Contacts of the strand formed by residues 167 - 179 (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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ARG 3.6 0.4 + - - -
166B GLN* 1.3 80.9 - - - +
168B LEU* 1.3 60.8 + - - -
169B TYR* 3.3 9.2 - - - -
230B GLU* 3.0 15.7 + - - +
231B LEU 2.5 44.1 + - - -
260B LYS* 4.6 4.3 - - - -
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Residues in contact with LEU 168 (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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121A GLN* 4.9 23.1 - - + +
123A ALA* 4.6 9.4 - - + -
147A THR* 4.0 11.4 - - + -
149A SER* 4.7 18.8 - - - -
167B GLY* 1.3 73.2 - - - -
169B TYR* 1.3 68.6 + - - +
228B VAL* 3.4 19.1 - - + -
229B PHE 2.9 33.7 - - - +
230B GLU* 3.4 29.2 - - + +
260B LYS* 3.7 5.5 - - - +
261B LEU* 3.6 32.9 + - + +
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE* 4.2 9.3 - - + +
152B LEU 5.3 0.7 + - - -
163B VAL* 3.7 25.2 - - + +
165B ARG* 2.4 35.4 + - - +
167B GLY* 3.3 22.2 - - - -
168B LEU* 1.3 87.0 - - - +
170B TYR* 1.3 62.6 + - - +
171B ILE* 3.6 12.5 + - + +
228B VAL* 3.4 3.5 - - - +
229B PHE* 2.6 32.7 + - - +
231B LEU* 3.5 33.9 - - + -
258B LEU* 3.9 14.4 - - + -
259B LEU 3.3 6.3 - - - +
260B LYS* 3.1 51.1 - - + +
261B LEU* 4.3 4.5 - - - -
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 3.8 28.7 + + - -
172A TYR* 4.6 4.8 - + - -
224A HIS* 4.0 9.4 + - - -
259A LEU* 4.2 11.0 - - + -
169B TYR* 1.3 72.0 - - - +
171B ILE* 1.3 57.7 + - - +
172B TYR* 4.2 13.6 - + + -
224B HIS* 4.6 2.3 + - - -
226B GLY* 3.2 19.4 - - - -
227B GLY* 2.9 34.7 + - - -
228B VAL* 4.0 15.0 - - + +
257B GLY 4.2 0.2 - - - +
258B LEU* 3.4 3.5 - - - -
259B LEU* 2.7 60.5 + - + +
261B LEU* 4.0 4.7 - - + +
170C TYR* 3.8 35.3 + + - -
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Residues in contact with ILE 171 (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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169B TYR* 4.2 9.0 - - + +
170B TYR* 1.3 77.5 - - - +
172B TYR* 1.3 67.5 + - - +
193B LEU* 3.2 33.2 - - + -
205B LEU* 4.8 4.0 - - + -
206B LEU* 4.4 1.2 - - - +
225B LEU 3.5 0.9 - - - +
226B GLY* 3.0 28.5 - - - +
227B GLY 3.2 11.4 + - - +
229B PHE* 4.4 15.5 - - + -
231B LEU* 3.7 34.5 - - + -
237B VAL* 4.2 21.3 - - + -
256B PHE* 4.6 7.0 - - + -
257B GLY 3.7 7.2 - - - +
258B LEU* 3.8 15.3 - - + -
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Residues in contact with TYR 172 (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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124B ALA 4.1 1.2 + - - -
125B HIS* 2.5 40.1 + + - +
170B TYR* 4.2 22.0 - + + +
171B ILE* 1.3 80.2 - - - +
173B ALA* 1.3 69.1 + - - +
174B GLN* 4.7 2.9 - - + -
193B LEU* 5.4 0.7 - - - -
224B HIS* 4.7 12.1 - + - +
225B LEU 3.0 12.8 - - - +
226B GLY* 4.2 6.5 - - - -
255B SER* 5.2 1.1 - - - -
256B PHE* 3.2 11.0 - - - -
257B GLY* 2.8 66.3 + - - -
258B LEU* 3.8 4.9 - - - -
259B LEU* 4.8 1.3 - - + -
170C TYR* 4.5 4.5 - + - -
226C GLY 4.6 2.2 - - - -
227C GLY* 3.2 22.4 - - - -
228C VAL* 2.6 31.8 + - + +
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Residues in contact with ALA 173 (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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172B TYR* 1.3 80.8 - - - +
174B GLN* 1.3 62.1 + - - +
175B VAL* 3.8 3.4 + - + +
193B LEU* 5.1 2.5 - - + -
223B ILE* 4.6 1.4 - - - +
224B HIS* 3.7 3.8 - - - -
