Contacts of the helix formed by residues 22 - 33 (chain S) 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 22 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13S ASN 5.6 1.9 - - - +
14S THR* 3.7 38.0 + - + +
16S SER* 3.4 37.2 - - - -
17S PRO* 4.7 5.8 - - + -
20S ARG 5.1 0.2 - - - -
21S LEU* 1.3 73.1 - - - +
23S GLN* 1.3 78.8 + - + +
24S VAL 3.2 1.6 - - - -
25S GLU* 3.0 7.8 + - + +
26S TYR* 3.0 61.3 + + + -
8T ASN* 5.4 6.3 - - - -
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Residues in contact with GLN 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R VAL* 3.9 17.2 - - + +
10R PHE* 3.0 41.6 + - + +
13S ASN 4.7 16.0 - - - +
21S LEU* 4.7 1.2 - - + +
22S PHE* 1.3 94.5 - - + +
24S VAL* 1.3 51.7 + - - +
26S TYR* 3.4 14.3 + - - +
27S ALA* 2.8 32.4 + - - +
123S PHE* 5.0 7.4 - - + -
136S PRO* 3.6 29.2 - - + +
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Residues in contact with VAL 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S LEU* 4.1 26.9 - - + +
22S PHE 3.2 0.6 - - - -
23S GLN* 1.3 77.7 - - - +
25S GLU* 1.3 63.0 + - - +
27S ALA* 3.0 8.1 + - + +
28S ILE* 2.9 30.0 + - + +
121S LEU* 3.7 26.9 - - + -
123S PHE* 4.2 12.8 - - + -
136S PRO* 4.6 3.1 - - + -
158S PRO* 4.1 7.0 - - + +
159S SER* 3.6 37.9 - - - +
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Residues in contact with GLU 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S ARG* 4.0 40.2 + - + +
21S LEU 3.1 19.5 - - - +
22S PHE* 3.0 9.4 + - + +
24S VAL* 1.3 81.9 - - + +
26S TYR* 1.3 64.3 + - + +
28S ILE* 3.4 20.8 + - - +
29S GLU* 3.1 29.1 + - - +
159S SER* 5.5 1.6 + - - -
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Residues in contact with TYR 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R PHE* 3.7 19.5 - - + -
11R SER 3.2 24.5 - - - +
12R PRO* 3.6 33.9 - - + +
14R GLY* 3.3 15.6 - - - +
22S PHE* 3.0 58.9 + + + -
23S GLN* 3.5 17.0 - - - +
25S GLU* 1.3 79.1 - - + +
27S ALA* 1.4 58.0 + - - +
29S GLU* 3.3 19.7 + - - +
30S ALA* 3.1 18.9 + - - +
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Residues in contact with ALA 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R PHE* 4.2 14.1 - - + -
23S GLN 2.8 16.4 + - - +
24S VAL* 3.0 13.9 + - + +
26S TYR* 1.4 69.5 - - - +
28S ILE* 1.3 59.1 + - - +
30S ALA* 3.0 26.8 + - - +
31S ILE* 3.3 12.6 + - - +
136S PRO* 4.6 3.6 - - + -
137S PHE 3.7 23.6 - - - +
138S GLY* 3.9 7.9 - - - +
158S PRO* 4.8 7.2 - - + -
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Residues in contact with ILE 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S VAL* 2.9 18.6 + - + +
25S GLU* 3.4 25.4 - - - +
26S TYR 3.3 0.2 - - - -
27S ALA* 1.3 73.5 - - - +
29S GLU* 1.4 63.7 + - + +
31S ILE* 3.3 18.3 + - + +
32S LYS* 3.2 35.4 + - - +
157S ASP* 5.2 5.2 - - - +
158S PRO* 3.6 31.6 - - + -
159S SER* 4.2 13.2 - - - +
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Residues in contact with GLU 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R PRO 3.1 26.2 - - - +
13R ASP* 3.2 18.9 - - - +
14R GLY* 4.6 1.9 - - - -
25S GLU* 3.1 17.2 + - - +
26S TYR* 3.4 26.6 - - - +
27S ALA 3.3 0.2 - - - -
28S ILE* 1.4 77.1 - - + +
30S ALA* 1.3 60.8 + - - +
32S LYS* 3.3 26.5 + - + +
33S LEU* 4.2 6.2 + - - +
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Residues in contact with ALA 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 4.2 10.3 - - + -
14R GLY* 3.6 22.7 - - - +
26S TYR 3.1 7.0 + - - +
27S ALA* 3.0 19.5 + - - +
29S GLU* 1.3 77.0 - - - +
31S ILE* 1.4 59.6 + - - +
33S LEU* 3.4 22.1 + - - +
34S GLY 4.0 0.3 + - - -
80S GLY* 4.2 8.1 - - - -
81S LEU* 4.4 21.5 - - + +
138S GLY* 4.6 2.9 - - - -
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Residues in contact with ILE 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ALA 3.7 4.9 - - - +
28S ILE* 3.4 18.8 - - + +
29S GLU 3.2 0.8 - - - -
30S ALA* 1.4 74.1 - - - +
32S LYS* 1.3 61.7 + - + +
34S GLY* 2.8 27.4 + - - +
79S SER* 4.3 6.3 - - - +
80S GLY* 4.0 7.9 - - - +
138S GLY 3.1 19.7 - - - +
140S ALA* 4.0 22.2 - - + +
158S PRO* 3.7 36.8 - - + -
170S ILE* 5.7 0.2 - - + -
171S GLY* 3.8 27.8 - - - +
172S SER 4.0 3.1 + - - -
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Residues in contact with LYS 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ILE* 3.2 42.7 + - - +
29S GLU* 3.5 16.2 - - + +
30S ALA 3.2 0.8 - - - -
31S ILE* 1.3 82.6 - - + +
33S LEU* 1.4 65.3 + - + +
34S GLY 3.3 0.9 - - - -
171S GLY 5.2 4.9 + - - +
172S SER* 2.9 36.2 - - - +
175S GLU* 4.5 17.9 - - - +
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Residues in contact with LEU 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R ASP 5.9 1.6 - - - +
14R GLY 6.1 1.6 - - - -
15R HIS* 3.7 32.3 - - + +
29S GLU 5.0 6.5 - - - +
30S ALA* 3.4 14.5 + - - +
31S ILE 3.1 0.6 - - - -
32S LYS* 1.4 81.7 - - + +
34S GLY* 1.3 56.4 + - - +
53S ARG* 4.4 14.9 + - - +
80S GLY 4.5 3.6 - - - +
82S ILE* 5.7 2.6 - - - +
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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