Contacts of the helix formed by residues 43 - 48 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I GLY 4.7 0.3 - - - +
36I ALA* 3.4 14.1 - - + -
37I SER* 3.0 47.1 + - - +
40I ASP* 2.9 21.4 + - - +
42I LYS* 1.3 76.4 - - - +
44I LEU* 1.3 52.7 + - - +
45I LYS 2.8 6.1 - - - -
46I PHE* 2.8 41.2 + - - +
47I ILE* 3.3 15.4 + - + +
225I ARG* 4.4 10.3 + - - -
229I GLN* 4.4 11.1 + - - -
234I ASN* 4.7 0.9 - - - +
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Residues in contact with LEU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ILE* 4.3 18.8 - - + +
40I ASP 3.9 1.6 + - - -
41I PRO* 3.1 21.2 + - + +
43I ASP* 1.3 77.1 - - - +
45I LYS* 1.3 57.1 + - - +
47I ILE* 3.8 6.0 - - - +
48I TYR* 3.0 59.8 + - + +
51I SER* 3.9 8.6 - - - +
199J ILE* 4.2 24.5 - - + +
200J ASP* 5.0 2.2 - - - +
201J PRO* 4.1 28.0 - - + -
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Residues in contact with LYS 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I LYS 3.4 16.5 + - - +
43I ASP 2.8 0.2 - - - -
44I LEU* 1.3 80.8 - - - +
46I PHE* 1.3 74.0 + - + +
51I SER* 4.0 11.8 + - - -
53I ASP* 3.4 43.1 + - + +
54I PHE* 3.2 10.7 - - - -
55I SER* 3.0 52.1 + - - +
233I ASP 4.9 1.2 + - - -
234I ASN* 2.5 38.2 + - + +
235I ASP* 4.3 4.6 - - - +
236I VAL* 4.4 2.7 - - - +
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Residues in contact with PHE 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I ALA 4.9 0.5 - - - +
28I ILE* 3.8 13.7 + - - +
31I ALA* 3.5 29.7 - - + +
36I ALA* 4.6 6.5 - - + -
42I LYS 4.5 4.7 - - - -
43I ASP* 2.8 30.3 + - - +
45I LYS* 1.3 94.3 - - + +
47I ILE* 1.3 59.9 + - - +
48I TYR 3.8 0.4 - - - -
54I PHE* 4.0 6.4 - - - -
55I SER 3.7 20.2 - - - +
57I LEU* 3.5 35.9 - - + +
225I ARG* 5.3 5.8 - - + -
228I LEU* 3.9 14.4 - - + -
234I ASN* 4.0 30.7 - - + -
236I VAL* 4.1 22.0 - - + -
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Residues in contact with ILE 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I ILE* 3.2 35.7 - - + +
31I ALA* 5.1 1.3 - - + -
32I LEU* 4.2 13.2 - - + -
36I ALA* 4.0 15.9 - - + +
37I SER* 3.6 17.9 - - - +
38I ILE* 3.5 42.4 - - + +
43I ASP 3.3 17.1 + - - +
44I LEU* 3.3 2.7 + - - +
46I PHE* 1.3 81.9 - - - +
48I TYR* 1.3 58.9 + - - +
186J ALA* 3.9 27.1 - - + +
189J ARG* 3.9 8.3 + - - -
199J ILE* 4.2 5.3 - - + +
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Residues in contact with TYR 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I LEU* 3.0 31.0 + - + +
47I ILE* 1.3 77.7 - - - +
49I GLU* 1.3 80.1 + - - +
50I GLY* 3.3 33.1 + - - -
51I SER* 3.0 32.2 + - - -
54I PHE* 3.0 15.4 - - - -
189J ARG* 3.8 6.3 - - - -
196J PRO* 3.5 28.4 - - + +
199J ILE* 3.7 35.2 - - + -
200J ASP* 3.8 32.2 - - + +
203J PHE* 5.2 1.0 - - - -
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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