Contacts of the helix formed by residues 43 - 48 (chain C) in PDB entry 1S9C
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 ASP 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY 4.7 0.3 - - - +
36C ALA* 3.4 13.8 - - + -
37C SER* 3.0 46.1 + - - +
38C ILE* 5.5 0.2 - - - -
40C ASP* 2.8 20.5 + - - +
42C LYS* 1.3 76.8 - - - +
44C LEU* 1.3 62.1 + - - +
45C LYS 2.8 6.5 - - - -
46C PHE* 2.8 32.5 + - - +
47C ILE* 3.2 17.1 + - + +
225C ARG* 4.4 10.8 + - - +
229C GLN* 4.3 12.3 + - - -
234C ASN* 4.4 1.0 - - - +
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Residues in contact with LEU 44 (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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38C ILE* 4.2 24.1 - - + +
40C ASP 3.9 1.6 + - - -
41C PRO* 3.0 20.1 + - + +
43C ASP* 1.3 78.2 - - - +
45C LYS* 1.3 56.9 + - - +
47C ILE* 3.8 4.2 - - - +
48C TYR* 2.9 61.3 + - + +
51C SER* 3.9 9.3 - - - +
199D ILE* 4.3 21.3 - - + +
200D ASP* 6.3 0.4 - - - -
201D PRO* 5.0 11.9 - - + -
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Residues in contact with LYS 45 (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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42C LYS 3.4 17.8 + - - +
43C ASP 2.8 0.2 - - - -
44C LEU* 1.3 79.0 - - - +
46C PHE* 1.3 69.8 - - + +
51C SER* 4.0 11.6 + - - -
53C ASP* 3.4 43.4 + - + +
54C PHE* 3.2 11.7 - - - -
55C SER* 3.1 52.1 + - - +
233C ASP 5.0 0.6 + - - -
234C ASN* 2.4 38.2 + - + +
235C ASP* 4.1 7.9 + - - +
236C VAL* 4.1 6.5 - - - +
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Residues in contact with PHE 46 (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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27C ALA 5.0 0.3 - - - +
28C ILE* 3.9 13.9 + - - +
31C ALA* 3.6 29.2 - - + +
36C ALA* 4.6 6.7 - - + -
42C LYS 4.5 4.5 - - - -
43C ASP* 2.8 32.6 + - - +
45C LYS* 1.3 97.0 - - + +
47C ILE* 1.3 61.4 + - - +
48C TYR 3.8 0.4 - - - -
54C PHE* 4.0 6.4 - - - -
55C SER* 3.8 20.4 - - - +
57C LEU* 3.5 35.4 - - + +
225C ARG* 5.4 4.7 - - + -
228C LEU* 3.8 15.0 - - + -
234C ASN* 4.0 25.6 - - - -
236C VAL* 3.8 22.4 - - + -
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Residues in contact with ILE 47 (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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28C ILE* 3.3 34.2 - - + +
31C ALA* 5.1 0.7 - - + -
32C LEU* 4.1 11.0 - - + -
36C ALA* 3.9 15.5 - - + +
37C SER* 3.6 18.6 - - - +
38C ILE* 3.5 42.2 - - + +
43C ASP 3.2 16.6 + - - +
44C LEU* 4.3 2.2 - - - +
46C PHE* 1.3 83.2 - - - +
48C TYR* 1.3 58.9 + - - +
183D ASN* 4.0 3.4 - - - +
186D ALA* 3.8 27.9 - - + +
189D ARG* 4.1 7.1 + - - -
199D ILE* 4.1 5.1 - - + +
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Residues in contact with TYR 48 (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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44C LEU* 2.9 34.4 + - + +
46C PHE 3.8 0.2 - - - -
47C ILE* 1.3 76.1 - - - +
49C GLU* 1.3 81.7 + - - +
50C GLY* 3.3 29.4 - - - -
51C SER* 3.0 30.6 + - - -
54C PHE* 3.0 14.9 - - - -
189D ARG* 4.0 1.6 - - - -
196D PRO* 3.5 24.8 - - + +
199D ILE* 3.5 39.0 - - + -
200D ASP* 3.4 37.2 + - + -
203D PHE* 4.2 4.3 - - - -
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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