Contacts of the strand formed by residues 191 - 196 (chain B) in PDB entry 1QQG
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 THR 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B CYS 3.8 0.4 - - - +
187B LEU* 3.5 7.8 - - - +
188B THR* 2.7 58.4 + - - +
190B LYS* 1.3 91.4 - - + +
192B ILE* 1.3 65.3 + - - +
193B SER* 4.2 4.7 + - - -
205B VAL* 4.1 15.4 - - + +
206B LEU 3.2 13.5 - - - +
207B GLN* 3.3 28.0 - - - +
208B LEU* 3.9 4.4 - - - +
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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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185B LEU* 3.3 32.1 - - + -
186B CYS 3.4 3.1 - - - -
187B LEU* 3.6 20.4 - - + -
191B THR* 1.3 73.2 - - - +
193B SER* 1.3 66.0 + - - +
194B PHE* 4.4 8.8 + - + -
204B VAL 4.2 0.5 - - - +
206B LEU* 2.8 43.8 + - + +
208B LEU* 3.8 6.7 - - + +
211B ILE* 3.9 17.5 - - + -
223B ILE* 3.9 17.5 - - + -
253B ILE* 3.7 39.0 - - + -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PHE* 4.5 11.1 - - - -
184B ARG 3.3 1.8 - - - +
185B LEU* 3.4 4.3 - - - -
186B CYS* 2.9 40.6 + - - -
191B THR* 4.7 4.5 + - - -
192B ILE* 1.3 76.1 - - - +
194B PHE* 1.3 63.5 + - - +
195B VAL* 3.9 9.9 - - - -
202B ALA* 4.3 13.2 - - - +
204B VAL 3.5 8.5 - - - -
205B VAL* 3.7 20.8 - - - +
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Residues in contact with PHE 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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166B VAL* 4.7 2.5 - - + -
168B LEU* 4.3 20.0 - - + -
179B LEU* 5.0 0.7 - - + -
183B TYR* 4.1 16.6 - - + -
184B ARG 3.5 2.0 - - - -
185B LEU* 3.8 35.0 - - + -
192B ILE* 4.7 3.8 - - + -
193B SER* 1.3 77.4 - - - +
195B VAL* 1.3 61.7 + - - +
196B LYS 4.0 0.2 - - - -
202B ALA* 3.8 0.7 - - - -
203B ALA* 2.9 31.1 + - + +
204B VAL* 3.0 33.6 + - + -
206B LEU* 3.9 15.9 - - + -
223B ILE* 4.3 7.4 - - + -
236B PHE* 3.8 32.8 - + - -
238B MET* 3.6 31.6 - - + -
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Residues in contact with VAL 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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70B PHE* 6.1 4.7 - - + -
160B PHE* 5.1 7.9 - - + -
183B TYR* 3.8 1.1 - - - -
184B ARG* 2.6 45.5 + - + +
186B CYS* 4.0 22.0 - - + -
193B SER* 4.5 7.2 - - - -
194B PHE* 1.3 74.1 - - - +
196B LYS* 1.3 65.9 + - - +
199B SER 3.6 23.8 - - - +
200B GLU 4.6 5.8 - - - +
201B ALA 3.9 13.0 - - - +
202B ALA* 4.2 20.2 - - + +
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Residues in contact with LYS 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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180B ILE 5.8 2.7 - - - -
182B ILE 3.9 9.2 + - - +
183B TYR* 3.4 41.6 - - + +
184B ARG* 5.4 0.5 + - - -
194B PHE 4.0 0.4 + - - -
195B VAL* 1.3 75.4 - - - +
197B LEU* 1.3 84.4 + - - +
198B ASN* 4.1 12.5 - - - +
199B SER* 2.9 40.0 + - - +
201B ALA 4.6 2.4 + - - +
203B ALA* 5.1 2.8 - - + +
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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