Contacts of the strand formed by residues 262 - 272 (chain A) in PDB entry 5JAU
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 ILE 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LYS* 3.7 15.9 + - - +
144A TYR 3.4 8.3 - - - +
146A LEU* 4.3 19.1 - - + -
173A ILE* 3.6 37.0 - - + -
236A ILE* 3.8 27.4 - - + -
237A LEU* 4.2 13.9 - - + -
240A ASP* 2.9 30.1 + - + +
258A LEU* 4.7 4.7 - - + +
261A SER* 1.3 82.8 - - - +
263A ASP* 1.4 73.9 + - - +
264A ARG* 3.1 23.0 + - - +
267A ILE* 5.2 1.6 - - + -
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Residues in contact with ASP 263 (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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143A LYS* 3.9 24.8 - - + +
144A TYR 2.7 28.3 + - - +
145A PRO* 4.0 4.5 - - - +
262A ILE* 1.4 71.1 - - - +
264A ARG* 1.3 60.4 + - - +
265A GLU* 3.3 4.0 + - - +
266A LYS* 2.9 67.5 + - + +
267A ILE* 4.7 0.2 - - - +
398A LEU* 5.3 0.3 - - - +
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Residues in contact with ARG 264 (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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143A LYS* 5.5 0.6 - - - +
237A LEU* 2.9 62.6 + - + +
238A ASP* 5.7 0.6 + - - -
240A ASP* 2.9 31.6 + - - +
241A HIS* 3.7 15.5 - - - +
262A ILE* 3.1 17.0 + - - +
263A ASP* 1.3 71.7 + - - +
265A GLU* 1.3 59.5 + - + +
266A LYS 3.4 0.2 - - - -
267A ILE* 3.1 24.3 - - - +
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Residues in contact with GLU 265 (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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263A ASP* 3.1 3.3 + - - +
264A ARG* 1.3 78.2 - - + +
266A LYS* 1.3 69.3 + - + +
267A ILE* 3.4 7.7 + - - -
290A ARG* 3.3 58.6 + - - +
396A LEU* 4.9 1.0 - - - +
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Residues in contact with LYS 266 (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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145A PRO* 3.4 19.4 - - + +
146A LEU 2.9 27.0 + - - +
263A ASP* 2.9 44.7 + - + +
264A ARG 3.4 0.2 - - - -
265A GLU* 1.3 82.2 - - + +
267A ILE* 1.3 60.4 + - - +
396A LEU* 3.0 42.8 + - + +
397A GLY* 3.8 14.5 + - - -
398A LEU* 3.5 19.3 - - + +
399A HIS* 5.7 4.3 - - - -
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Residues in contact with ILE 267 (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 LEU* 3.4 21.5 - - + +
148A VAL* 5.0 0.2 - - + -
233A LEU* 3.7 38.6 - - + -
237A LEU* 4.3 12.3 - - + -
262A ILE* 5.2 0.7 - - + -
263A ASP 4.7 1.3 - - - +
264A ARG* 3.1 27.6 - - - +
265A GLU* 3.4 6.3 + - - -
266A LYS* 1.3 80.2 - - - +
268A ALA* 1.3 62.0 - - - +
288A ARG* 3.8 19.1 - - + +
289A PHE* 3.6 27.1 - - + -
290A ARG* 2.9 26.8 + - - +
396A LEU* 3.5 10.7 - - - +
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Residues in contact with ALA 268 (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 LEU 2.9 9.9 + - - +
147A VAL* 3.4 9.6 - - + -
148A VAL 2.9 24.1 + - - -
266A LYS 4.3 0.2 + - - -
267A ILE* 1.3 75.8 - - - +
269A VAL* 1.3 63.2 + - - +
270A ILE* 4.3 1.8 - - + -
289A PHE* 3.7 9.2 - - - -
291A CYS* 3.5 17.9 - - - +
292A GLY* 5.4 0.2 - - - -
392A LEU* 3.5 32.3 - - + -
396A LEU* 4.2 4.5 - - + -
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Residues in contact with VAL 269 (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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148A VAL 3.3 10.8 - - - +
150A SER* 5.5 1.3 - - - -
229A CYS* 4.5 15.9 - - - -
268A ALA* 1.3 73.8 - - - +
270A ILE* 1.3 68.4 + - - +
279A VAL* 3.8 41.8 - - + +
282A THR* 4.2 16.2 - - + -
283A LEU* 3.9 22.7 - - + -
289A PHE* 3.6 22.2 - - + -
291A CYS 3.3 3.0 + - - +
292A GLY* 3.2 7.4 - - - -
293A ILE 3.1 21.1 + - - -
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Residues in contact with ILE 270 (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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147A VAL* 3.7 37.0 - - + -
148A VAL 2.9 6.3 + - - +
149A PHE* 3.2 26.3 - - + -
150A SER* 2.8 23.0 + - - -
163A ILE* 5.3 2.9 - - + -
167A LEU* 4.1 11.7 - - + -
268A ALA* 4.8 2.5 - - + -
269A VAL* 1.3 79.8 - - - +
271A GLY* 1.3 62.6 + - - +
279A VAL* 3.4 5.9 - - - +
293A ILE* 3.3 43.5 - - + +
295A LEU* 4.0 16.4 - - + -
388A SER* 5.1 3.8 - - - +
392A LEU* 4.0 12.8 - - + -
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Residues in contact with GLY 271 (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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149A PHE* 4.2 5.4 - - - -
150A SER 3.2 14.4 - - - -
270A ILE* 1.3 81.2 - - - +
272A HIS* 1.3 55.4 + - - -
275A GLY 3.5 10.8 - - - -
276A GLY* 3.4 12.4 - - - -
279A VAL* 3.3 2.0 - - - +
293A ILE 3.2 4.6 + - - -
294A ALA 3.7 0.2 - - - -
295A LEU* 2.8 34.5 + - - +
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Residues in contact with HIS 272 (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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149A PHE* 4.1 3.2 - - + -
150A SER 3.1 6.5 + - - -
152A GLY* 3.5 10.4 + - - -
160A TYR* 2.7 45.7 + + + +
271A GLY* 1.3 70.3 - - - -
273A SER* 1.4 72.5 + - - +
274A PHE 3.2 0.3 + - - -
275A GLY* 2.8 21.3 + - - -
276A GLY 3.4 2.7 - - - -
295A LEU* 3.2 28.5 - - + +
296A ASP* 4.1 2.9 - - + -
351A HIS* 2.9 39.9 + + - -
352A GLN* 4.4 2.9 - - - -
354A PHE* 3.5 24.4 - + + -
355A ALA* 4.7 4.5 - - + -
504A 6HU 3.5 23.1 + - - -
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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