Contacts of the helix formed by residues 43 - 48 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G ALA* 3.4 14.2 - - + -
37G SER* 3.0 45.7 + - - +
40G ASP* 2.9 22.2 + - - +
42G LYS* 1.3 76.6 - - - +
44G LEU* 1.3 63.9 + - - +
45G LYS 2.8 5.6 - - - -
46G PHE* 2.8 31.6 + - - +
47G ILE* 3.3 15.6 + - + +
225G ARG* 4.5 10.8 + - - +
229G GLN* 4.3 11.9 + - - -
234G ASN* 4.5 0.9 - - - +
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G ILE* 4.3 18.7 - - + +
40G ASP 3.9 1.4 + - - -
41G PRO* 3.0 20.8 + - + +
43G ASP* 1.3 78.4 - - - +
45G LYS* 1.3 57.6 + - - +
47G ILE* 4.5 4.5 - - - +
48G TYR* 2.9 63.2 + - + +
51G SER* 4.0 8.0 - - - +
199H ILE* 4.1 24.7 - - + +
200H ASP* 5.5 1.1 - - - +
201H PRO* 4.6 19.7 - - + -
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Residues in contact with LYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G PRO 4.5 0.2 + - - -
42G LYS 3.4 16.7 + - - +
44G LEU* 1.3 80.1 - - - +
46G PHE* 1.3 70.9 + - + +
51G SER* 4.1 12.5 + - - -
53G ASP* 3.4 42.5 + - + +
54G PHE* 3.2 11.4 - - - -
55G SER* 3.1 51.9 + - - +
233G ASP 4.9 0.6 + - - -
234G ASN* 2.4 39.8 + - + +
235G ASP* 4.1 6.7 + - - +
236G VAL* 4.3 5.9 - - - +
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Residues in contact with PHE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ALA 4.9 0.9 - - - +
28G ILE* 3.9 13.7 - - - +
31G ALA* 3.6 29.5 - - + +
36G ALA* 4.6 7.0 - - + -
42G LYS 4.4 4.5 - - - -
43G ASP* 2.8 33.7 + - - +
45G LYS* 1.3 89.7 - - + +
47G ILE* 1.3 61.2 + - - +
48G TYR 3.8 0.2 - - - -
54G PHE* 4.1 6.0 - - - -
55G SER* 3.7 20.7 - - - +
57G LEU* 3.5 36.8 - - + +
225G ARG* 5.3 4.7 - - + -
228G LEU* 3.8 14.1 - - + -
234G ASN* 3.9 32.3 - - + -
236G VAL* 3.9 22.4 - - + -
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Residues in contact with ILE 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ILE* 3.2 36.1 - - + +
31G ALA* 5.1 0.9 - - + -
32G LEU* 4.1 12.3 - - + -
36G ALA* 3.9 15.5 - - + +
37G SER* 3.6 18.2 - - - +
38G ILE* 3.5 39.7 - - + +
43G ASP 3.4 14.6 - - - +
44G LEU* 3.2 4.1 + - - +
46G PHE* 1.3 84.1 - - - +
48G TYR* 1.3 58.3 + - - +
186H ALA* 3.9 26.7 - - + +
189H ARG* 3.8 8.1 + - - -
199H ILE* 4.0 9.3 - - + +
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Residues in contact with TYR 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G LEU* 2.9 38.0 + - + +
47G ILE* 1.3 77.2 - - - +
49G GLU* 1.3 84.3 + - - +
50G GLY* 3.3 32.7 + - - -
51G SER* 3.0 31.9 + - - -
54G PHE* 3.0 15.7 - - - -
189H ARG* 4.0 3.1 - - - -
196H PRO* 3.3 25.3 - - + +
199H ILE* 3.7 29.4 - - + -
200H ASP* 2.8 41.4 + - + -
203H PHE* 4.5 3.5 - - - -
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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