Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 1DT0
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 SER 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C HIS 4.4 0.4 - - - -
15C GLN* 3.9 12.1 - - - -
16C PRO* 5.3 1.9 - - - -
18C ILE* 1.3 75.5 - - - +
20C LYS* 1.3 63.8 + - - +
21C GLU* 3.7 10.3 + - - +
22C THR* 3.0 20.4 + - - -
23C LEU* 3.3 19.8 + - - +
164C ILE* 4.3 0.6 - - - +
165C ASP* 2.4 35.1 + - - -
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C HIS* 3.2 37.1 + - + +
12C ASP* 3.9 21.6 + - + +
15C GLN* 3.3 18.3 + - - +
19C SER* 1.3 70.8 - - - +
21C GLU* 1.3 65.6 + - - +
23C LEU* 3.2 3.6 + - - +
24C GLU* 2.9 46.6 + - - +
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 3.2 9.6 - - - +
20C LYS* 1.3 79.5 - - - +
22C THR* 1.3 64.8 + - - +
24C GLU* 3.2 16.2 + - - +
25C PHE* 3.0 48.6 + - + -
164C ILE* 3.5 32.4 - - + +
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 3.7 16.2 - - + -
19C SER* 3.0 12.2 + - - -
20C LYS 3.3 0.2 - - - -
21C GLU* 1.3 79.8 - - - +
23C LEU* 1.3 54.7 + - + +
25C PHE* 3.9 0.7 - - - +
26C HIS* 2.7 47.2 + - + +
160C HIS 4.4 7.4 - - - +
161C ALA 3.5 28.3 + - - +
162C TYR* 5.3 0.6 - - - -
164C ILE* 3.5 21.7 + - + +
165C ASP* 2.6 29.0 + - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C LEU* 3.7 22.0 - - + -
9C TYR* 4.0 18.4 - - + -
10C ALA 4.1 1.3 - - - +
11C HIS* 3.2 35.7 - - + +
14C LEU* 4.3 13.5 - - + -
18C ILE* 3.5 25.6 - - + +
19C SER 3.3 6.9 + - - +
20C LYS 3.2 8.6 + - - +
22C THR* 1.3 78.6 - - + +
24C GLU* 1.3 58.6 + - - +
26C HIS* 4.5 0.2 - - - -
27C HIS* 2.7 39.2 + - - +
77C TRP* 3.6 28.0 - - + -
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C HIS* 3.8 12.5 - - + +
20C LYS* 2.9 45.2 + - - +
21C GLU* 3.5 19.3 - - - +
23C LEU* 1.3 75.1 - - - +
25C PHE* 1.3 62.8 + - + +
28C ASP* 2.8 52.6 + - + +
29C LYS* 3.5 7.2 + - - +
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU* 3.0 46.7 + - + +
22C THR* 3.9 2.9 - - - +
24C GLU* 1.3 81.1 - - + +
26C HIS* 1.3 62.9 + - - +
29C LYS* 3.0 46.2 + - + +
30C HIS* 3.0 37.8 + + + +
160C HIS 6.1 0.9 - - - +
164C ILE* 3.8 20.9 - - + -
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Residues in contact with HIS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 2.7 29.0 + - + +
25C PHE* 1.3 72.5 - - - +
27C HIS* 1.3 57.2 + - - +
30C HIS* 3.5 8.2 - - + +
31C HIS* 3.0 25.8 + - - +
73C HIS* 2.8 16.7 + + - -
76C TYR* 4.3 13.2 + + - -
77C TRP* 3.6 19.1 - + + -
156C ASP* 2.8 18.5 + - - -
160C HIS* 3.0 15.6 + + + +
161C ALA* 3.3 36.7 + - + -
1603C FE 2.3 26.5 - - - -
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Residues in contact with HIS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.6 27.5 - - + +
5C PRO 2.9 28.9 + - - -
6C PRO* 4.2 2.8 - - - +
7C LEU* 3.5 41.2 + - + +
11C HIS* 3.6 15.0 - + - -
23C LEU 2.7 24.7 + - - +
26C HIS* 1.3 74.1 - - - +
28C ASP* 1.3 84.1 + - - -
29C LYS 3.3 1.3 + - - -
31C HIS* 3.1 34.0 + - - +
32C ASN 3.4 4.2 + - - -
77C TRP* 3.8 13.2 + + + -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.6 5.9 - - - +
11C HIS* 3.0 22.0 + - - -
24C GLU* 2.8 35.8 + - + +
27C HIS* 1.3 97.2 - - - +
29C LYS* 1.3 65.1 + - + +
32C ASN* 3.1 22.0 + - - +
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Residues in contact with LYS 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU* 4.6 8.5 - - - +
25C PHE* 3.0 57.5 + - + +
27C HIS 3.3 0.2 - - - -
28C ASP* 1.3 84.5 - - - +
30C HIS* 1.3 65.0 + - + +
31C HIS 3.4 1.1 - - - -
32C ASN* 3.2 3.8 + - - +
33C THR* 2.8 35.7 + - - +
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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