Contacts of the strand formed by residues 262 - 275 (chain A) in PDB entry 1S8B
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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233A GLU* 3.4 25.4 - - - +
234A GLU* 2.4 62.1 - - + +
235A LYS* 4.1 16.2 - - + -
257A LYS* 5.6 3.4 - - - +
260A GLU* 4.3 2.7 - - + +
261A ASP* 1.3 91.6 + - - +
263A GLU* 1.4 82.7 + - + +
264A ILE* 5.1 2.5 - - + -
297A PRO* 4.2 7.6 + - - +
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Residues in contact with GLU 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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234A GLU 3.0 14.6 - - - +
235A LYS* 3.6 9.1 - - + +
236A LYS 3.2 15.2 + - - +
257A LYS* 6.1 1.1 - - - +
262A ILE* 1.4 91.9 - - + +
264A ILE* 1.3 76.6 + - - +
265A ILE* 2.9 43.7 - - + +
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Residues in contact with ILE 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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227A ILE* 5.8 2.9 - - + -
230A LEU* 3.5 9.4 - - + -
234A GLU* 5.0 2.0 - - + -
236A LYS* 3.2 49.4 - - + +
255A GLN* 4.1 29.2 - - + +
257A LYS* 3.6 25.8 - - - +
262A ILE* 5.1 0.2 - - + -
263A GLU* 1.3 84.8 - - - +
265A ILE* 1.3 67.7 + - - +
267A ILE* 5.1 19.5 - - + +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS* 5.1 5.4 - - - +
236A LYS 2.9 7.5 + - - +
237A GLU* 3.0 64.7 - - + +
238A GLN 3.2 0.3 + - - -
263A GLU* 2.9 49.6 - - + +
264A ILE* 1.3 71.4 - - - +
266A PRO* 1.4 79.6 - - + +
267A ILE* 3.6 7.9 - - - +
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Residues in contact with PRO 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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4A PRO* 5.3 0.9 - - - +
237A GLU* 3.8 15.5 - - - +
238A GLN* 2.7 34.1 + - - +
239A THR 3.1 22.3 + - - +
240A ILE* 5.6 0.5 - - - +
265A ILE* 1.4 102.8 - - + +
267A ILE* 1.3 60.7 + - - +
268A GLN 4.4 0.2 + - - -
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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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227A ILE* 6.3 4.0 - - + -
236A LYS* 5.5 2.7 - - + +
237A GLU* 5.5 1.3 - - - -
239A THR* 3.2 24.0 - - + +
255A GLN* 4.4 16.8 - - + +
264A ILE* 5.1 18.2 - - + +
265A ILE* 3.9 18.2 - - - +
266A PRO* 1.3 83.5 - - - +
268A GLN* 1.3 63.4 + - - +
269A GLU* 4.4 14.0 + - + +
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Residues in contact with GLN 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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239A THR 3.0 6.3 + - - -
240A ILE* 3.3 22.2 - - + +
241A GLU 2.9 27.0 + - - +
242A ILE* 5.2 0.7 - - + -
266A PRO 4.3 0.2 - - - -
267A ILE* 1.3 76.3 + - - +
269A GLU* 1.3 74.4 + - - +
270A GLU* 3.9 28.6 - - + +
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Residues in contact with GLU 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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239A THR* 4.4 9.5 - - - +
240A ILE 4.4 0.5 - - - -
241A GLU* 2.4 61.4 + - - +
253A SER* 4.4 9.8 + - - +
267A ILE* 4.2 13.9 + - + +
268A GLN* 1.3 87.2 + - - +
270A GLU* 1.3 59.9 + - - +
272A GLU* 3.2 29.2 - - - +
281A GLU* 5.6 9.2 - - - +
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Residues in contact with GLU 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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241A GLU 3.0 7.3 + - - +
242A ILE* 2.7 66.9 - - + +
268A GLN* 4.4 21.4 - - + +
269A GLU* 1.3 75.6 - - - +
271A GLU* 1.3 77.9 + - + +
272A GLU* 3.6 3.2 - - - +
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Residues in contact with GLU 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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242A ILE* 4.0 8.1 - - + -
243A LYS* 2.9 55.2 + - + +
244A GLU 3.1 2.6 + - - -
270A GLU* 1.3 84.4 - - + +
272A GLU* 1.3 60.4 + - - +
273A GLU* 3.5 19.4 - - - +
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Residues in contact with GLU 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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244A GLU* 2.6 51.9 - - + +
252A THR* 3.2 29.7 + - + +
253A SER* 4.1 5.4 - - - -
269A GLU* 3.2 29.6 - - - +
270A GLU 4.2 9.6 - - - +
271A GLU* 1.3 76.4 - - - +
273A GLU* 1.3 67.8 + - - +
281A GLU* 4.2 6.9 - - - +
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Residues in contact with GLU 273 (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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243A LYS* 4.5 13.4 + - - -
244A GLU 2.9 13.3 + - - +
245A GLU* 2.6 33.2 - - - +
246A VAL* 2.8 28.6 + - - +
271A GLU* 3.5 26.9 - - - +
272A GLU* 1.3 82.2 - - - +
274A GLU* 1.3 61.2 + - - +
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Residues in contact with GLU 274 (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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224A LYS* 3.3 1.0 - - - -
245A GLU* 5.0 1.3 - - - -
246A VAL* 3.2 14.8 - - + -
251A GLU 3.1 1.0 - - - -
252A THR* 2.8 40.6 + - + +
272A GLU 5.8 0.2 - - - -
273A GLU* 1.3 73.7 - - - +
275A THR* 1.3 75.2 + - - +
277A THR* 2.5 47.8 + - + +
279A PHE 3.2 6.3 - - - +
280A PRO* 3.2 19.1 - - - +
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Residues in contact with THR 275 (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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245A GLU* 4.9 6.1 + - - -
246A VAL 3.1 5.7 + - - +
247A VAL* 3.4 13.3 - - + +
248A GLY 2.9 23.2 + - - -
274A GLU* 1.3 85.0 + - - +
276A GLU* 1.3 72.0 + - + +
277A THR* 3.2 2.9 + - - +
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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