Contacts of the helix formed by residues 28 - 39 (chain R) in PDB entry 1G4Y
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 28 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26R THR* 4.0 3.5 + - - -
27R ILE* 1.3 77.6 - - - +
29R THR* 1.3 73.5 + - - +
30R LYS* 3.4 14.8 + - + +
31R GLU* 3.1 41.4 + - + +
32R LEU* 3.0 23.2 + - - +
52R ILE* 4.0 4.0 - - - -
61R GLY 5.5 0.5 + - - -
62R THR* 4.3 16.5 - - - +
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Residues in contact with THR 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R THR* 1.3 81.5 + - - +
30R LYS* 1.3 59.2 + - - +
32R LEU* 3.6 5.4 - - - +
33R GLY* 2.8 28.2 + - - -
45R GLU* 4.2 14.2 + - - -
48R LEU* 3.7 19.4 - - - +
49R GLN* 3.9 37.2 - - + +
52R ILE* 3.5 24.3 - - + +
61R GLY 4.9 4.6 + - - +
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Residues in contact with LYS 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28R THR* 3.1 12.8 + - + +
29R THR* 1.3 84.4 + - - +
31R GLU* 1.3 63.2 + - + +
33R GLY* 3.4 1.6 + - - -
34R THR* 3.1 29.7 + - - +
37R ARG* 4.9 2.2 + - - +
48R LEU* 5.7 0.4 - - - -
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Residues in contact with GLU 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19R PHE 3.5 16.4 - - - +
20R ASP* 3.8 1.4 - - - +
21R LYS* 3.3 23.6 + - + +
22R ASP* 3.0 29.1 + - - +
26R THR 3.0 9.7 - - - +
27R ILE* 3.6 4.0 - - + -
28R THR* 3.1 28.8 + - + +
30R LYS* 1.3 76.3 - - + +
32R LEU* 1.3 65.4 + - - +
34R THR* 3.1 6.9 + - - -
35R VAL* 3.1 25.5 + - - +
1001R CA 2.3 30.7 - - - -
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Residues in contact with LEU 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.4 42.2 - - + -
19R PHE* 4.6 8.1 - - + -
27R ILE* 4.2 13.1 - - + +
28R THR 3.0 16.3 + - - +
29R THR 3.6 3.8 - - - +
31R GLU* 1.3 76.2 - - - +
33R GLY* 1.3 58.3 + - - +
35R VAL* 3.3 4.6 + - - +
36R MET* 2.8 37.9 + - + +
48R LEU* 4.0 26.7 - - + +
51R MET* 3.5 33.9 - - + -
52R ILE* 4.3 12.8 - - + -
63R ILE* 5.4 3.4 - - + -
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Residues in contact with GLY 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29R THR 2.8 17.8 + - - -
30R LYS* 3.8 1.8 - - - -
31R GLU 3.2 0.2 - - - -
32R LEU* 1.3 76.7 - - - +
34R THR* 1.3 61.0 + - - +
36R MET* 3.9 2.0 - - - +
37R ARG* 3.0 48.2 + - - +
43R PRO* 4.8 0.7 - - - -
48R LEU* 3.8 19.9 - - - +
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Residues in contact with THR 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R LYS* 3.3 28.9 - - + +
30R LYS* 3.1 16.8 + - - +
31R GLU* 3.1 10.9 + - - -
33R GLY* 1.3 76.1 - - - +
35R VAL* 1.3 59.0 + - - +
37R ARG* 3.4 19.6 + - - +
38R SER* 3.0 26.5 + - - -
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Residues in contact with VAL 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 5.0 1.6 - - + -
483B LEU* 3.7 20.2 - - + -
18R LEU 3.4 24.5 - - - +
19R PHE* 3.6 38.6 - - + -
21R LYS* 3.6 16.6 - - - +
31R GLU 3.1 14.5 + - - +
32R LEU* 3.8 6.5 - - - +
34R THR* 1.3 74.3 - - - +
36R MET* 1.3 67.6 + - - +
38R SER* 2.6 29.8 + - - +
39R LEU* 3.2 10.6 + - + +
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Residues in contact with MET 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B GLN* 3.7 35.9 - - + +
479B THR* 4.3 11.2 - - - -
480B LEU* 3.9 22.4 - - + -
32R LEU* 2.8 37.8 + - + +
33R GLY 3.9 0.7 - - - +
35R VAL* 1.3 72.0 - - - +
37R ARG* 1.3 62.2 + - - +
39R LEU* 3.1 18.5 + - - +
41R GLN* 3.1 49.3 + - + +
43R PRO* 3.6 29.6 - - + -
48R LEU* 4.6 1.1 - - + -
51R MET* 4.2 5.6 - - + -
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Residues in contact with ARG 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R LYS* 4.9 2.6 + - - +
33R GLY* 3.0 36.2 + - - +
34R THR* 3.8 28.8 + - - +
36R MET* 1.3 70.6 - - - +
38R SER* 1.3 57.4 + - - +
39R LEU 2.9 5.6 - - - -
40R GLY* 2.8 19.1 + - - -
41R GLN 3.2 18.8 - - - +
42R ASN* 4.1 18.6 - - - +
43R PRO* 4.8 8.6 + - + +
48R LEU* 5.1 5.5 - - - +
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Residues in contact with SER 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 5.8 0.2 - - - +
21R LYS* 5.7 3.6 - - - -
34R THR* 3.0 14.0 + - - -
35R VAL* 2.6 27.2 + - - +
37R ARG* 1.3 76.0 - - - +
39R LEU* 1.3 64.9 + - - +
40R GLY 3.3 2.3 + - - -
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Residues in contact with LEU 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B THR* 3.4 33.7 - - + +
480B LEU* 5.6 1.3 - - + -
483B LEU* 4.0 41.3 - - + -
35R VAL* 3.5 15.9 - - + +
36R MET* 3.1 15.0 + - - +
37R ARG 2.9 0.8 - - - -
38R SER* 1.3 85.8 - - - +
40R GLY* 1.3 61.9 + - - +
41R GLN* 3.3 7.3 + - + +
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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