Contacts of the strand formed by residues 182 - 189 (chain F) in PDB entry 3QS7
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 LEU 182 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173F PHE* 4.1 13.2 - - + -
174F ARG 3.9 3.4 - - - +
175F LYS* 3.9 15.3 - - + +
181F ALA* 1.3 71.8 - - - +
183F VAL* 1.4 66.4 + - - +
196F TRP* 3.7 28.5 - - + -
220F VAL* 3.6 1.4 - - - +
221F LEU* 2.9 35.9 + - + +
224F LEU* 3.7 25.8 - - + +
244F LEU* 3.8 28.0 - - + -
269F TRP* 3.5 38.4 - - + -
314F PHE* 5.2 3.4 - - + -
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Residues in contact with VAL 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 3.5 5.6 - - - -
174F ARG* 2.9 45.2 + - + +
176F MET* 4.0 20.2 - - + +
182F LEU* 1.4 79.2 - - - +
184F CYS* 1.3 68.6 + - - +
185F ILE* 3.7 11.8 + - + +
196F TRP* 4.1 4.7 - - - -
219F LYS* 3.4 12.8 - - + +
220F VAL* 3.8 28.3 - - + -
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Residues in contact with CYS 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F PRO* 3.4 23.1 - - - -
172F TYR 3.6 4.9 - - - -
173F PHE* 4.3 1.3 - - - -
183F VAL* 1.3 72.7 - - - +
185F ILE* 1.4 59.3 + - - +
186F SER* 3.7 5.3 + - - -
194F VAL* 3.6 25.3 - - + +
196F TRP* 3.7 18.9 - - + +
219F LYS* 2.9 15.6 + - - +
231F CYS* 2.0 50.0 - - - -
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Residues in contact with ILE 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ARG 4.3 1.2 - - - +
172F TYR* 2.8 47.2 + - + +
173F PHE 5.2 0.4 - - - -
174F ARG* 3.7 27.6 - - + -
183F VAL* 3.7 14.1 + - + +
184F CYS* 1.4 71.4 - - - +
186F SER* 1.3 57.7 + - - +
187F GLU* 4.2 2.8 + - + +
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Residues in contact with SER 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F ARG 4.0 2.0 - - - -
171F PRO* 3.7 23.8 - - - -
184F CYS* 3.7 6.0 + - - -
185F ILE* 1.3 74.3 - - - +
187F GLU* 1.4 61.9 + - - +
188F SER 4.2 0.3 + - - -
192F PRO* 4.3 11.5 - - - +
194F VAL* 4.2 18.8 - - - +
233F ALA* 3.6 31.0 - - - -
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Residues in contact with GLU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F LEU* 3.7 0.9 - - - +
169F ARG* 2.8 46.9 + - + +
170F ARG 4.7 0.6 + - - -
185F ILE* 4.2 3.4 + - + +
186F SER* 1.4 74.2 - - - +
188F SER* 1.4 64.0 + - - +
192F PRO* 4.8 0.5 - - - +
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Residues in contact with SER 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F THR* 3.3 20.4 - - - -
168F LEU* 3.8 8.3 - - - +
169F ARG 4.6 0.2 - - - +
186F SER 4.2 0.4 + - - -
187F GLU* 1.4 77.5 - - - +
189F VAL* 1.3 67.7 + - - +
190F PRO 3.3 15.1 - - - +
191F GLU* 3.6 8.1 + - - +
192F PRO* 3.7 19.5 - - - +
235F ASN* 3.4 15.5 - - - -
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Residues in contact with VAL 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU* 4.0 17.9 - - + +
165F LEU 3.4 26.7 - - - +
166F TYR* 3.2 16.7 - - + +
167F THR* 2.9 38.3 + - - +
188F SER* 1.3 78.3 - - - +
190F PRO* 1.4 65.0 - - + +
237F LEU* 3.3 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