Contacts of the strand formed by residues 271 - 282 (chain A) in PDB entry 5C58
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 GLY 271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A GLY* 3.3 0.5 - - - -
268A ASN* 2.8 32.3 + - - +
269A GLU 3.4 2.0 - - - -
270A THR* 1.3 85.4 + - - +
272A ASP* 1.3 66.8 + - - +
332A GLY 3.1 15.0 - - - -
333A TRP* 4.2 4.0 - - - -
334A ASN* 4.3 3.8 + - - -
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Residues in contact with ASP 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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233A ALA* 3.3 23.3 - - + +
237A LEU* 4.1 14.4 - - + -
266A LEU 3.4 12.1 - - - +
267A GLY* 3.7 6.1 - - - -
268A ASN 5.4 1.9 - - - +
271A GLY* 1.3 76.6 - - - +
273A ILE* 1.3 65.3 + - - +
330A LYS* 4.5 4.2 - - - +
331A VAL* 3.8 6.2 - - - +
332A GLY* 3.0 29.8 + - - +
334A ASN* 4.3 2.1 + - - +
340A ARG* 3.1 37.3 + - - -
342A GLN* 5.1 0.2 - - - +
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Residues in contact with ILE 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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233A ALA* 4.5 1.6 - - - +
264A LEU 4.0 0.5 - - - +
265A ALA* 3.3 6.2 - - - +
266A LEU* 2.8 67.3 + - + +
272A ASP* 1.3 78.8 - - - +
274A LEU* 1.3 68.5 + - - +
275A LEU* 4.1 28.5 - - + -
329A ALA* 5.4 0.9 - - + -
330A LYS 3.3 20.2 - - - +
331A VAL* 3.6 23.3 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A VAL* 3.8 19.3 - - + +
232A SER 4.4 0.7 - - - +
233A ALA* 4.0 26.0 - - + +
236A PHE* 4.6 1.1 - - + -
263A ILE* 3.8 16.8 - - + -
264A LEU 3.3 15.7 - - - +
265A ALA* 3.7 15.9 - - + -
273A ILE* 1.3 73.6 - - - +
275A LEU* 1.3 64.6 + - - +
276A ALA* 4.2 11.0 - - + -
328A LEU* 3.8 33.7 - - + -
329A ALA* 3.2 7.3 - - - -
330A LYS* 2.8 50.5 + - + +
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Residues in contact with LEU 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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262A GLY 4.7 0.2 - - - -
263A ILE* 3.4 1.0 - - - +
264A LEU* 2.6 58.0 + - + +
273A ILE* 4.1 23.9 - - + -
274A LEU* 1.3 82.0 - - - +
276A ALA* 1.3 60.8 + - - +
328A LEU 3.6 1.6 - - - +
329A ALA* 3.9 19.5 - - + -
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Residues in contact with ALA 276 (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 LEU* 4.0 13.2 - - + -
231A VAL* 5.8 0.2 - - + -
262A GLY 3.2 11.2 - - - +
263A ILE* 3.8 22.0 - - + -
274A LEU* 4.2 6.7 - - + -
275A LEU* 1.3 76.7 - - - +
277A ALA* 1.3 64.1 + - - +
327A ARG* 3.7 3.8 - - - +
328A LEU* 2.9 45.9 + - + +
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Residues in contact with ALA 277 (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 LEU* 4.3 3.5 - - - +
261A SER* 3.2 5.1 - - - -
262A GLY* 2.8 34.4 + - - +
276A ALA* 1.3 77.1 - - - +
278A SER* 1.3 61.7 + - - +
279A GLU* 5.9 0.7 - - + -
326A SER 3.3 6.7 - - - -
327A ARG* 3.4 28.7 - - - +
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Residues in contact with SER 278 (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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199A ASP* 2.8 38.0 + - - +
201A GLU* 4.0 7.2 - - - -
202A LEU* 3.6 8.4 - - - +
260A GLY 3.3 11.9 - - - -
261A SER* 3.7 10.5 - - - +
277A ALA* 1.3 76.2 - - - +
279A GLU* 1.3 71.0 + - - +
325A HIS* 3.7 4.0 - - - -
326A SER* 3.1 37.9 + - - +
327A ARG* 4.2 0.5 + - - -
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Residues in contact with GLU 279 (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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258A PHE* 3.6 25.6 - - + +
259A ILE* 3.5 2.4 - - - -
260A GLY 2.8 34.5 + - - +
277A ALA* 5.9 0.9 - - + -
278A SER* 1.3 76.3 - - - +
280A ARG* 1.3 66.5 + - - +
281A HIS* 2.9 20.0 + - + +
324A MET 3.9 1.3 - - - +
325A HIS* 2.6 30.6 + - - -
327A ARG* 2.5 32.3 + - - +
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Residues in contact with ARG 280 (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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136A ALA* 3.0 34.9 + - - +
137A ARG 3.9 12.5 + - - -
138A HIS 5.7 2.2 - - - -
139A ALA* 6.2 1.3 - - - -
199A ASP* 2.9 40.8 + - - +
200A SER* 3.8 13.9 + - - -
201A GLU* 4.2 7.3 + - - +
258A PHE 3.5 2.7 - - - -
259A ILE* 3.6 37.1 - - + +
279A GLU* 1.3 76.9 - - - +
281A HIS* 1.3 65.6 + - - +
282A LEU* 4.2 5.6 - - + +
322A TYR* 3.9 11.2 + - + +
323A ARG* 3.1 7.6 - - - +
324A MET* 3.0 60.0 + - + -
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Residues in contact with HIS 281 (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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257A HIS* 3.2 19.5 + - + +
258A PHE* 2.8 48.0 + + + +
279A GLU* 2.9 31.5 + - + +
280A ARG* 1.3 79.5 - - - +
282A LEU* 1.3 65.6 + - - +
322A TYR 3.9 2.5 - - - -
323A ARG* 4.0 17.9 - - + +
325A HIS* 3.6 23.0 - + - -
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Residues in contact with LEU 282 (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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137A ARG* 3.3 55.6 - - + +
255A GLY 3.2 15.3 - - - +
256A THR* 3.7 23.1 - - + -
257A HIS* 4.3 3.8 - - - +
259A ILE* 4.2 12.3 - - + -
280A ARG* 4.6 9.2 - - + +
281A HIS* 1.3 83.8 - - - +
283A GLY* 1.3 62.8 + - - +
321A HIS* 3.1 5.1 - - - +
322A TYR* 3.0 60.0 + - + +
853A ARG* 5.3 0.2 - - - +
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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