Contacts of the strand formed by residues 282 - 293 (chain A) in PDB entry 4X8G
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 ALA 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A LEU* 3.2 5.1 - - - -
273A ASP* 2.7 50.3 + - + +
280A PRO 3.5 4.4 + - - +
281A GLU* 1.3 73.0 - - - +
283A VAL* 1.3 65.2 + - - +
284A VAL* 4.7 0.4 - - + -
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Residues in contact with VAL 283 (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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270A SER* 5.1 2.2 - - - -
271A LEU 4.1 3.6 - - - +
272A LEU* 3.6 20.6 - - + -
281A GLU 5.1 2.7 - - - +
282A ALA* 1.3 76.3 - - - +
284A VAL* 1.3 65.2 + - - +
285A PHE 4.0 9.9 - - - +
286A GLN* 4.1 29.6 - - + +
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Residues in contact with VAL 284 (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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5A THR* 5.6 5.7 - - - -
18A VAL* 4.4 29.2 - - + +
20A VAL* 5.8 2.2 - - + -
197A HIS* 4.4 8.7 - - + +
271A LEU* 2.8 31.8 + - + +
272A LEU 4.2 1.6 - - - -
273A ASP* 3.8 32.8 - - + +
282A ALA* 3.9 0.9 - - + +
283A VAL* 1.3 79.3 - - - +
285A PHE* 1.3 60.2 + - + +
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Residues in contact with PHE 285 (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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3A GLN* 6.0 1.8 - - - -
20A VAL* 3.7 37.7 - - + -
23A THR* 3.6 27.6 - - + -
115A ILE* 3.6 37.9 - - + -
269A ILE* 4.9 2.5 - - + -
270A SER* 3.3 4.0 - - - -
271A LEU* 2.7 44.5 + - + +
283A VAL* 3.9 2.8 - - - +
284A VAL* 1.3 83.6 - - + +
286A GLN* 1.3 79.1 + - - +
287A ASP* 3.8 24.9 - - + -
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Residues in contact with GLN 286 (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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202A HIS* 3.8 18.2 + - - -
268A THR* 4.2 7.3 - - + +
269A ILE 3.3 5.4 - - - +
270A SER* 3.0 28.6 + - - +
283A VAL* 4.1 17.6 - - + +
285A PHE* 1.3 93.3 - - - +
287A ASP* 1.3 63.0 + - - +
288A SER* 5.7 0.7 - - - +
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Residues in contact with ASP 287 (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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115A ILE 4.5 3.6 - - - +
116A SER* 4.7 0.2 - - - -
117A LEU* 3.6 23.0 + - - +
130A THR* 2.9 28.5 + - - -
268A THR* 3.4 0.5 - - - +
269A ILE* 2.8 48.5 + - + +
285A PHE* 3.8 18.6 - - + -
286A GLN* 1.3 77.5 - - - +
288A SER* 1.3 74.3 + - - +
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Residues in contact with SER 288 (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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117A LEU* 4.6 1.8 - - - -
130A THR* 4.3 8.0 - - - +
137A ARG* 4.6 22.3 - - - +
266A THR* 4.1 13.6 - - - +
267A LEU 3.2 10.8 - - - -
268A THR* 2.9 24.7 + - - +
286A GLN* 5.4 0.7 - - - +
287A ASP* 1.3 89.1 + - - +
289A VAL* 1.3 70.9 + - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.0 31.6 - - + +
118A CYS 4.8 0.4 - - - -
119A ALA* 4.2 22.2 - - + +
121A ILE* 5.0 6.3 - - + -
130A THR* 4.1 10.1 - - + -
137A ARG* 5.8 1.1 - - - +
148A ALA* 6.2 0.4 - - + -
183A MET* 3.7 29.4 - - + -
265A ILE 3.8 0.5 - - - +
266A THR* 3.5 2.1 - - - -
267A LEU* 3.0 35.9 + - + +
288A SER* 1.3 80.7 - - - +
290A VAL* 1.3 65.7 + - - +
291A PHE* 3.8 15.5 + - + -
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Residues in contact with VAL 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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121A ILE* 5.9 2.1 - - - +
137A ARG* 3.3 36.9 - - + +
138A THR 5.1 0.7 - - - +
139A TRP* 3.5 33.5 - - + +
147A GLY* 4.2 2.1 - - - -
148A ALA* 3.4 23.2 + - - +
264A LEU* 4.3 12.8 - - + -
265A ILE 3.3 8.5 - - - +
266A THR* 3.9 24.2 - - + +
289A VAL* 1.3 76.6 - - - +
291A PHE* 1.3 70.0 + - - +
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Residues in contact with PHE 291 (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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119A ALA* 4.0 18.8 - - + -
120A ASP 5.7 0.2 - - - -
139A TRP* 4.3 1.6 - - - -
148A ALA* 3.5 24.0 - - + -
149A ILE 4.2 4.0 - - - -
150A LEU* 4.0 31.4 - - + -
181A SER* 3.9 22.2 - - - -
182A LEU 4.7 3.1 - - - -
183A MET* 4.4 8.3 - - + -
251A VAL* 4.4 15.3 - - + -
264A LEU* 3.4 6.8 - - - +
265A ILE* 2.6 51.4 + - + +
267A LEU* 3.9 22.9 - - + -
289A VAL* 3.8 29.6 - - + -
290A VAL* 1.3 77.6 - - - +
292A ARG* 1.3 59.4 + - - +
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Residues in contact with ARG 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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139A TRP* 3.3 52.2 + - + +
141A TRP* 3.6 35.0 - - - +
148A ALA 3.0 8.0 + - - +
149A ILE* 3.6 5.0 - - - +
150A LEU* 2.8 25.5 + - - +
262A PRO* 3.3 28.3 + - - +
263A GLY* 3.3 7.9 + - - +
264A LEU* 3.6 31.9 - - + +
291A PHE* 1.3 73.6 - - - +
293A VAL* 1.3 72.6 + - - +
294A ALA 3.4 0.7 + - - -
455A GLN* 4.4 10.7 + - - +
658A TRP* 3.9 14.5 - - + -
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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
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150A LEU* 3.2 11.9 - - + +
152A VAL* 3.5 31.2 - - + -
210A LYS 5.8 0.4 - - - +
253A ALA* 4.1 14.8 - - + -
255A ALA 3.6 11.0 - - - +
257A PRO* 3.7 19.5 - - + +
261A PHE* 3.6 34.1 - - + -
263A GLY 2.8 15.3 + - - +
265A ILE* 4.2 14.1 - - + -
292A ARG* 1.3 79.4 + - - +
294A ALA* 1.3 68.7 + - - +
295A PRO* 3.5 5.0 - - - +
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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