Contacts of the helix formed by residues 18 - 25 (chain D) in PDB entry 3G03
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLN* 3.4 15.7 - - - +
17D LEU* 1.3 77.9 - - - +
19D PHE* 1.3 69.6 + - - +
20D GLU* 3.5 17.1 + - - +
21D HIS* 2.7 30.7 + - - +
22D TYR* 3.1 12.4 + - - -
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLY* 3.6 9.4 - - - -
61C ILE* 3.5 31.0 - - + -
62C MET* 3.1 35.2 - - + -
67C TYR* 3.8 30.5 - + + -
72C GLN* 3.0 40.6 + - - +
75C VAL* 4.4 2.7 - - + -
93C VAL* 4.0 13.0 - - + -
18D THR* 1.3 70.6 - - - +
20D GLU* 1.3 70.9 + - + +
22D TYR* 3.0 4.9 + - - +
23D TRP* 2.8 65.8 + + + +
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Residues in contact with GLU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B THR* 4.7 15.0 - - - +
59C GLN* 6.0 0.4 - - - +
62C MET* 3.6 32.6 - - - +
67C TYR* 5.5 2.4 + - - -
72C GLN* 4.8 1.0 - - - +
18D THR* 3.1 19.4 + - - +
19D PHE* 1.3 81.7 + - + +
21D HIS* 1.3 64.5 + - - +
23D TRP* 4.0 3.8 - - - +
24D ALA* 2.9 27.3 + - - +
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Residues in contact with HIS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 3.4 35.6 - - + +
18D THR* 2.7 32.1 + - - +
20D GLU* 1.3 74.5 - - - +
22D TYR* 1.3 71.1 + + - +
24D ALA* 3.5 11.1 + - - +
25D GLN* 2.7 44.3 + - - +
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C GLN 4.0 4.9 - - - -
73C HIS* 3.6 46.5 - + + -
93C VAL* 3.4 26.3 - - + +
94C LYS* 3.5 28.9 - - + -
96C HIS* 4.7 2.6 + - - -
17D LEU* 3.5 40.4 - - + +
18D THR 3.1 16.8 + - - -
19D PHE 3.0 5.4 + - - +
21D HIS* 1.3 88.9 - + - +
23D TRP* 1.3 62.9 + - - +
25D GLN* 3.1 32.6 + - - +
26D LEU 4.0 1.6 + - - -
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Residues in contact with TRP 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 2.8 36.4 + - + +
55C PHE* 5.3 2.9 - - - -
57C LEU* 3.6 27.6 - - + -
58C GLY* 3.3 26.4 - - - -
61C ILE* 3.6 19.3 - - + -
91C PHE* 4.9 2.7 - + - -
93C VAL* 3.8 17.0 - - + +
99C ILE* 4.4 13.0 - - + -
19D PHE* 2.8 46.2 + + + +
20D GLU* 4.0 4.0 - - - +
22D TYR* 1.3 76.6 - - - +
24D ALA* 1.3 61.1 + - - +
26D LEU* 2.9 56.7 + - + +
27D THR* 4.3 2.8 + - - -
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA* 4.8 18.2 - - + -
20D GLU 2.9 18.2 + - - +
21D HIS* 3.7 7.0 - - - +
22D TYR 3.2 0.2 - - - -
23D TRP* 1.3 78.7 - - - +
25D GLN* 1.3 61.5 + - + +
26D LEU 3.1 1.9 + - - -
27D THR* 3.3 23.3 + - - +
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Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 5.7 2.1 - - - +
96C HIS* 3.2 29.1 + - + -
21D HIS* 2.7 45.1 + - - +
22D TYR* 3.1 26.4 + - - +
23D TRP 3.1 1.4 - - - -
24D ALA* 1.3 77.1 - - + +
26D LEU* 1.3 59.5 + - - +
27D THR 3.2 5.8 - - - +
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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