Contacts of the helix formed by residues 43 - 48 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J GLY 4.7 0.5 - - - +
36J ALA* 3.4 13.0 - - + -
37J SER* 3.0 46.9 + - - +
40J ASP* 2.8 20.6 + - - +
42J LYS* 1.3 76.2 - - - +
44J LEU* 1.3 61.7 + - - +
45J LYS 2.9 6.1 - - - -
46J PHE* 2.9 32.2 + - - +
47J ILE* 3.3 15.6 + - + +
225J ARG* 4.4 10.4 + - - +
229J GLN* 4.3 12.1 + - - -
234J ASN* 4.5 0.9 - - - +
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Residues in contact with LEU 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199I ILE* 3.9 35.9 - - + +
200I ASP* 5.4 1.3 - - - +
201I PRO* 3.9 26.0 - - + -
38J ILE* 4.2 14.8 - - + +
40J ASP 3.9 2.0 + - - -
41J PRO* 3.0 19.9 + - + +
43J ASP* 1.3 78.0 - - - +
45J LYS* 1.3 57.6 + - - +
47J ILE* 4.4 3.8 - - - +
48J TYR* 2.9 54.2 + - + +
51J SER* 4.0 8.9 - - - +
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Residues in contact with LYS 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J LYS 3.4 15.8 + - - +
43J ASP 2.9 0.2 - - - -
44J LEU* 1.3 79.3 - - - +
46J PHE* 1.3 72.2 + - + +
51J SER* 4.1 11.4 + - - -
53J ASP* 3.5 42.9 + - + +
54J PHE* 3.2 10.9 - - - -
55J SER* 3.0 53.0 + - - +
233J ASP 4.9 0.6 + - - -
234J ASN* 2.4 41.6 + - + +
235J ASP* 4.1 5.7 + - - +
236J VAL* 4.3 3.7 - - - +
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Residues in contact with PHE 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ALA 4.8 0.7 - - - +
28J ILE* 3.8 13.7 - - - +
31J ALA* 3.5 29.5 - - + +
36J ALA* 4.6 6.7 - - + -
42J LYS 4.5 4.0 - - - -
43J ASP* 2.9 29.3 + - - +
45J LYS* 1.3 91.7 - - + +
47J ILE* 1.3 61.6 + - - +
48J TYR 3.8 0.7 - - - -
54J PHE* 4.0 5.7 - - - -
55J SER* 3.7 20.4 - - - +
57J LEU* 3.6 36.3 - - + +
225J ARG* 5.2 5.2 - - + -
228J LEU* 3.8 14.6 - - + -
234J ASN* 4.0 32.1 - - + -
236J VAL* 3.9 22.7 - - + -
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Residues in contact with ILE 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I ALA* 3.9 26.0 - - + +
189I ARG* 3.7 7.8 + - - -
199I ILE* 4.1 9.2 - - + -
28J ILE* 3.2 35.9 - - + +
31J ALA* 5.1 0.9 - - + -
32J LEU* 4.1 13.7 - - + -
36J ALA* 3.8 15.5 - - + +
37J SER* 3.6 19.7 - - - +
38J ILE* 3.6 37.2 - - + +
43J ASP 3.3 15.5 - - - +
44J LEU* 3.2 3.6 + - - +
46J PHE* 1.3 83.4 - - - +
48J TYR* 1.3 60.8 + - - +
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Residues in contact with TYR 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I ARG* 3.6 27.1 - - - +
194I TRP 4.8 1.1 - - - -
196I PRO* 3.3 30.9 - - + +
199I ILE* 3.7 25.4 - - + -
200I ASP* 3.8 31.4 + - + +
44J LEU* 2.9 31.5 + - + +
47J ILE* 1.3 78.5 - - - +
49J GLU* 1.3 70.1 + - - +
50J GLY* 3.3 34.0 - - - -
51J SER* 3.1 31.3 + - - -
54J PHE* 3.0 15.6 - - - -
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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