Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 5W4A
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 PHE 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C THR* 3.0 12.9 + - - +
18C PHE* 1.3 92.8 - - + +
20C PRO* 1.3 65.5 - - - +
21C ASN 3.4 2.7 - - - -
22C LEU* 3.2 11.5 + - + +
23C ALA* 3.0 20.8 + - - +
43C PHE* 3.9 23.6 - + - -
63C ILE* 6.5 0.2 - - - -
64C LEU* 4.4 11.0 - - + -
80C THR* 3.5 28.5 - - + -
84C LEU* 5.1 6.7 - - + -
170C PHE* 3.9 11.4 - - + -
171C ASP* 3.5 19.1 - - - -
174C VAL* 3.5 39.9 - - + -
175C PHE* 3.7 26.9 - + - -
178C ILE* 5.9 0.9 - - + -
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Residues in contact with PRO 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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9C VAL* 3.8 24.7 - - + -
11C PHE* 3.4 16.9 - - + -
16C THR* 3.6 11.8 - - + +
17C TYR 3.4 17.5 - - - +
18C PHE 3.4 4.5 - - - +
19C PHE* 1.3 89.3 - - - +
21C ASN* 1.3 59.1 + - - +
23C ALA* 3.3 1.2 + - - +
24C LEU* 3.0 24.4 + - - +
73C THR* 6.3 3.4 - - + -
76C THR* 4.6 11.0 - - + -
77C SER* 5.8 3.6 - - - +
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Residues in contact with ASN 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 PHE 3.4 0.6 - - - -
20C PRO* 1.3 79.1 - - + +
22C LEU* 1.3 60.8 + - - +
24C LEU* 4.4 16.9 - - - +
25C TYR* 2.9 30.6 + - - +
63C ILE* 2.9 46.6 + - + +
64C LEU* 5.5 1.3 - - - +
66C PRO* 3.7 26.6 - - + +
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Residues in contact with LEU 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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19C PHE* 3.2 17.5 + - + +
21C ASN* 1.3 76.4 - - - +
23C ALA* 1.3 66.0 + - - +
25C TYR* 3.3 6.0 + - + +
26C ALA* 3.0 22.5 + - - +
41C ASN* 5.2 1.1 - - - +
43C PHE* 3.9 34.3 - - + -
44C ALA* 3.7 38.8 - - + +
47C VAL* 4.2 7.2 - - + -
48C PHE* 4.7 5.8 - - + -
63C ILE* 3.9 18.4 - - + +
170C PHE* 3.9 21.5 - - + -
174C VAL* 3.9 17.7 - - + -
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Residues in contact with ALA 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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11C PHE* 3.9 15.7 - - + -
14C ILE* 3.6 36.5 - - + +
16C THR* 4.0 7.9 - - + -
19C PHE 3.0 12.6 + - - +
20C PRO 3.6 7.6 - - - +
22C LEU* 1.3 76.9 - - - +
24C LEU* 1.3 61.8 + - - +
26C ALA* 3.2 3.7 + - - +
27C VAL* 3.0 28.5 + - - +
170C PHE* 4.2 5.8 - - + -
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Residues in contact with LEU 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 PHE* 3.9 39.2 - - + -
20C PRO 3.0 16.5 + - - +
21C ASN* 3.8 17.9 - - - +
23C ALA* 1.3 75.4 - - - +
25C TYR* 1.3 65.3 + - - +
27C VAL* 3.3 7.0 + - + +
28C ASN* 3.0 44.4 + - - +
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Residues in contact with TYR 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 ASN* 2.9 20.9 + - - +
22C LEU* 3.6 7.9 - - - +
24C LEU* 1.3 77.7 - - - +
26C ALA* 1.3 59.1 + - - +
28C ASN* 4.8 0.9 - - - +
29C ASN* 2.9 69.7 + - + +
32C LEU* 4.1 5.5 - - - +
33C LEU* 4.5 9.6 - - + -
40C ALA* 3.5 10.9 - - - +
41C ASN* 2.9 38.1 + - + -
44C ALA* 3.6 31.4 - - + -
63C ILE* 4.6 14.1 - - + -
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Residues in contact with ALA 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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14C ILE* 4.4 5.6 - - + -
22C LEU 3.0 12.5 + - - +
23C ALA 3.2 4.2 + - - +
25C TYR* 1.3 82.9 - - + +
27C VAL* 1.3 63.0 + - - +
30C ASP* 3.2 29.5 + - - +
33C LEU* 4.2 10.4 - - + +
44C ALA* 5.5 0.9 - - + -
48C PHE* 3.5 42.6 - - + -
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Residues in contact with VAL 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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11C PHE* 3.5 30.5 - - + +
12C LEU* 4.0 35.8 - - + +
14C ILE* 4.0 13.5 - - + -
23C ALA 3.0 19.7 + - - +
24C LEU* 3.3 10.1 + - + +
26C ALA* 1.3 77.1 - - - +
28C ASN* 1.3 65.8 + - - +
30C ASP* 3.9 12.3 - - - +
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Residues in contact with ASN 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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24C LEU* 3.0 45.0 + - - +
25C TYR* 5.2 0.6 - - - +
27C VAL* 1.3 84.0 - - - +
29C ASN* 1.3 73.8 + - - +
30C ASP* 3.6 3.8 + - - +
31C GLU 5.4 0.2 + - - -
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Residues in contact with ASN 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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25C TYR* 2.9 68.1 + - + +
26C ALA 3.8 1.6 - - - -
27C VAL 3.4 0.2 - - - -
28C ASN* 1.3 90.3 - - - +
30C ASP* 1.3 64.9 + - - +
31C GLU 3.3 3.4 - - - -
32C LEU* 3.2 22.8 + - + +
33C LEU* 3.0 23.3 + - + +
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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