Contacts of the strand formed by residues 191 - 199 (chain B) in PDB entry 3Q5H
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 GLN 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B LEU* 3.5 9.7 - - - +
185B ILE* 3.1 32.4 + - + +
186B LYS* 4.8 8.0 + - - -
189B VAL* 2.8 36.2 + - + +
190B TRP* 1.3 74.5 - - - +
192B ILE* 1.3 67.0 + - - +
211B LEU* 3.4 20.1 - - - +
212B ALA 3.3 17.0 - - - +
213B LEU* 4.0 6.6 - - + +
295B THR* 3.2 33.3 + - - +
298B THR* 2.9 30.5 + - - +
320B ILE* 5.2 0.2 - - - -
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Residues in contact with ILE 192 (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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182B ILE* 3.9 29.8 - - + +
183B ASN 3.3 24.2 - - - +
184B LEU* 4.1 9.4 - - + -
185B ILE* 3.6 14.1 - - - +
191B GLN* 1.3 77.5 - - - +
193B GLN* 1.3 61.9 + - - +
211B LEU* 3.8 0.5 - - - -
212B ALA* 2.9 47.6 + - + +
214B VAL* 4.3 7.4 - - + -
262B LEU* 4.1 18.6 - - + -
301B LEU* 5.3 0.4 - - + -
320B ILE* 4.2 10.5 - - + -
322B PHE* 3.9 31.9 - - + -
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Residues in contact with GLN 193 (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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182B ILE* 4.9 3.5 - - + +
183B ASN 4.9 1.6 + - - -
185B ILE* 3.8 20.6 - - + +
192B ILE* 1.3 78.0 - - - +
194B MET* 1.3 77.9 + - - +
195B LYS* 4.5 15.1 - - + +
209B GLY* 4.0 10.7 - - - -
210B CYS* 2.9 29.1 + - - +
211B LEU* 4.2 6.0 - - + +
261B HIS 4.4 0.2 - - - +
262B LEU* 4.2 16.6 - - - +
263B GLY 4.5 4.5 + - - -
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Residues in contact with MET 194 (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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192B ILE 3.8 0.4 + - - -
193B GLN* 1.3 79.8 + - - +
195B LYS* 1.3 63.1 + - - +
196B GLY 3.6 15.3 - - - +
197B VAL* 3.9 7.6 - - + -
206B CYS* 3.2 2.2 - - - -
210B CYS* 2.7 44.7 + - - +
211B LEU 4.0 3.4 - - - +
212B ALA* 4.2 10.5 - - + -
260B PHE* 3.7 25.4 - - + -
261B HIS 3.4 13.0 - - - +
262B LEU* 3.6 20.6 - - + -
299B TRP* 3.3 52.7 - - + +
301B LEU* 5.1 2.2 - - + -
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Residues in contact with LYS 195 (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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193B GLN* 4.5 14.8 - - + +
194B MET* 1.3 75.5 - - - +
196B GLY* 1.3 55.6 + - - +
203B THR* 5.4 0.9 - - - +
206B CYS 3.5 9.0 - - - +
207B GLU* 4.9 8.2 - - - +
209B GLY* 4.3 7.0 - - - +
261B HIS* 2.8 32.0 + - + +
263B GLY 6.0 1.6 - - - +
264B GLY* 5.6 9.4 - - - +
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Residues in contact with GLY 196 (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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194B MET* 3.6 2.1 - - - +
195B LYS* 1.3 78.6 - - - +
197B VAL* 1.3 68.9 + - - +
198B SER* 4.1 0.9 - - - -
203B THR* 4.4 9.4 - - - -
205B LEU 3.7 3.8 - - - -
206B CYS* 3.2 21.9 + - - -
259B SER 3.7 0.2 - - - +
260B PHE* 3.6 0.9 - - - -
261B HIS* 3.0 32.4 + - - -
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Residues in contact with VAL 197 (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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194B MET* 3.9 18.8 - - + -
196B GLY* 1.3 79.6 - - - +
198B SER* 1.3 63.8 + - - +
203B THR* 3.8 0.9 - - - +
204B LEU* 2.9 27.0 + - + +
205B LEU* 3.3 20.8 + - + +
206B CYS* 4.3 5.6 - - + -
231B LEU* 5.1 6.5 - - + -
258B ILE* 4.1 13.0 - - + -
259B SER 3.2 5.8 - - - +
260B PHE* 3.8 34.1 - - + -
299B TRP* 3.9 28.9 - - + -
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Residues in contact with SER 198 (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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196B GLY 5.0 0.2 - - - -
197B VAL* 1.3 75.1 + - - +
199B VAL* 1.3 60.9 + - - +
200B GLY 4.0 13.5 - - - -
201B SER 4.8 1.9 + - - -
202B SER 3.2 13.5 - - - -
203B THR* 3.3 21.8 + - - +
257B ASP 3.9 0.2 - - - +
258B ILE* 3.3 10.0 - - - +
259B SER* 2.7 46.0 + - - +
261B HIS* 4.1 17.4 + - - -
266B GLU* 5.1 1.6 - - - -
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Residues in contact with VAL 199 (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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198B SER* 1.3 73.4 - - - +
200B GLY* 1.3 64.4 + - - +
201B SER 3.2 0.2 + - - -
202B SER* 3.0 25.8 + - - +
204B LEU* 3.7 20.6 - - + +
231B LEU* 3.6 31.6 - - + -
234B ALA* 4.0 18.6 - - + +
235B LEU* 4.0 8.7 - - + -
256B PRO* 3.2 32.5 - - + -
257B ASP 3.4 6.3 - - - +
258B ILE* 4.6 2.5 - - + -
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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