Contacts of the strand formed by residues 226 - 230 (chain X) 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 SER 226 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X CYS* 3.5 6.4 - - - -
182X CYS* 3.6 0.3 - - - -
183X ALA 3.0 29.3 + - - -
192X GLU 5.6 1.4 + - - -
193X HIS* 4.7 19.8 - - - -
213X THR* 5.8 1.3 - - - -
215X TRP 6.1 0.7 - - - -
224X GLU 4.8 2.3 + - - -
225X PRO* 1.3 75.9 - - - +
227X VAL* 1.3 64.8 + - - +
228X TYR* 3.8 26.1 + - - -
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Residues in contact with VAL 227 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168X CYS* 3.6 32.1 - - + +
174X MET* 4.0 28.5 - - + -
176X VAL* 4.1 14.1 - - + -
180X MET* 3.6 32.3 - - + -
181X LEU 3.5 12.8 - - - +
193X HIS* 5.7 0.3 + - - -
213X THR* 4.3 2.4 - - - +
214X SER* 3.1 27.2 + - - -
215X TRP 4.2 6.3 + - - +
225X PRO 5.5 0.4 - - - +
226X SER* 1.3 74.1 - - - +
228X TYR* 1.3 69.0 + - - +
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Residues in contact with TYR 228 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X ALA* 4.0 11.0 - - + +
160X LEU* 3.2 20.4 - - - +
180X MET* 3.5 6.6 - - - +
181X LEU* 2.8 35.7 + - + +
182X CYS 4.9 0.7 - - - -
183X ALA* 3.7 28.5 - - + -
198X PRO 4.8 0.9 - - - -
199X LEU* 3.8 42.2 - - + -
211X GLY* 4.6 0.4 - - - -
212X ILE 3.5 13.2 - - - +
213X THR* 3.2 40.6 - - + -
214X SER* 4.6 1.3 - - - -
226X SER* 3.8 33.8 + - - -
227X VAL* 1.3 77.7 - - - +
229X THR* 1.3 62.8 + - - +
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Residues in contact with THR 229 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101X ASN* 5.4 0.9 - - - +
102X ASP* 3.1 47.2 + - - +
103X LEU* 4.2 12.1 - - + -
179X ALA 4.2 10.8 - - - +
180X MET* 4.7 4.0 - - + +
181X LEU* 4.8 0.9 - - - -
211X GLY* 3.1 9.1 - - - -
212X ILE* 2.7 42.4 + - - +
214X SER* 3.9 5.9 - - - -
228X TYR* 1.3 72.6 - - - +
230X LYS* 1.3 72.2 + - - +
231X LEU* 4.5 0.7 - - - +
234X PHE* 4.3 11.7 - - + -
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Residues in contact with LYS 230 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X GLU* 5.8 4.5 - - - +
130X PRO* 5.0 16.2 - - + -
178X ASP* 2.9 28.3 + - - +
179X ALA 3.4 18.9 + - - +
180X MET* 4.1 5.8 + - - +
181X LEU* 3.9 36.6 - - + -
210X GLN 3.9 4.0 - - - +
228X TYR 3.8 2.2 + - - -
229X THR* 1.3 75.3 - - - +
231X LEU* 1.3 64.6 + - - +
232X ILE* 3.6 12.3 - - + +
233X LYS* 4.3 22.3 + - + +
234X PHE* 3.1 26.9 - - - -
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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