Contacts of the helix formed by residues 235 - 243 (chain Z) in PDB entry 1SGF
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 THR 235 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123Z LEU* 3.9 17.3 - - + -
124Z PRO* 3.1 43.3 + - + +
231Z LEU 3.3 5.2 + - - +
232Z ASN* 2.9 26.3 + - - +
233Z LYS 3.9 0.4 - - - -
234Z PHE* 1.3 72.0 - - - +
236Z SER* 1.3 60.0 + - - +
238Z ILE* 4.1 8.2 - - - +
239Z LYS* 3.5 43.3 + - - +
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Residues in contact with SER 236 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233Z LYS 5.6 2.0 + - - -
234Z PHE* 2.7 7.0 + - - -
235Z THR* 1.3 72.8 + - - +
237Z TRP* 1.3 64.6 + - - -
238Z ILE 3.0 1.8 + - - -
239Z LYS* 3.2 3.9 + - - +
240Z ASP* 3.0 38.0 + - - +
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Residues in contact with TRP 237 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Z LEU* 5.2 0.2 - - + -
89Z ILE* 3.4 34.4 - - + +
90Z PRO 3.8 2.0 - - - -
91Z HIS* 3.5 50.3 - + + +
92Z PRO* 4.0 15.0 - - + +
103Z LEU* 3.6 38.4 - - + -
105Z LEU* 3.9 28.0 - - + -
234Z PHE* 3.0 9.9 + - + +
236Z SER* 1.3 78.9 - - - +
238Z ILE* 1.3 67.4 + - + +
240Z ASP* 4.5 6.7 + - - -
241Z THR* 3.0 45.5 + - - -
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Residues in contact with ILE 238 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Z LEU* 4.1 10.3 - - + -
53Z LEU* 4.8 7.4 - - + -
103Z LEU* 4.0 7.9 - - + -
105Z LEU* 4.1 13.7 - - + -
123Z LEU* 4.0 22.7 - - + -
231Z LEU* 4.4 15.5 - - + +
234Z PHE* 3.2 38.4 + - + +
235Z THR* 4.2 7.6 - - - +
236Z SER 3.0 1.4 - - - -
237Z TRP* 1.3 98.4 - - + +
239Z LYS* 1.3 60.9 + - - +
241Z THR* 3.3 1.6 + - - -
242Z MET* 2.8 58.8 + - + +
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Residues in contact with LYS 239 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123Z LEU* 4.0 22.9 - - + +
125Z THR* 5.2 11.5 - - - +
235Z THR* 3.5 35.8 + - - +
236Z SER* 3.2 5.3 + - - +
238Z ILE* 1.3 78.3 - - + +
240Z ASP* 1.3 66.3 + - - +
242Z MET* 4.0 8.7 - - - +
243Z ALA* 3.8 15.2 + - - +
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Residues in contact with ASP 240 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236Z SER* 3.0 26.9 + - - +
237Z TRP* 4.0 7.1 - - + +
239Z LYS* 1.3 82.0 - - - +
241Z THR* 1.3 62.4 + - - +
242Z MET 3.0 6.4 + - - -
243Z ALA* 3.2 10.6 + - - +
244Z LYS* 3.3 35.9 + - - +
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Residues in contact with THR 241 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Z TRP* 3.5 3.8 - - + -
89Z ILE* 4.1 26.9 - - + +
105Z LEU* 3.7 20.9 - - + -
237Z TRP* 3.0 35.5 + - - -
240Z ASP* 1.3 80.0 - - - +
242Z MET* 1.3 60.9 + - - +
244Z LYS* 3.9 14.6 + - + +
246Z PRO* 3.5 34.5 - - + +
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Residues in contact with MET 242 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Z LEU* 4.2 16.8 - - + +
48Z ASP* 3.6 36.3 - - + +
51Z TRP* 3.3 51.0 + - + +
105Z LEU* 4.5 3.8 - - + -
123Z LEU* 5.0 6.5 - - + -
238Z ILE* 2.8 47.9 + - + +
239Z LYS* 4.2 9.9 - - + +
240Z ASP 3.0 0.6 + - - -
241Z THR* 1.3 73.3 - - - +
243Z ALA* 1.3 64.4 + - - +
245Z ASN* 3.9 6.4 + - - +
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Residues in contact with ALA 243 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239Z LYS 3.8 8.8 + - - +
240Z ASP 3.2 7.3 + - - +
242Z MET* 1.3 74.8 - - - +
244Z LYS* 1.3 66.7 + - + +
245Z ASN* 2.8 13.9 + - - +
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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