Contacts of the strand formed by residues 208 - 213 (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 ILE 208 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X ILE* 5.8 0.7 - - - -
122X THR* 6.1 0.9 - - - +
124X PRO* 5.7 4.0 - - + -
125X THR* 5.6 4.7 - - - +
128X GLU* 3.6 41.5 - - + +
200X ILE* 3.8 4.5 - - - -
201X CYS 2.8 48.0 + - - +
202X ASP* 3.4 12.3 - - + +
207X GLY* 1.3 78.5 - - - +
209X LEU* 1.3 65.8 + - - +
210X GLN* 3.3 22.1 - - - +
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Residues in contact with LEU 209 (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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45X VAL* 4.4 11.4 - - + -
47X LEU* 4.2 16.8 - - + -
53X LEU* 5.1 0.2 - - + -
121X ILE* 3.8 30.7 - - + +
122X THR 3.6 22.9 + - - +
123X LEU* 4.5 6.5 - - + -
124X PRO* 3.0 25.6 - - + +
198X PRO* 4.0 23.8 - - + -
199X LEU 4.0 10.8 - - - +
200X ILE* 4.2 10.7 - - + +
208X ILE* 1.3 74.7 - - - +
210X GLN* 1.3 70.1 + - - +
211X GLY 4.0 9.4 - - - +
231X LEU* 3.6 22.4 - - + -
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Residues in contact with GLN 210 (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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124X PRO* 3.4 21.2 - - - +
128X GLU 3.3 18.7 + - - +
129X GLU 4.9 0.4 - - - -
130X PRO* 3.6 38.8 - - + +
181X LEU* 4.0 11.4 - - + +
199X LEU 3.0 10.6 + - - +
201X CYS* 4.1 25.2 + - + +
208X ILE* 3.3 37.6 + - - +
209X LEU* 1.3 74.5 + - - +
211X GLY* 1.3 59.1 + - - +
230X LYS* 3.9 4.0 - - + +
231X LEU* 2.9 30.2 + - - +
232X ILE* 4.0 8.0 + - - +
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Residues in contact with GLY 211 (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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181X LEU* 4.7 1.8 - - - -
198X PRO* 3.6 2.4 - - - +
199X LEU* 3.0 40.6 + - - +
209X LEU* 4.0 5.4 - - - +
210X GLN* 1.3 81.6 - - - +
212X ILE* 1.3 68.9 + - - +
228X TYR* 4.6 4.7 - - - -
229X THR 3.1 11.7 - - - -
231X LEU* 4.1 6.2 - - - +
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Residues in contact with ILE 212 (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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45X VAL* 4.0 9.6 - - + -
53X LEU* 3.4 49.8 - - + +
54X THR 3.9 6.5 - - - +
55X ALA* 4.3 16.6 - - + -
102X ASP 4.4 0.7 - - - +
103X LEU* 4.3 13.9 - - + -
196X GLY* 3.6 15.3 - - - +
197X GLY 3.5 3.8 - - - +
211X GLY* 1.3 78.8 - - - +
213X THR* 1.3 71.5 + - - +
214X SER 3.1 0.3 + - - -
228X TYR* 4.0 2.4 - - - +
229X THR* 2.7 48.2 + - - +
231X LEU* 4.4 9.9 - - + -
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Residues in contact with THR 213 (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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55X ALA* 4.0 5.0 - - - +
57X HIS* 4.0 0.3 - - - -
193X HIS* 3.4 36.3 - - + +
194X ASP* 3.1 29.5 + - - +
195X SER 4.0 0.3 - - - -
196X GLY* 3.0 19.2 + - - -
197X GLY 3.0 17.3 + - - +
198X PRO 4.5 1.6 + - - -
212X ILE* 1.3 73.0 - - - +
214X SER* 1.3 62.7 + - - +
226X SER* 5.8 1.3 - - - -
227X VAL 4.8 2.0 - - - +
228X TYR* 3.2 34.7 - - + -
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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