.5 3.1 - - - +
150F SER* 3.9 29.2 - - - +
80G LEU* 6.0 5.6 - - + -
129G ARG* 5.1 2.2 - - - +
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Residues in contact with GLU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG* 3.9 24.1 + - + +
19F ILE 3.5 9.0 - - - +
20F HIS* 3.1 40.7 + - - +
22F ILE* 1.4 77.1 - - + +
24F TYR* 1.3 68.7 + - + +
26F MET* 3.5 30.8 + - + +
27F GLU* 3.7 13.2 - - - +
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Residues in contact with TYR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 3.3 28.7 - - + +
16E SER 3.5 14.4 - - - +
17E PRO* 3.6 48.4 - - + +
19E GLY* 3.6 9.4 - - - +
7F ASP 5.0 1.6 - - - -
8F ASN* 5.5 3.8 - - - -
20F HIS* 3.0 47.6 + + + +
21F GLN* 3.7 14.4 - - - +
23F GLU* 1.3 86.2 - - + +
25F ALA* 1.3 64.4 + - - +
26F MET 3.2 0.7 - - - -
27F GLU* 3.2 11.7 + - + +
28F ALA* 3.2 16.3 + - - +
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Residues in contact with ALA 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 3.7 24.4 - - + -
21F GLN 2.9 14.9 + - - +
22F ILE* 3.2 15.9 - - - +
24F TYR* 1.3 75.4 - - - +
26F MET* 1.4 60.5 + - - -
28F ALA* 3.3 12.3 + - - +
29F VAL* 3.5 0.9 - - - +
127F PRO* 4.3 5.4 - - + -
129F GLY* 3.2 26.0 - - - +
149F PRO* 3.5 19.9 - - + +
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Residues in contact with MET 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ILE* 3.2 36.8 + - + +
23F GLU* 3.5 22.9 - - + +
24F TYR 3.2 0.4 - - - -
25F ALA* 1.4 75.1 - - - +
27F GLU* 1.3 67.3 + - - +
28F ALA 3.2 0.2 - - - -
29F VAL* 3.3 17.5 - - - +
30F LYS* 3.0 25.2 + - - +
148F CYS* 5.1 4.9 - - + -
149F PRO* 3.7 29.2 - - - -
150F SER* 4.7 10.3 - - - +
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E PRO 4.3 13.2 - - - +
18E GLU* 4.6 2.5 - - - -
19E GLY* 3.8 16.6 - - - +
23F GLU 3.7 13.5 - - - +
24F TYR* 3.2 12.2 + - + +
26F MET* 1.3 84.4 - - - +
28F ALA* 1.3 64.2 + - - +
29F VAL 3.1 2.0 - - - -
30F LYS* 3.2 30.3 + - + +
31F GLN* 3.2 20.3 + - - +
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Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E PHE* 4.8 5.6 - - + -
19E GLY* 3.8 12.3 - - - +
20E ARG* 4.8 5.6 - - + +
24F TYR 3.2 9.2 + - - +
25F ALA* 3.3 18.4 - - - +
26F MET 3.2 0.2 - - - -
27F GLU* 1.3 78.2 - - - +
29F VAL* 1.4 60.2 + - - +
30F LYS 3.5 0.5 + - - -
31F GLN* 3.8 17.5 + - - +
32F GLY 4.4 0.3 + - - -
76F GLY* 3.2 16.2 - - - -
77F LEU* 3.9 18.0 + - + -
129F GLY* 4.0 12.6 - - - +
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Residues in contact with VAL 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ALA 3.5 5.6 - - - +
26F MET* 3.3 15.7 - - - +
28F ALA* 1.4 76.6 - - - +
30F LYS* 1.3 66.7 + - + +
31F GLN 3.3 0.2 - - - -
32F GLY 3.4 14.4 + - - +
75F ALA* 3.8 24.2 - - + +
76F GLY* 3.4 13.6 + - - -
129F GLY 3.2 20.2 - - - +
131F GLY* 3.8 15.3 - - - +
149F PRO* 3.6 17.3 - - + -
161F ILE* 4.8 4.9 - - + -
162F GLY* 3.9 15.4 - - - +
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F MET* 3.0 29.9 + - - +
27F GLU* 3.2 32.3 + - - +
29F VAL* 1.3 85.1 - - + +
31F GLN* 1.3 68.6 + - - +
32F GLY 3.3 6.8 - - - +
162F GLY 4.0 17.0 - - - +
163F ALA* 3.5 20.9 - - - +
164F ARG 5.9 0.4 - - - +
166F GLN* 5.3 10.1 - - - +
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Residues in contact with GLN 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E GLU 4.0 11.2 + - - +
20E ARG* 3.3 60.6 + - + +
27F GLU* 3.2 25.9 + - - +
28F ALA* 3.8 7.4 + - - +
29F VAL 3.3 0.8 - - - -
30F LYS* 1.3 82.6 - - - +
32F GLY* 1.4 63.4 + - - +
33F SER* 3.8 1.6 + - - -
76F GLY 6.2 0.2 - - - -
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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