Contacts of the helix formed by residues 12 - 20 (chain A) in PDB entry 1DCT
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 GLY 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA 3.9 0.4 - - - -
11A GLY* 1.3 74.4 - - - +
13A LEU* 1.3 57.4 + - - +
15A LEU* 2.9 20.4 + - - +
16A GLY* 3.0 10.9 + - - -
286A PHE* 3.9 23.6 - - - -
307A ALA* 4.6 6.7 - - - +
308A VAL 3.8 21.1 - - - -
310A VAL* 4.1 7.7 - - - +
313A ALA* 4.3 2.6 - - - +
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Residues in contact with LEU 13 (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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5A SER* 5.4 0.9 - - - +
11A GLY* 4.5 0.2 - - - -
12A GLY* 1.3 73.8 - - - +
14A ASP* 1.3 67.8 + - - +
15A LEU 3.2 0.2 + - - -
16A GLY 3.2 1.0 + - - -
17A PHE* 2.9 68.5 + - + -
66A ILE* 3.7 25.6 - - + -
67A GLY* 4.9 13.5 - - - +
68A GLY* 5.3 0.9 - - - +
107A LEU* 4.1 20.9 - - + -
109A GLU* 4.5 6.5 - - + -
157A PHE* 5.3 1.6 - - + -
308A VAL* 3.6 36.6 + - + +
313A ALA* 4.2 11.7 - - + -
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Residues in contact with ASP 14 (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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5A SER* 2.8 27.0 + - - -
8A SER* 3.7 5.5 - - - -
11A GLY* 3.2 20.8 + - - +
13A LEU* 1.3 77.4 + - - +
15A LEU* 1.3 57.5 + - - +
17A PHE 3.8 0.5 - - - -
18A GLN* 2.9 37.1 + - - +
24A ILE* 3.2 37.5 - - + +
38A TYR* 3.0 24.7 + - - -
42A HIS* 3.8 15.3 - - + +
66A ILE* 4.5 0.9 - - - -
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Residues in contact with LEU 15 (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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11A GLY 2.9 17.7 + - - +
12A GLY 2.9 7.5 + - - +
14A ASP* 1.3 74.0 - - - +
16A GLY* 1.3 65.4 + - - +
18A GLN* 2.9 16.5 + - - +
19A LYS* 2.9 23.6 + - - +
41A ASN 5.7 2.2 - - - +
42A HIS* 3.9 18.2 - - + -
286A PHE* 3.8 20.6 - - + -
287A PRO* 4.1 17.5 - - + -
290A PHE* 4.5 11.2 - - + -
310A VAL* 3.7 31.4 - - + -
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Residues in contact with GLY 16 (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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12A GLY 3.0 11.1 + - - -
13A LEU 3.2 0.2 + - - -
15A LEU* 1.3 73.9 - - - +
17A PHE* 1.3 64.0 + - - +
19A LYS* 3.0 18.7 + - - +
20A ALA 3.4 5.0 + - - -
310A VAL* 3.7 9.7 - - - +
313A ALA* 3.6 9.6 - - - -
314A TYR* 3.4 38.4 - - - -
317A ALA* 4.2 0.7 - - - +
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Residues in contact with PHE 17 (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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3A LEU* 3.5 18.8 - - + -
13A LEU* 2.9 50.0 + - + +
14A ASP 4.0 2.7 - - - +
16A GLY* 1.3 74.8 - - - +
18A GLN* 1.3 60.6 + - - +
20A ALA 3.2 6.2 + - - -
22A PHE* 3.1 51.5 + + + -
24A ILE* 4.4 2.7 - - + -
66A ILE* 3.8 26.7 - - + -
105A PHE* 4.1 15.3 - + - -
107A LEU* 4.1 17.3 - - + -
313A ALA* 4.4 7.9 - - + -
316A ILE* 5.3 1.6 - - + -
317A ALA* 4.0 33.0 - - + -
320A ILE* 4.3 9.4 - - + -
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Residues in contact with GLN 18 (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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14A ASP 2.9 27.3 + - - +
15A LEU* 2.9 23.0 + - - +
17A PHE* 1.3 72.9 - - - +
19A LYS* 1.3 62.7 + - - +
20A ALA 3.0 5.7 + - - -
21A GLY* 3.1 13.2 + - - -
22A PHE 3.4 17.9 - - - +
23A ARG* 5.2 1.1 - - - -
24A ILE* 3.6 29.1 + - + +
42A HIS* 4.4 12.6 + - - +
43A SER* 5.8 0.3 + - - -
44A ALA* 5.5 2.1 + - - +
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Residues in contact with LYS 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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15A LEU 2.9 10.9 + - - +
16A GLY* 3.0 12.5 + - - +
18A GLN* 1.3 75.9 - - - +
20A ALA* 1.3 57.8 + - - +
310A VAL* 4.4 19.6 + - - +
311A ASN* 4.6 12.7 + - - +
314A TYR* 3.2 47.5 + - + +
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Residues in contact with ALA 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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16A GLY 3.4 2.2 + - - +
17A PHE 3.2 10.2 + - - +
18A GLN 3.0 0.8 - - - -
19A LYS* 1.3 79.8 - - - +
21A GLY* 1.3 57.8 + - - +
22A PHE* 3.6 21.3 - - + -
314A TYR* 4.1 7.9 - - + -
317A ALA* 3.9 17.9 - - + -
318A LYS* 4.3 10.3 - - + +
321A LYS* 2.9 38.4 + - + +
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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