Contacts of the helix formed by residues 43 - 48 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L GLY 4.7 0.2 - - - +
36L ALA* 3.4 13.6 - - + -
37L SER* 3.0 46.5 + - - +
40L ASP* 2.8 17.0 + - - +
42L LYS* 1.3 75.1 - - - +
44L LEU* 1.3 61.9 + - - +
45L LYS 2.8 6.3 - - - -
46L PHE* 2.8 33.0 + - - +
47L ILE* 3.3 16.1 + - + +
225L ARG* 4.5 10.3 + - - +
229L GLN* 4.3 16.4 + - - -
234L ASN* 4.3 1.4 - - - +
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Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K ILE* 3.9 34.3 - - + +
200K ASP* 5.2 1.1 - - - +
201K PRO* 3.6 29.4 - - + -
38L ILE* 4.2 17.4 - - + +
40L ASP 3.9 1.4 + - - -
41L PRO* 3.0 19.0 + - + +
43L ASP* 1.3 76.7 - - - +
45L LYS* 1.3 57.0 + - - +
47L ILE* 3.8 5.1 - - - +
48L TYR* 3.0 52.4 + - + +
51L SER* 3.9 9.1 - - - +
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Residues in contact with LYS 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41L PRO 4.5 0.2 + - - -
42L LYS 3.5 16.9 + - - +
44L LEU* 1.3 79.5 - - - +
46L PHE* 1.3 69.4 + - + +
51L SER* 4.0 11.2 + - - -
53L ASP* 3.4 44.9 + - + +
54L PHE* 3.1 10.9 - - - -
55L SER* 3.0 52.8 + - - +
233L ASP 5.0 0.4 + - - -
234L ASN* 2.5 36.2 + - + +
235L ASP* 4.1 8.1 + - - +
236L VAL* 4.2 6.4 - - - +
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Residues in contact with PHE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ALA 5.0 0.5 - - - -
28L ILE* 3.8 14.2 - - - +
31L ALA* 3.6 28.4 - - + +
36L ALA* 4.7 6.7 - - + -
42L LYS 4.5 4.3 - - - -
43L ASP* 2.8 28.6 + - - +
45L LYS* 1.3 93.5 - - + +
47L ILE* 1.3 61.5 + - - +
48L TYR 3.8 0.4 - - - -
54L PHE* 4.0 5.7 - - - -
55L SER* 3.7 21.1 - - - +
57L LEU* 3.6 30.5 - - + +
225L ARG* 5.4 4.5 - - + -
228L LEU* 3.8 20.9 - - + -
234L ASN* 3.9 31.9 - - - -
236L VAL* 3.7 22.9 - - + -
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Residues in contact with ILE 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K ASN* 4.1 3.1 - - - +
186K ALA* 3.7 27.6 - - + +
189K ARG* 3.8 7.6 + - - -
199K ILE* 4.0 10.2 - - + +
28L ILE* 3.2 35.7 - - + +
31L ALA* 5.2 0.7 - - + -
32L LEU* 4.1 9.6 - - + -
36L ALA* 3.9 15.5 - - + +
37L SER* 3.6 17.7 - - - +
38L ILE* 3.5 40.4 - - + +
43L ASP 3.4 15.5 - - - +
44L LEU* 3.3 3.0 + - - +
46L PHE* 1.3 82.7 - - - +
48L TYR* 1.3 59.8 + - - +
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Residues in contact with TYR 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K ARG* 3.8 10.1 - - - -
194K TRP 5.1 0.2 - - - -
196K PRO* 3.3 26.3 - - + +
199K ILE* 3.7 30.1 - - + -
200K ASP* 3.1 40.1 + - + -
44L LEU* 3.0 31.7 + - + +
47L ILE* 1.3 76.5 - - - +
49L GLU* 1.3 81.8 + - - +
50L GLY* 3.3 33.3 - - - -
51L SER* 3.0 32.0 + - - -
54L PHE* 3.0 15.8 - - - -
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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