Contacts of the helix formed by residues 21 - 32 (chain G) 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 PHE 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8G ASP* 3.4 23.3 + - + +
15G SER* 3.2 26.7 + - - +
17G ASP* 4.0 11.4 - - - -
19G ARG* 3.4 32.1 - - + -
20G VAL* 1.3 70.1 - - - +
22G GLN* 1.3 62.3 + - - +
23G VAL 3.3 0.2 - - - -
24G GLU* 3.1 23.9 + - - +
25G TYR* 3.1 53.5 + + + -
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Residues in contact with GLN 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F THR* 4.7 4.7 - - + -
12F VAL* 3.8 8.5 - - - +
13F TRP* 2.4 70.9 + - - +
8G ASP 4.3 3.6 + - - -
9G LEU* 2.5 32.4 - - - +
10G SER* 4.6 1.1 - - - +
11G ALA* 4.1 17.3 - - + +
20G VAL* 3.3 14.0 - - + +
21G PHE* 1.3 75.9 - - - +
23G VAL* 1.3 62.5 + - - +
25G TYR* 3.2 7.1 + - - -
26G ALA* 3.1 20.4 + - - +
130G PRO* 3.8 21.8 - - + -
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Residues in contact with VAL 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A MET* 6.2 2.7 - - + -
132A ARG* 5.5 2.2 - - - +
11G ALA* 5.7 0.4 - - + -
20G VAL* 3.5 29.8 + - + +
21G PHE 3.3 0.4 - - - -
22G GLN* 1.3 75.5 - - + +
24G GLU* 1.3 59.5 + - + +
26G ALA* 3.5 4.0 + - - +
27G MET* 3.0 34.7 + - + +
123G THR* 4.1 38.8 - - + +
130G PRO* 4.1 18.4 - - + -
153G PRO* 5.1 1.9 - - + +
154G SER* 4.5 20.2 - - - +
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Residues in contact with GLU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ARG* 3.5 27.5 + - + -
20G VAL 3.8 10.5 - - - +
21G PHE* 3.1 45.8 + - - +
22G GLN 3.2 0.2 - - - -
23G VAL* 1.3 76.0 - - + +
25G TYR* 1.4 61.2 + - + +
27G MET* 3.2 16.5 + - - +
28G LYS* 3.0 29.6 + - - +
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Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F VAL* 6.0 0.2 - - + -
13F TRP* 3.2 42.1 - - + -
14F SER 3.5 15.8 - - - +
15F PRO* 3.2 49.5 - - + +
17F GLY* 4.7 2.4 - - - +
8G ASP 3.9 18.9 + - - -
9G LEU* 5.0 7.2 - - + -
21G PHE* 3.1 41.5 + + + -
22G GLN* 3.2 12.1 + - - +
24G GLU* 1.4 77.6 - - + +
26G ALA* 1.3 61.0 + - - +
28G LYS* 3.5 22.3 + - - +
29G ALA 3.8 2.6 + - - -
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F TRP* 3.6 32.5 - - + +
22G GLN 3.1 7.3 + - - +
23G VAL 3.5 8.3 - - - +
25G TYR* 1.3 74.5 - - - +
27G MET* 1.3 61.1 + - - +
28G LYS 3.3 0.4 - - - -
29G ALA* 3.4 9.2 - - - +
130G PRO* 3.6 16.2 - - + -
131G PHE 3.2 21.5 - - - +
132G GLY* 3.4 22.7 - - - +
153G PRO* 5.3 0.9 - - + -
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Residues in contact with MET 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G VAL* 3.0 21.8 + - + +
24G GLU* 3.2 18.8 + - - +
26G ALA* 1.3 72.9 - - - +
28G LYS* 1.3 65.0 + - - +
30G VAL* 3.1 21.9 - - + +
31G GLU* 3.4 10.4 - - + +
152G ASP* 3.9 12.8 - - + +
153G PRO* 3.4 32.5 - - + -
154G SER* 3.4 34.3 - - - +
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Residues in contact with LYS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F PRO 2.9 28.0 - - - +
16F GLN 3.8 15.9 - - - +
17F GLY* 4.6 4.7 - - - -
24G GLU 3.0 11.1 + - - +
25G TYR* 3.5 22.6 - - - +
26G ALA 3.3 0.6 - - - -
27G MET* 1.3 75.2 - - - +
29G ALA* 1.3 59.9 + - - +
31G GLU* 2.9 29.9 + - + +
32G ASN* 3.3 23.7 - - - +
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Residues in contact with ALA 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F TRP* 3.7 26.9 - - + -
18F ARG* 4.6 9.7 + - + +
25G TYR 3.8 2.2 + - - -
26G ALA 3.4 15.4 + - - +
27G MET 3.2 0.2 - - - -
28G LYS* 1.3 80.0 - - - +
30G VAL* 1.4 58.9 + - - +
32G ASN* 3.5 24.5 + - - +
33G SER* 3.6 5.2 + - - -
79G GLY* 4.0 6.2 - - - -
80G LEU* 4.4 13.9 + - + +
132G GLY* 3.8 9.6 - - - +
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Residues in contact with VAL 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G MET* 3.1 22.6 + - + +
29G ALA* 1.4 74.2 - - - +
31G GLU* 1.3 68.2 + - - +
32G ASN 3.1 6.2 + - - -
33G SER 3.5 5.3 - - - +
78G ALA* 3.5 20.2 - - + +
79G GLY* 3.4 24.7 - - - +
132G GLY 3.5 17.6 + - - +
133G CYS 4.7 0.7 - - - +
134G SER* 4.1 23.8 - - - +
152G ASP* 6.0 0.7 - - - +
153G PRO* 5.0 4.5 - - + -
165G ILE* 4.6 3.1 - - + -
166G GLY* 3.3 24.6 - - - +
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Residues in contact with GLU 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G MET* 3.4 18.2 - - + +
28G LYS* 2.9 20.3 + - + +
30G VAL* 1.3 89.5 - - - +
32G ASN* 1.4 60.6 + - - +
165G ILE* 5.9 1.0 - - - +
166G GLY 3.8 10.1 + - - +
167G LYS* 3.5 21.0 - - - +
169G ARG* 3.0 41.1 + - - -
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLY* 5.3 6.3 - - - -
18F ARG* 3.2 41.3 - - - +
28G LYS* 3.3 29.2 + - - +
29G ALA* 3.6 11.0 - - - +
30G VAL 3.1 0.4 - - - -
31G GLU* 1.4 80.2 - - - +
33G SER* 1.4 67.0 + - - +
34G SER 3.8 0.2 + - - -
167G LYS* 3.4 26.9 + - - +
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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