Contacts of the helix formed by residues 19 - 28 (chain A) in PDB entry 4HFX
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 THR 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG 3.9 1.7 + - - +
18A CYS* 1.3 76.8 - - - +
20A PRO* 1.3 74.9 - - + +
21A ASP* 2.7 20.1 + - - -
22A GLN* 3.2 25.5 + - - +
23A LEU* 3.0 17.5 + - - +
44A HIS* 4.1 1.3 - - - -
20D PRO* 4.7 13.7 - - + -
21D ASP* 3.2 20.1 - - + +
64D TYR* 4.5 8.5 - - - +
68D GLN* 4.2 17.7 - - - +
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Residues in contact with PRO 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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19A THR* 1.3 88.2 - - + +
21A ASP* 1.3 51.3 + - - +
23A LEU* 3.1 5.6 + - + +
24A TYR* 2.7 34.2 + - - +
41A TRP* 3.5 28.3 - - + -
44A HIS* 4.0 21.8 - - + +
64A TYR* 3.6 35.4 - - + +
68A GLN* 4.9 4.0 - - + +
19D THR* 4.9 12.8 - - + +
21D ASP* 3.9 8.3 - - - +
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Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 2.7 28.1 + - - -
20A PRO* 1.3 74.5 - - - +
22A GLN* 1.3 63.7 + - - +
24A TYR* 3.9 9.6 - - + -
25A ARG* 2.4 66.2 + - + +
21D ASP* 2.9 30.1 + - - +
25D ARG* 4.2 19.3 + - - +
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Residues in contact with GLN 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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18A CYS* 3.5 17.6 - - + +
19A THR* 3.2 38.1 + - - +
21A ASP* 1.3 83.2 + - - +
23A LEU* 1.3 58.7 + - - +
25A ARG* 3.8 21.7 + - - +
26A ILE* 2.9 36.5 + - + +
68D GLN* 2.7 35.5 + - - +
71D ARG* 4.2 7.6 - - - +
72D GLU* 3.3 30.1 + - + +
75D LEU* 4.6 9.6 - - + -
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Residues in contact with LEU 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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15A LEU* 4.3 30.5 - - + +
18A CYS* 4.1 6.9 - - + +
19A THR 3.0 12.7 + - - +
20A PRO 3.3 8.1 - - - +
22A GLN* 1.3 76.4 - - - +
24A TYR* 1.3 58.6 + - - +
26A ILE* 3.4 9.0 + - + +
27A GLU* 3.1 38.7 + - + +
37A THR 5.3 0.2 - - - +
40A LEU* 3.7 38.4 - - + -
41A TRP* 3.8 24.9 - - + +
44A HIS* 3.7 23.8 - - - +
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Residues in contact with TYR 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 PRO 2.7 20.6 + - - +
21A ASP* 3.7 10.3 - - + +
23A LEU* 1.3 70.8 - - - +
25A ARG* 1.3 71.2 + - + +
27A GLU* 3.0 12.3 + - - +
28A GLU* 3.0 37.0 + - + +
41A TRP* 4.3 5.4 - + + -
61A ARG* 3.3 31.2 - - - -
65A LEU* 3.7 35.7 - - + +
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Residues in contact with ARG 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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21A ASP* 2.4 56.4 + - + +
22A GLN* 3.8 21.1 - - - +
24A TYR* 1.3 82.3 - - + +
26A ILE* 1.3 68.2 + - + +
28A GLU* 3.7 11.8 + - - +
29A TYR* 3.8 9.9 + - - +
72D GLU* 3.4 32.1 + - - -
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Residues in contact with ILE 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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15A LEU* 4.4 26.7 - - + -
18A CYS* 5.4 3.1 - - - -
22A GLN* 2.9 25.0 + - + +
23A LEU* 3.4 13.5 - - + +
24A TYR 3.1 0.8 - - - -
25A ARG* 1.3 82.3 - - + +
27A GLU* 1.3 64.4 + - + +
29A TYR* 3.2 24.0 + - - +
75D LEU* 5.1 21.5 - - + +
76D ARG* 6.0 0.9 - - - +
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Residues in contact with GLU 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 LEU* 3.1 28.4 + - + +
24A TYR* 3.0 7.3 + - - +
26A ILE* 1.3 73.5 - - + +
28A GLU* 1.3 61.7 + - - +
29A TYR 3.0 15.9 - - - +
37A THR* 5.2 10.0 + - - +
41A TRP* 3.3 30.0 + - - -
61A ARG* 3.0 38.8 + - - +
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Residues in contact with GLU 28 (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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24A TYR* 3.0 27.2 + - + +
25A ARG* 4.1 9.0 - - - +
26A ILE 3.4 0.4 - - - -
27A GLU* 1.3 75.5 - - - +
29A TYR* 1.3 50.0 + - - +
61A ARG* 5.1 2.0 - - - +
76C ARG* 2.3 31.4 + - - -
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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