Contacts of the strand formed by residues 204 - 210 (chain B) in PDB entry 1I9R
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 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A THR* 4.2 20.5 + - + +
252A GLY* 4.4 2.1 + - - -
192B SER* 4.2 11.2 - - - +
193B LEU 4.1 4.9 - - - +
194B CYS* 4.3 11.2 - - - +
203B ARG* 1.3 107.2 + - - +
205B LEU* 1.3 66.6 + - - +
206B LEU 3.4 23.8 - - - +
207B ARG* 3.9 35.0 - - + +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A HIS* 5.1 1.9 + - - -
145A TYR* 3.6 43.1 - - + -
252A GLY* 3.6 12.4 - - - +
171B ILE* 4.8 8.5 - - + -
193B LEU* 3.0 24.6 + - + +
195B LEU* 3.8 36.1 - - + -
203B ARG* 4.4 2.7 - - + +
204B ILE* 1.3 79.5 - - - +
206B LEU* 1.3 72.1 + - + +
229B PHE* 3.7 44.7 - - + -
231B LEU* 5.2 1.3 - - + -
237B VAL* 4.9 1.1 - - + -
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A HIS* 4.1 12.3 - - + +
174A GLN* 5.2 4.7 - - + +
252A GLY* 3.2 9.6 - - - +
255A SER* 4.6 8.7 - - - +
193B LEU* 3.1 49.5 + - + -
204B ILE* 3.4 4.7 - - - +
205B LEU* 1.3 96.1 - - - +
207B ARG* 1.3 73.7 + - - +
225B LEU* 3.7 28.0 - - + +
226B GLY 2.6 31.2 - - - +
229B PHE* 3.0 30.1 - - + -
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 3.4 9.9 + - - +
250A GLY* 5.9 0.2 - - - -
251A THR* 3.7 20.7 + - - +
252A GLY 2.7 22.2 + - - +
253A PHE* 3.5 43.9 - - + +
190B ILE* 2.8 36.1 - - + +
191B ALA 3.1 6.7 - - - +
192B SER* 3.2 21.6 + - - +
204B ILE* 3.9 22.6 - - + +
206B LEU* 1.3 85.0 - - - +
208B ALA* 1.3 60.4 + - - +
225B LEU* 3.8 5.1 - - - +
59H ASN* 5.6 2.6 + - - -
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 3.6 5.6 - - - +
222A SER* 3.2 17.3 - - - +
253A PHE* 4.3 1.8 - - - -
190B ILE* 3.2 2.9 - - - +
191B ALA 2.9 27.2 + - - +
207B ARG* 1.3 73.3 - - - +
209B ALA* 1.3 66.7 + - - +
223B ILE* 3.7 27.4 - - + -
224B HIS 4.8 2.7 - - - +
225B LEU* 3.2 23.7 - - + +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 4.9 0.4 + - - +
220A GLN* 3.2 14.5 - - + +
221A GLN* 3.0 31.7 + - - -
222A SER* 3.1 8.1 + - - -
253A PHE* 3.8 15.7 - - + -
188B PRO* 4.7 2.9 - - + -
189B PHE 3.4 6.5 - - - +
190B ILE* 3.5 27.1 - - + -
208B ALA* 1.3 79.8 - - - +
210B ASN* 1.3 64.9 + - - +
223B ILE* 4.3 0.9 - - - -
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Residues in contact with ASN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASN* 5.0 5.1 - - - +
220A GLN 3.6 5.8 - - - -
221A GLN* 4.4 12.0 + - - +
222A SER* 3.6 16.1 + - - +
177B PHE* 4.1 9.6 - - + -
188B PRO* 2.9 21.8 - - - +
189B PHE* 3.1 17.2 + - - +
209B ALA* 1.3 80.6 + - - +
211B THR* 1.3 64.2 + - - +
212B HIS 4.0 0.6 + - - -
221B GLN* 3.0 37.6 + - - +
222B SER 4.3 11.0 + - - +
223B ILE* 3.7 21.7 - - - +
210C ASN* 5.0 4.8 - - - +
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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