Contacts of the strand formed by residues 219 - 225 (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 GLY 219 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B PHE* 3.9 0.7 - - - +
178B CYS* 3.5 2.3 - - - -
179B SER* 2.7 29.1 + - - +
213B SER* 3.5 11.8 + - - -
215B ALA* 3.1 24.1 + - - +
218B CYS* 1.3 74.9 - - - +
220B GLN* 1.3 68.2 + - - +
221B GLN* 4.5 2.9 - - - +
188C PRO* 6.3 0.7 - - - -
211C THR* 3.7 7.9 - - - -
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Residues in contact with GLN 220 (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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176B THR* 3.7 5.6 + - - +
177B PHE 2.9 9.0 - - - +
178B CYS* 3.6 19.4 - - - +
218B CYS 4.2 0.2 + - - -
219B GLY* 1.3 74.5 - - - -
221B GLN* 1.3 62.8 + - - +
248B SER* 3.3 22.7 + - - +
253B PHE* 2.9 47.8 - - - -
188C PRO* 4.0 25.0 - - + +
190C ILE* 5.1 1.4 - - - +
209C ALA* 3.4 19.1 - - + +
210C ASN* 3.7 0.7 - - - -
211C THR* 2.8 24.6 + - - +
57K ASP* 4.8 7.0 + - - +
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Residues in contact with GLN 221 (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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221A GLN* 4.7 5.9 - - - +
176B THR* 3.1 1.5 - - - -
177B PHE* 2.9 57.4 + - + +
179B SER* 5.5 0.2 + - - -
210B ASN* 3.0 42.0 + - - +
211B THR 3.6 22.1 + - - +
212B HIS 4.2 0.8 - - - +
213B SER* 4.3 12.2 - - - +
219B GLY 4.5 4.0 - - - +
220B GLN* 1.3 84.1 - - - +
222B SER* 1.3 60.5 + - - +
209C ALA 3.1 8.9 + - - -
210C ASN* 4.3 14.9 + - - +
211C THR* 4.4 6.7 - - - +
221C GLN* 4.8 3.6 - - - +
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Residues in contact with SER 222 (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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174B GLN* 4.1 5.6 + - - -
175B VAL 3.3 3.4 - - - -
176B THR* 3.0 23.7 - - - +
210B ASN* 4.3 12.1 + - - +
221B GLN* 1.3 72.5 - - - +
223B ILE* 1.3 69.9 + - - +
208C ALA* 3.1 24.5 - - - -
209C ALA 3.0 22.5 + - - -
210C ASN* 3.7 13.0 + - - +
223C ILE* 5.2 2.0 - - - -
224C HIS 6.1 1.8 - - - -
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Residues in contact with ILE 223 (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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222A SER* 5.2 2.5 - - - -
173B ALA 4.6 1.3 - - - +
174B GLN* 3.4 6.3 - - - +
175B VAL* 2.5 52.4 + - + +
177B PHE* 4.2 5.2 - - + -
189B PHE* 4.0 32.8 - - + +
191B ALA* 4.2 7.9 - - + -
208B ALA* 3.7 40.4 - - + +
209B ALA 4.0 1.1 - - - +
210B ASN* 3.7 19.5 - - - +
222B SER* 1.3 80.2 - - - +
224B HIS* 1.3 67.0 + - - +
225B LEU* 4.1 10.1 - - + -
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Residues in contact with HIS 224 (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 9.5 - - - +
222A SER* 6.0 1.3 - - - -
224A HIS* 3.0 50.4 + + + +
170B TYR* 4.6 3.6 + - - -
172B TYR* 4.7 12.2 - + + +
173B ALA 3.7 4.7 - - - -
174B GLN* 3.4 17.2 - - + +
208B ALA* 4.8 1.3 - - - +
223B ILE* 1.3 78.3 - - - +
225B LEU* 1.3 71.8 + - - +
170C TYR* 3.9 8.7 + - - -
224C HIS* 2.8 43.9 + + + +
225C LEU* 3.8 0.2 - - - -
226C GLY* 3.1 34.8 - - - -
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Residues in contact with LEU 225 (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* 3.5 12.6 - - + +
224A HIS* 3.8 3.6 - - - -
171B ILE 3.5 0.7 - - - +
172B TYR* 3.0 22.6 - - - -
173B ALA* 3.2 28.3 + - + +
191B ALA* 4.3 6.1 - - + +
192B SER* 4.9 2.0 - - - -
193B LEU* 3.8 33.2 - - + +
206B LEU* 3.7 17.1 - - + +
207B ARG* 3.8 5.6 - - - -
208B ALA* 3.2 43.7 - - + +
223B ILE* 4.1 7.6 - - + -
224B HIS* 1.3 79.3 - - - +
226B GLY* 1.3 60.2 + - - +
239B VAL* 5.9 1.3 - - + -
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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