Contacts of the strand formed by residues 181 - 187 (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 GLY 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B VAL 3.5 0.7 - - - +
167B ILE* 3.2 11.0 - - - -
168B LEU* 2.7 40.1 + - - +
180B ILE* 1.3 81.0 - - - +
182B ILE* 1.3 68.9 + - - -
183B TYR* 3.6 1.3 + - - -
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Residues in contact with ILE 182 (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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165B GLN* 3.8 36.8 - - + +
166B VAL 3.5 2.0 - - - +
167B ILE* 3.7 31.9 - - + -
180B ILE 4.1 0.8 + - - -
181B GLY* 1.3 71.6 - - - -
183B TYR* 1.3 68.7 + - - +
196B LYS* 3.9 5.5 + - - +
197B LEU* 3.2 48.7 + - + +
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Residues in contact with TYR 183 (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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165B GLN* 3.6 4.9 - - - +
166B VAL* 2.9 40.1 + - + -
168B LEU* 3.7 22.9 - - + -
178B ASN 4.1 3.1 + - - -
179B LEU* 3.5 30.6 - - + +
180B ILE 3.3 32.9 + - - -
181B GLY 4.0 4.7 - - - -
182B ILE* 1.3 81.3 - - - +
184B ARG* 1.3 66.8 + - - +
185B LEU 4.2 0.2 - - - -
194B PHE* 4.1 13.5 - - + -
195B VAL 3.4 9.9 - - - +
196B LYS* 3.4 46.6 - - + +
197B LEU 4.2 0.4 - - - +
203B ALA* 3.8 21.7 - - + +
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Residues in contact with ARG 184 (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* 4.1 11.4 - - + -
87B TYR* 3.7 12.9 - - + -
88B THR 2.4 28.8 + - - -
89B ARG* 3.3 21.0 + - - +
91B GLU 3.1 20.4 + - - +
163B VAL* 3.8 18.6 - - + -
164B TRP 3.3 9.9 - - - +
165B GLN* 2.7 38.0 + - - -
183B TYR* 1.3 82.0 - - - +
185B LEU* 1.3 60.8 + - - +
186B CYS* 3.4 15.2 + - - -
193B SER 3.3 5.4 - - - +
194B PHE* 3.5 2.3 - - - -
195B VAL* 2.6 41.9 + - + +
196B LYS 5.4 0.2 - - - -
197B LEU* 3.3 25.7 - - - +
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Residues in contact with LEU 185 (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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163B VAL* 3.3 3.5 - - - -
164B TRP* 2.7 57.3 + - + +
166B VAL* 4.5 6.1 - - + +
183B TYR 4.2 1.0 + - - -
184B ARG* 1.3 69.2 - - - +
186B CYS* 1.3 64.2 + - - +
187B LEU* 4.3 0.7 - - + +
192B ILE* 3.3 31.9 - - + -
193B SER 3.4 3.6 - - - -
194B PHE* 3.8 14.8 - - + -
221B PHE* 4.0 12.1 - - + -
223B ILE* 4.2 5.6 - - + -
238B MET* 3.8 20.6 - - + -
249B MET* 3.5 29.6 - - + -
253B ILE* 4.1 9.0 - - + -
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Residues in contact with CYS 186 (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* 4.4 5.6 - - - -
160B PHE* 3.5 45.8 - - + -
162B GLU 3.5 4.7 - - - +
163B VAL* 4.2 10.3 - - + -
184B ARG* 3.4 29.6 - - - -
185B LEU* 1.3 76.5 - - - +
187B LEU* 1.3 58.9 + - - +
188B THR* 4.1 0.5 + - - +
191B THR 3.8 1.2 - - - +
192B ILE* 3.4 2.9 - - - -
193B SER* 2.9 39.5 + - - +
195B VAL* 4.0 16.6 - - - -
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Residues in contact with LEU 187 (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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160B PHE* 3.5 1.9 - - - +
161B LYS* 2.7 52.1 + - - +
162B GLU* 2.8 24.6 + - + +
164B TRP* 4.2 10.5 - - + -
185B LEU* 3.9 1.7 + - + -
186B CYS* 1.3 72.7 - - - +
188B THR* 1.3 74.8 + - - +
191B THR 3.5 11.4 - - - +
192B ILE* 3.6 22.4 - - + +
208B LEU* 4.0 16.8 - - + -
252B THR* 4.1 19.7 - - + -
253B ILE* 4.1 19.5 - - + -
256B ALA* 4.2 10.3 - - + -
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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