Contacts of the helix formed by residues 19 - 26 (chain C) in PDB entry 4DQ0
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 HIS 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C ARG 3.2 4.0 + - - -
18C THR* 1.3 71.5 - - - +
20C SER* 1.3 73.3 + - - +
21C GLU* 3.0 50.7 + - + +
22C VAL* 2.9 21.0 + - + +
23C LEU* 3.3 8.7 + - - +
43C ARG* 3.8 19.7 - - - +
44C ASN* 3.1 27.6 + - - +
102C THR* 4.1 16.9 - - + +
103C VAL* 5.0 4.3 - - + +
133C VAL* 4.2 24.2 - - + +
201C NHE 3.8 22.5 + - - -
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Residues in contact with SER 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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17C ARG* 3.9 21.1 - - - +
18C THR 3.2 5.3 + - - -
19C HIS* 1.3 77.9 + - - +
21C GLU* 1.3 73.3 + - - +
23C LEU* 3.4 15.5 - - - +
24C GLU* 3.3 24.1 + - - +
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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 HIS* 3.0 28.1 + - + +
20C SER* 1.3 80.9 + - - +
22C VAL* 1.3 60.1 + - - +
24C GLU* 3.4 4.9 + - - +
25C ALA* 2.8 28.6 + - - +
131C LEU* 3.9 18.3 - - + +
133C VAL* 4.2 14.4 - - + -
167C LYS* 3.0 30.3 + - - +
169C ASN* 5.5 1.6 + - - -
191C THR* 3.7 24.1 + - + +
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Residues in contact with VAL 22 (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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18C THR* 4.1 15.3 - - + -
19C HIS* 2.9 14.5 + - + +
21C GLU* 1.3 74.9 - - - +
23C LEU* 1.3 67.9 + - - +
25C ALA* 3.1 15.7 + - + +
26C VAL* 3.2 15.7 + - + +
44C ASN* 3.8 30.1 - - + +
47C TYR* 4.3 6.5 - - + -
48C LEU* 4.2 29.6 - - + -
98C PHE* 5.6 2.5 - - + -
100C LEU* 3.9 18.8 - - + -
102C THR* 4.3 3.6 - - + -
131C LEU* 4.1 12.1 - - + -
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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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6C GLU* 3.3 38.6 - - + +
17C ARG* 3.6 22.9 - - - +
18C THR* 3.5 29.4 - - + +
19C HIS 3.5 7.6 - - - +
20C SER* 3.4 13.7 - - - +
22C VAL* 1.3 76.4 - - - +
24C GLU* 1.3 64.7 + - - +
26C VAL* 3.1 24.7 - - - +
27C LYS* 3.6 14.0 - - - +
47C TYR* 3.5 20.4 - - + +
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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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20C SER 3.3 11.9 + - - +
21C GLU* 3.8 8.7 - - - +
22C VAL 3.1 0.6 - - - -
23C LEU* 1.3 82.5 - - - +
25C ALA* 1.3 67.9 + - - +
26C VAL 3.2 0.4 - - - -
27C LYS* 3.2 44.8 + - + +
28C VAL* 4.5 1.7 + - - +
167C LYS* 4.1 25.1 - - - +
193C LEU* 5.3 1.5 - - - +
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Residues in contact with ALA 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 2.8 19.5 + - - +
22C VAL* 3.1 8.2 + - - +
24C GLU* 1.3 77.6 - - - +
26C VAL* 1.3 56.4 + - - +
27C LYS 3.1 2.6 + - - -
28C VAL* 3.4 5.7 + - - +
29C VAL* 3.1 29.6 + - + +
98C PHE* 3.9 27.1 - - + -
131C LEU* 4.2 8.1 - - + -
193C LEU* 4.1 23.8 - - + -
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Residues in contact with VAL 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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0C ALA* 6.0 2.4 - - - +
2C ILE* 4.5 15.0 - - + -
22C VAL* 3.2 11.8 + - + +
23C LEU* 3.1 24.0 - - - +
25C ALA* 1.3 74.2 - - - +
27C LYS* 1.3 66.2 + - + +
28C VAL 3.3 0.7 - - - -
29C VAL* 3.3 18.6 - - - +
47C TYR* 4.5 17.3 - - + +
48C LEU* 3.5 27.4 - - + -
53C TYR* 3.4 23.7 + - + +
98C PHE* 5.1 4.9 - - + -
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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