Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 3DFG
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLN* 1.3 76.9 - - - +
19A PRO* 1.3 75.5 - - + +
20A VAL* 3.7 8.2 + - - +
21A GLN* 3.0 39.2 + - - +
22A ARG* 2.9 21.8 + - - +
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Residues in contact with PRO 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 GLN 4.5 0.9 - - - +
18A THR* 1.3 88.2 - - - +
20A VAL* 1.3 58.9 + - + +
22A ARG* 3.3 3.9 + - + +
23A ALA* 2.9 31.4 + - - +
41A LEU* 3.8 5.2 - - + +
46A ILE* 3.5 49.6 - - + -
50A ALA* 4.6 7.9 - - + +
54A ALA* 3.9 19.1 - - + -
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Residues in contact with VAL 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 THR* 3.2 8.2 + - - +
19A PRO* 1.3 80.0 - - + +
21A GLN* 1.3 59.1 + - + +
23A ALA* 3.4 3.5 + - - +
24A LEU* 2.9 32.0 + - + +
54A ALA* 3.9 24.0 - - + +
57A ARG* 3.9 31.2 - - - +
58A LEU* 3.9 23.1 - - + +
61A GLU* 5.6 1.3 - - - +
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Residues in contact with GLN 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 GLN* 3.4 33.2 + - + +
18A THR* 3.0 49.2 + - - +
20A VAL* 1.3 76.9 - - + +
22A ARG* 1.3 63.0 + - - +
24A LEU* 3.4 8.9 + - - +
25A GLY* 3.0 19.6 + - - -
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Residues in contact with ARG 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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17A GLN* 3.3 46.9 + - + +
18A THR 2.9 17.0 + - - +
19A PRO 3.6 6.1 - - - +
21A GLN* 1.3 76.6 - - - +
23A ALA* 1.3 61.2 + - - +
25A GLY* 3.2 3.0 + - - -
26A LEU* 3.2 28.1 + - + +
41A LEU* 4.0 9.2 - - + -
44A ARG* 3.0 59.4 + - - +
46A ILE* 3.7 25.2 - - - +
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Residues in contact with ALA 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 PRO 2.9 17.0 + - - +
20A VAL* 3.9 0.7 - - - +
22A ARG* 1.3 75.0 - - - +
24A LEU* 1.3 65.9 + - - +
26A LEU* 3.1 14.9 + - - +
27A LEU* 3.0 24.8 + - - +
37A LEU* 4.3 13.8 - - + +
41A LEU* 4.2 17.9 - - + +
54A ALA* 5.2 2.9 - - + +
55A VAL* 5.6 0.9 - - + -
58A LEU* 3.2 24.5 - - + -
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Residues in contact with LEU 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 VAL* 2.9 21.9 + - + +
21A GLN* 3.7 7.6 - - - +
23A ALA* 1.3 76.6 - - - +
25A GLY* 1.3 62.9 + - - +
27A LEU* 3.1 4.8 + - + +
28A VAL* 2.9 34.1 + - + +
58A LEU* 3.7 13.4 - - + +
63A TRP* 3.4 62.1 - - + +
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Residues in contact with GLY 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 GLN 3.0 15.2 + - - -
22A ARG* 3.2 4.0 + - - -
24A LEU* 1.3 76.8 - - - +
26A LEU* 1.3 62.8 + - - +
28A VAL* 3.5 17.2 + - - +
29A HIS* 3.6 9.7 + - - +
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Residues in contact with LEU 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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22A ARG* 3.2 16.0 + - + +
23A ALA* 3.1 10.6 + - - +
25A GLY* 1.3 77.7 - - - +
27A LEU* 1.3 56.9 + - - +
29A HIS* 3.0 22.7 + - + +
30A ARG 3.2 2.8 + - - -
32A HIS* 3.1 36.5 - - + +
37A LEU* 3.8 22.2 - - + -
40A LYS* 3.9 35.0 - - + +
41A LEU* 5.3 7.0 - - + -
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Residues in contact with LEU 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 ALA 3.0 14.8 + - - +
24A LEU* 3.6 8.5 - - - +
26A LEU* 1.3 73.6 - - - +
28A VAL* 1.3 65.5 + - - +
29A HIS 3.3 0.2 + - - -
30A ARG* 3.3 17.7 + - - +
31A GLU* 4.4 5.9 - - - +
32A HIS* 3.7 37.2 - - + +
37A LEU* 4.2 13.0 - - + -
58A LEU* 4.0 19.1 - - + -
63A TRP* 3.8 44.6 - - + +
64A GLN* 4.0 18.2 - - + -
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Residues in contact with VAL 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 LEU* 2.9 35.4 + - + +
25A GLY* 3.6 12.1 - - - +
26A LEU 3.2 0.2 - - - -
27A LEU* 1.3 78.0 - - - +
29A HIS* 1.3 62.0 + - - +
63A TRP* 4.5 13.7 - - + -
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Residues in contact with HIS 29 (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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25A GLY 3.6 6.6 + - - +
26A LEU* 3.0 12.9 + - + +
28A VAL* 1.3 83.3 - - - +
30A ARG* 1.3 91.6 + - + +
32A HIS* 4.7 4.5 - + - -
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Residues in contact with ARG 30 (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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26A LEU 3.2 4.7 + - - +
27A LEU* 3.3 16.2 + - - -
29A HIS* 1.3 102.4 + - + +
31A GLU* 1.3 80.2 + - - +
32A HIS* 2.8 33.7 + - + -
36A GLU* 2.9 36.6 + - - -
40A LYS* 3.4 19.0 - - - +
69A PHE* 4.2 5.5 - - - -
76A ASN* 6.0 1.8 - - - -
77A ARG* 6.2 2.2 - - - -
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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