Contacts of the helix formed by residues 18 - 27 (chain A) in PDB entry 6A08
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 PRO 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A VAL 3.6 5.4 - - - +
17A LEU* 1.3 93.1 - - + +
19A GLY* 1.3 65.2 + - - +
20A GLU* 3.3 26.5 - - - +
21A ILE* 3.1 24.8 + - + +
22A PHE* 2.9 19.2 + - - +
83A LEU 5.7 0.2 - - - +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU 3.5 2.9 + - - -
18A PRO* 1.3 72.6 - - - +
20A GLU* 1.3 59.5 + - - +
22A PHE* 3.3 8.2 + - - +
23A ASP* 2.9 36.1 + - - -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO* 3.3 23.9 - - - +
19A GLY* 1.3 78.0 + - - +
21A ILE* 1.3 63.3 + - + +
23A ASP* 3.3 3.3 + - - +
24A PHE* 2.9 27.0 + - - +
166A ASP* 4.7 0.7 - - - +
169A ASN* 3.8 30.2 + - + +
171A PHE* 3.7 31.2 - - + -
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.2 8.5 - - + -
18A PRO* 3.1 30.8 + - + +
20A GLU* 1.3 82.9 - - + +
22A PHE* 1.3 66.0 + - - +
24A PHE* 3.2 8.5 + - + +
25A LEU* 3.1 21.5 + - - +
83A LEU* 3.6 44.0 - - + +
84A PHE* 3.8 23.5 - - + -
171A PHE* 3.9 19.5 - - + -
174A PRO* 5.0 8.7 - - + -
176A TRP* 5.2 8.3 - - + -
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Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 3.9 33.4 - - + -
13A ALA* 4.3 2.9 - - + -
14A ARG* 3.9 52.9 - - + +
17A LEU* 4.2 26.4 - - + +
18A PRO 2.9 12.6 + - - +
19A GLY* 3.3 10.1 + - - +
21A ILE* 1.3 76.0 - - - +
23A ASP* 1.3 64.9 + - - +
25A LEU* 3.3 6.8 + - + +
26A ALA* 2.8 44.1 + - + +
165A ARG* 5.0 3.6 - - - -
311A TRP* 4.7 10.3 - + - -
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLY 2.9 16.6 + - - +
20A GLU 3.5 3.4 - - - +
21A ILE 3.1 0.2 - - - -
22A PHE* 1.3 79.7 - - - +
24A PHE* 1.3 59.9 + - - +
27A GLY* 2.9 30.0 + - - -
165A ARG* 3.1 43.0 + - + +
166A ASP* 4.2 4.6 - - - +
169A ASN* 3.0 33.6 + - - +
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLU 2.9 13.1 + - - +
21A ILE* 3.2 8.3 + - + +
23A ASP* 1.3 76.3 - - - +
25A LEU* 1.3 58.6 + - - +
27A GLY* 4.9 0.2 - - - -
79A ALA 4.7 5.6 - - - -
80A TYR* 5.0 6.3 - + + -
83A LEU* 3.6 32.5 - - + -
84A PHE* 4.4 9.0 - + - -
163A ARG* 3.8 16.1 - - - -
166A ASP* 3.3 26.7 + - - +
171A PHE* 3.6 26.9 - + + -
173A LEU* 6.1 0.4 - - + -
255A ARG* 2.8 47.6 + - - -
402A FMN 3.8 18.4 - + + -
404A 173 3.9 32.1 - + - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.4 13.0 - - + -
21A ILE 3.1 13.0 + - - +
22A PHE* 3.6 11.2 - - + +
24A PHE* 1.3 79.3 - - - +
26A ALA* 1.3 59.3 + - - +
84A PHE* 3.9 24.9 - - + -
255A ARG* 3.5 1.2 + - - -
307A ARG* 2.8 40.9 + - + -
310A MET* 3.7 38.8 - - + -
311A TRP* 3.7 30.1 - - + +
402A FMN 3.3 27.0 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 5.4 3.8 - - - +
22A PHE* 2.8 40.4 + - + +
25A LEU* 1.3 76.8 - - + +
27A GLY* 1.3 64.5 + - - +
35A LEU* 3.5 17.0 - - - +
165A ARG* 3.8 21.2 + - - +
307A ARG* 3.4 16.5 + - - +
311A TRP* 6.0 2.5 - - - +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP 2.9 18.6 + - - -
24A PHE 4.2 0.6 + - - -
25A LEU 3.4 1.4 - - - -
26A ALA* 1.3 78.1 - - - +
28A GLY* 1.3 60.7 + - - -
32A GLU* 3.4 12.1 - - - -
35A LEU* 4.2 1.3 - - - -
163A ARG* 5.4 4.3 - - - -
165A ARG* 3.5 11.2 - - - -
255A ARG* 2.9 15.6 + - - +
307A ARG* 2.9 21.8 + - - -
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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