Contacts of the strand formed by residues 320 - 331 (chain A) in PDB entry 5E8R
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 GLN 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A VAL* 3.6 5.3 - - - +
239A GLN 3.0 33.6 + - - +
240A GLY* 3.6 1.1 - - - -
241A LEU* 2.7 38.0 + - + +
289A ALA* 4.5 6.5 - - + -
290A ILE 3.7 8.3 - - - +
291A TRP* 3.9 23.8 - - + +
309A THR 2.9 25.3 + - - +
310A SER 3.6 1.6 + - - -
311A PRO* 3.4 26.7 - - + +
315A ALA* 6.3 1.0 - - - +
318A TRP 4.0 4.7 - - - -
319A LYS* 1.3 85.9 + - - +
321A ALA* 1.3 61.8 + - - +
322A LEU* 4.0 11.4 + - + -
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Residues in contact with ALA 321 (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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159A TYR* 5.2 0.7 - - + -
160A GLY* 4.3 20.0 - - - +
236A ILE* 3.7 21.5 - - + -
237A VAL 3.7 5.4 - - - -
238A VAL* 4.7 4.7 - - + +
288A PHE 3.9 0.5 - - - +
289A ALA* 3.4 1.0 - - - -
290A ILE* 2.8 58.4 + - + +
320A GLN* 1.3 71.2 - - - +
322A LEU* 1.3 63.1 + - - +
323A LEU* 4.1 1.3 + - - +
353A LEU* 6.2 0.2 - - + -
373A MET* 5.2 2.2 - - + -
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Residues in contact with LEU 322 (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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196A ILE* 4.7 6.5 - - + -
198A ASP* 3.5 13.9 - - - +
235A GLU 4.3 1.6 - - - +
236A ILE* 3.7 8.7 - - - +
237A VAL* 2.8 46.3 + - + +
239A GLN* 3.8 29.4 - - + +
241A LEU* 3.5 37.0 - - + -
288A PHE 3.4 3.6 - - - +
289A ALA* 3.7 13.9 - - + -
320A GLN* 4.4 2.7 - - + -
321A ALA* 1.3 75.0 - - - +
323A LEU* 1.3 61.5 + - - +
324A TYR* 3.4 37.4 + - + +
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Residues in contact with LEU 323 (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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236A ILE* 3.9 21.5 - - + -
287A GLY* 3.2 3.7 - - - -
288A PHE* 2.6 49.1 + - + +
290A ILE* 4.2 17.0 - - + -
321A ALA 4.6 4.3 - - - +
322A LEU* 1.3 79.8 - - - +
324A TYR* 1.3 63.4 + - - +
325A LEU* 5.1 0.2 - - - +
341A ILE* 3.7 30.3 - - + -
355A VAL* 3.9 12.6 - - + -
357A LEU* 4.6 11.3 - - + +
371A PHE* 3.8 39.1 - - + -
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Residues in contact with TYR 324 (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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196A ILE* 4.8 3.6 - - + -
198A ASP* 2.8 30.9 + - + -
201A LEU* 3.7 35.3 - - + +
230A LEU 4.1 18.2 - - - -
231A MET* 4.3 11.2 - - + +
233A HIS 5.6 2.9 - - - +
235A GLU 5.3 4.3 + - - +
237A VAL* 3.7 34.4 - - + +
239A GLN* 4.2 3.5 + - - -
286A HIS* 3.5 17.5 - - + +
287A GLY* 4.9 0.9 - - - -
322A LEU* 3.4 26.2 + - + +
323A LEU* 1.3 73.9 - - - +
325A LEU* 1.3 68.8 + - - +
357A LEU* 6.3 0.2 - - - -
369A LYS* 3.2 19.0 + - - +
371A PHE* 3.3 19.6 - - + -
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Residues in contact with LEU 325 (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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231A MET* 3.0 22.8 - - + +
285A MET* 3.7 31.0 - - + +
286A HIS 3.1 16.2 + - - +
287A GLY* 3.8 13.0 - - - +
288A PHE* 4.3 12.8 - - + -
323A LEU 3.9 0.2 + - - -
324A TYR* 1.3 78.0 - - - +
326A ASN* 1.3 63.8 + - - +
327A GLU* 3.3 22.2 - - - +
329A VAL* 4.3 15.5 - - + -
357A LEU* 5.5 1.6 - - + -
359A TYR* 3.5 43.7 - - + +
361A VAL* 5.4 2.0 - - + -
364A GLN* 6.3 0.2 - - - +
369A LYS* 3.6 4.3 - - - +
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Residues in contact with ASN 326 (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 THR* 3.9 7.4 - - - +
228A ARG* 5.2 2.1 - - - +
231A MET* 3.6 17.7 - - - +
232A GLY* 4.2 14.1 + - - +
325A LEU* 1.3 74.3 - - - +
327A GLU* 1.3 79.0 + - - +
359A TYR* 4.5 9.6 + - - +
367A LYS* 6.1 1.6 - - - +
368A THR 5.8 2.6 + - - -
369A LYS* 2.7 40.6 + - - +
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Residues in contact with GLU 327 (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 THR* 4.0 8.1 - - + -
231A MET* 3.7 10.7 - - - +
325A LEU* 3.3 22.6 - - - +
326A ASN* 1.3 93.7 + - - +
328A PRO* 1.3 86.5 - - + +
329A VAL* 5.0 0.2 - - - +
367A LYS* 4.0 19.0 + - - -
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Residues in contact with PRO 328 (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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205A LEU* 4.3 9.9 - - + -
227A THR* 4.0 9.9 - - + +
231A MET* 3.8 11.2 - - + -
284A PRO* 4.9 8.7 - - + -
285A MET 3.6 8.5 - - - +
286A HIS* 4.0 27.8 - - + +
327A GLU* 1.3 103.7 - - + +
329A VAL* 1.3 61.0 + - - +
330A GLN 4.2 0.4 - - - -
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Residues in contact with VAL 329 (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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284A PRO* 4.6 1.8 - - - -
285A MET* 2.9 36.0 + - + +
325A LEU* 4.3 16.8 - - + -
327A GLU 3.7 0.2 + - - -
328A PRO* 1.3 74.6 - - - +
330A GLN* 1.3 64.4 + - - +
331A VAL* 3.9 0.5 - - - +
361A VAL* 4.7 21.3 - - + -
364A GLN* 5.0 13.9 - - - +
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Residues in contact with GLN 330 (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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282A SER* 3.2 23.2 + - - -
283A ALA* 3.3 19.5 + - - +
284A PRO* 3.6 21.4 - - - +
328A PRO* 4.2 1.2 - - - +
329A VAL* 1.3 71.5 - - - +
331A VAL* 1.3 61.4 + - - +
332A GLU* 4.0 15.0 - - - +
335A THR* 5.9 0.2 - - - +
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Residues in contact with VAL 331 (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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247A LEU* 4.4 16.4 - - + -
279A CYS* 4.1 21.1 - - - -
281A GLY 4.2 8.5 - - - +
282A SER* 3.4 3.3 + - - -
283A ALA* 2.9 44.7 + - + +
285A MET* 4.1 12.6 - - + -
329A VAL 3.5 8.7 + - - +
330A GLN* 1.3 84.4 - - - +
332A GLU* 1.3 65.2 + - - +
335A THR* 4.0 15.5 - - + +
361A VAL* 3.9 27.4 - - + -
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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