Contacts of the strand formed by residues 289 - 298 (chain A) in PDB entry 4FO9
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 TYR 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.7 5.5 - - - -
166A LEU* 3.1 45.3 + - + +
168A GLN* 4.9 9.3 + - - +
213A LEU* 5.5 0.7 - - + -
214A CYS* 3.3 18.2 - - - -
215A LEU* 3.8 27.8 - - + +
216A ALA* 4.5 4.4 - - - +
225A ASN* 3.8 18.2 - - + +
226A TYR 3.2 29.7 + - - -
227A PRO* 3.7 27.0 - - + +
228A ASN* 4.9 3.3 + - - -
281A TRP* 5.4 2.2 - + - +
284A GLU* 5.9 4.3 - - + -
287A LYS* 3.8 32.4 - - + +
288A ASN* 1.3 78.7 - - - +
290A SER* 1.3 63.3 + - - +
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Residues in contact with SER 290 (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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146A GLY* 3.6 30.9 + - - -
148A LEU* 5.8 0.4 - - - +
163A PRO* 3.9 3.8 - - - +
164A THR 3.4 26.0 + - - -
165A SER* 4.3 2.2 - - - +
166A LEU* 4.4 2.0 - - - +
212A ARG 4.2 0.2 - - - +
213A LEU* 3.4 7.7 - - - +
214A CYS* 2.9 37.1 + - - -
216A ALA* 4.6 9.6 - - - -
289A TYR* 1.3 76.4 - - - +
291A MET* 1.3 59.9 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ILE* 3.7 27.1 - - + -
162A LYS 3.5 0.5 - - - +
163A PRO* 3.4 1.4 - - - +
164A THR* 3.0 34.6 + - - +
166A LEU* 4.0 9.0 - - + +
179A PHE* 3.6 53.6 - - + -
211A LEU* 4.1 5.8 - - + -
212A ARG 3.4 6.5 - - - +
213A LEU* 3.7 20.9 - - + -
277A ILE* 4.5 5.6 - - + -
279A ILE* 3.8 15.3 - - + -
290A SER* 1.3 72.5 - - - +
292A SER* 1.3 65.3 + - - +
293A VAL* 3.9 21.5 - - + -
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Residues in contact with SER 292 (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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146A GLY 4.6 0.3 + - - -
148A LEU* 3.4 16.6 - - - +
161A ILE 3.3 14.6 - - - -
163A PRO* 3.7 15.9 - - - +
211A LEU* 3.6 0.9 - - - +
212A ARG 3.0 30.0 + - - +
291A MET* 1.3 79.8 - - - +
293A VAL* 1.3 68.2 + - - +
294A TYR* 2.7 35.3 + - - -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.7 1.0 - - - -
160A LEU* 2.7 40.2 + - + -
161A ILE* 2.9 35.8 + - + +
181A PHE* 4.6 8.5 - - + -
209A VAL* 3.7 29.4 - - + -
210A GLN 3.4 8.3 - - - +
211A LEU* 3.8 16.6 - - + -
263A ILE* 4.9 0.2 - - + -
277A ILE* 3.8 24.9 - - + -
291A MET* 3.9 3.4 - - + -
292A SER* 1.3 79.0 - - - +
294A TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN* 4.7 7.0 + - - -
148A LEU* 3.8 13.5 + - + +
156A VAL* 4.0 24.7 - - + -
158A ASP 3.4 7.9 - - - +
159A VAL* 4.1 28.0 - - + -
160A LEU* 4.0 7.2 - - - +
163A PRO* 4.2 9.0 - - + +
209A VAL* 3.5 4.5 - - - +
210A GLN* 2.9 42.8 + - - +
212A ARG* 4.1 27.4 - - - -
292A SER* 2.7 42.3 + - - -
293A VAL* 1.3 76.0 - - - +
295A LEU* 1.3 61.0 + - - +
296A VAL* 3.8 18.8 - - + -
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Residues in contact with LEU 295 (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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156A VAL* 3.7 0.3 - - - -
157A LEU* 2.7 54.2 + - + -
158A ASP* 3.0 22.3 + - + +
160A LEU* 4.1 12.0 - - + +
183A LEU* 4.8 4.0 - - + -
187A GLN* 3.9 35.7 - - + +
190A GLU* 5.2 2.9 - - + -
191A ILE* 4.0 31.4 - - + -
207A VAL* 4.1 10.5 - - + -
208A GLN 3.4 15.3 - - - +
209A VAL* 4.4 7.4 - - + -
294A TYR* 1.3 72.6 - - - +
296A VAL* 1.3 56.8 - - - +
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Residues in contact with VAL 296 (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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154A TYR* 3.7 29.6 - - + -
155A ASP 3.2 11.9 - - - +
156A VAL* 4.5 9.4 - - + -
157A LEU* 4.2 4.7 - - - -
207A VAL* 3.3 7.1 - - - +
208A GLN* 2.9 45.2 + - + +
210A GLN* 3.5 37.2 - - + +
294A TYR* 3.8 15.3 - - + -
295A LEU* 1.3 80.1 - - - +
297A ARG* 1.3 60.5 + - - +
506A UNX 3.9 7.9 - - - -
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Residues in contact with ARG 297 (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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154A TYR* 3.3 5.9 - - - -
155A ASP* 2.9 37.5 + - + +
157A LEU* 4.2 18.8 - - + +
190A GLU* 5.1 2.8 - - - +
194A SER* 5.4 1.2 - - - +
206A THR* 3.3 18.8 + - - +
207A VAL* 3.8 20.9 - - + +
296A VAL* 1.3 74.6 - - - +
298A GLN* 1.3 71.7 + - - +
299A LEU* 3.7 18.2 + - + +
303A MET* 4.6 11.7 - - - -
307A ARG* 6.2 0.2 - - - +
507A UNX 3.7 18.0 - - - -
516A UNX 3.8 15.3 - - - -
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Residues in contact with GLN 298 (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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153A PHE* 3.4 9.4 - - + +
154A TYR* 3.6 31.7 + - + -
198A LEU* 4.1 16.7 - - + +
199A PRO* 4.0 27.2 - - + +
206A THR* 2.9 22.5 + - + +
208A GLN* 2.9 31.5 + - - +
296A VAL* 4.1 1.0 - - - +
297A ARG* 1.3 82.4 - - - +
299A LEU* 1.3 71.8 + - - +
300A THR* 4.3 1.8 + - + +
303A MET* 4.8 3.3 - - - +
378A GLU* 5.5 3.8 + - - +
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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