225B LEU* 3.2 44.1 + - + +
239B VAL* 3.6 34.1 - - + -
255B SER 3.5 9.6 - - - +
256B PHE* 3.9 4.7 - - + +
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Residues in contact with GLN 174 (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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172B TYR* 4.7 4.8 - - + -
173B ALA* 1.3 73.0 - - - +
175B VAL* 1.3 78.0 + - - +
176B THR* 3.6 11.7 - - - +
222B SER* 4.1 4.5 + - - -
223B ILE 3.4 8.0 + - - +
224B HIS* 3.4 28.3 - - + +
252B GLY 5.2 1.6 - - - -
253B PHE 2.6 29.5 + - - -
254B THR* 3.4 0.5 - - - +
255B SER* 3.0 46.0 + - - +
206C LEU* 5.5 3.8 - - + -
207C ARG 3.5 9.4 + - - +
208C ALA* 3.6 6.6 - - - +
224C HIS 3.7 4.9 - - - +
225C LEU* 3.4 33.0 - - + +
226C GLY 5.0 2.7 - - - +
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Residues in contact with VAL 175 (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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138B LEU* 4.0 17.0 - - + -
140B TRP* 4.6 2.7 - - + -
173B ALA* 3.8 4.2 + - + +
174B GLN* 1.3 86.6 - - - +
176B THR* 1.3 71.8 + - - +
177B PHE* 4.6 1.0 - - + -
189B PHE* 4.3 26.5 - - + -
191B ALA* 4.9 6.7 - - + -
221B GLN 4.1 0.5 - - - +
222B SER 3.3 0.5 - - - -
223B ILE* 2.5 57.5 + - + +
239B VAL* 4.4 11.4 - - + -
241B VAL* 5.1 2.5 - - + -
247B VAL* 4.6 7.2 - - + -
254B THR* 3.5 18.8 - - + +
255B SER 4.8 0.2 - - - +
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Residues in contact with THR 176 (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* 3.6 2.5 - - - +
175B VAL* 1.3 75.9 - - - +
177B PHE* 1.3 65.2 + - - +
220B GLN* 3.7 8.3 + - - +
221B GLN 3.1 9.7 + - - -
222B SER* 3.0 25.1 - - - +
247B VAL* 3.6 2.6 - - - -
248B SER* 2.8 30.8 + - - -
253B PHE* 2.9 60.4 - - + +
254B THR* 3.3 8.0 + - - -
207C ARG 3.9 0.4 - - - +
209C ALA 4.9 0.6 + - - -
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Residues in contact with PHE 177 (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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175B VAL 4.6 3.6 - - - -
176B THR* 1.3 77.9 + - - +
178B CYS* 1.3 63.3 + - - +
179B SER* 3.6 25.6 - - - -
189B PHE* 3.4 65.7 - + + -
210B ASN* 4.1 8.5 - - + -
212B HIS* 3.8 5.2 - + - -
219B GLY 3.9 0.2 - - - +
220B GLN* 2.9 22.9 - - - +
221B GLN* 2.9 54.4 + - + +
223B ILE* 4.2 13.7 - - + -
246B GLN* 3.2 16.8 - - + +
247B VAL* 3.6 7.0 - - - -
248B SER* 3.5 7.6 - - - +
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Residues in contact with CYS 178 (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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177B PHE* 1.3 76.0 - - - +
179B SER* 1.3 60.4 + - - +
218B CYS* 2.0 55.4 - - - -
219B GLY 3.5 3.4 - - - -
220B GLN* 3.6 24.9 - - + -
246B GLN* 2.9 15.1 + - - +
248B SER* 3.8 6.5 + - - +
55K ASN* 2.5 34.9 - - - +
57K ASP* 3.9 7.4 - - - +
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Residues in contact with SER 179 (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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177B PHE* 3.6 11.0 - - - -
178B CYS* 1.3 76.0 - - - +
180B ASN* 1.3 57.7 + - - +
184B SER* 5.9 1.6 - - - -
212B HIS* 2.9 38.9 - - - +
213B SER* 4.3 4.2 + - - +
215B ALA 3.8 0.3 - - - +
218B CYS* 2.8 17.6 - - - +
219B GLY* 2.7 31.4 + - - +
246B GLN* 3.7 20.2 - - - +
55K ASN* 4.1 1.6 - - - -
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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