Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 2FQQ
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 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU 2.8 20.7 + - - -
198A TYR* 4.0 3.1 - - - -
218A PHE* 3.6 19.1 - - - -
224A HIS* 4.1 9.4 - - - -
229A SER* 1.3 77.9 - - - +
231A PHE* 1.3 77.4 + - - +
232A LEU* 3.9 13.0 - - + +
265A LEU* 5.3 0.2 - - + -
273A LEU* 3.7 18.8 - - + -
277A PRO 3.3 3.1 + - - +
278A LYS* 3.7 30.7 - - + -
279A VAL* 3.1 25.1 + - - +
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU 3.9 3.6 + - - -
165A ALA* 3.4 11.5 - - + +
166A LEU 3.0 27.1 + - - +
193A LEU* 3.6 31.6 - - + -
196A LEU* 5.0 2.7 - - + -
198A TYR* 3.3 42.6 - + - -
229A SER* 5.6 0.2 - - - -
230A THR* 1.3 80.7 + - - +
232A LEU* 1.3 65.1 + - - +
233A VAL* 5.1 2.7 - - + -
279A VAL* 3.4 43.3 - - + -
281A ILE* 4.0 20.0 - - + -
357B MET* 4.5 12.3 - - + -
366B VAL* 4.7 6.5 - - + -
398B PHE* 4.4 2.5 - + - -
400B LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 3.4 28.9 - - + +
168A ILE* 6.0 0.2 - - + -
215A LEU* 3.9 27.1 - - + -
218A PHE* 3.8 13.5 - - + -
230A THR* 3.9 24.5 - - + +
231A PHE* 1.3 78.9 - - - +
233A VAL* 1.3 59.3 + - - +
234A PHE* 4.1 16.6 - - + -
261A ILE* 5.3 0.4 - - + -
265A LEU* 4.3 20.6 - - + -
278A LYS* 5.5 1.6 - - + -
279A VAL 2.7 17.4 + - - +
280A ILE* 3.4 16.1 - - + +
281A ILE* 2.7 34.5 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU 2.9 10.5 + - - +
167A ILE* 3.7 31.4 - - + -
168A ILE* 2.8 33.6 + - - +
189A MET* 3.8 32.5 - - + -
193A LEU* 4.4 9.9 - - + -
231A PHE* 5.1 1.1 - - + -
232A LEU* 1.3 80.4 - - - +
234A PHE* 1.3 61.6 + - - +
235A MET* 4.0 25.8 - - + -
281A ILE* 3.2 21.8 - - + +
350B ILE* 5.4 1.8 - - + -
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Residues in contact with PHE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.5 32.5 - - + -
211A MET* 4.7 6.1 - - + -
215A LEU* 3.9 24.9 - - + -
232A LEU* 4.1 12.8 - - + -
233A VAL* 1.3 77.1 - - - +
235A MET* 1.3 61.9 + - - +
236A SER 4.2 0.9 - - - -
243A ILE* 4.3 17.0 - - + -
256A LEU* 3.7 26.2 - - + -
261A ILE* 3.9 29.6 - - + -
280A ILE* 4.0 20.9 - - + -
281A ILE 2.8 9.3 + - - +
282A ILE* 3.5 23.2 - - + -
283A GLN* 2.6 32.8 + - - +
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Residues in contact with MET 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 3.7 28.3 - - + -
168A ILE 3.0 9.8 + - - +
169A CYS* 3.4 27.3 - - + -
170A ASN* 2.8 32.2 + - - -
179A ARG* 3.3 10.6 + - - +
185A ASP* 3.6 24.5 - - - +
186A ILE* 3.8 20.6 - - + +
189A MET* 5.2 1.8 - - + -
233A VAL* 4.0 13.2 - - + -
234A PHE* 1.3 79.4 - - - +
236A SER* 1.3 57.0 + - - +
243A ILE* 5.8 0.2 - - - +
283A GLN* 3.4 30.7 - - + +
350B ILE* 4.2 10.5 - - + -
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASN* 3.4 26.2 + - - +
173A PHE* 3.6 8.3 - - - -
179A ARG* 3.7 22.8 + - - +
234A PHE 4.2 0.4 - - - -
235A MET* 1.3 75.9 - - - +
237A HIS* 1.3 71.5 + - - +
243A ILE* 3.8 15.8 - - - +
244A CYS* 2.9 23.4 + - - +
283A GLN* 2.9 21.2 + - - +
284A ALA* 3.7 4.5 - - - -
285A ALA* 3.9 3.5 + - - +
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.5 29.6 - + - -
176A ILE* 3.7 18.6 - - + +
177A PRO* 2.8 41.2 + - + -
178A ARG 5.4 0.9 - - - -
179A ARG* 3.4 19.4 - - + +
236A SER* 1.3 82.9 + - - +
238A GLY* 1.3 59.5 + - - +
243A ILE* 3.9 4.0 - - - +
244A CYS* 2.9 43.8 + - + -
284A ALA* 4.6 1.2 - - - +
285A ALA* 4.4 15.9 + - + +
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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