Contacts of the strand formed by residues 292 - 301 (chain A) in PDB entry 5E8M
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 SER 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A TYR* 3.6 16.6 - - - +
265A GLY 3.5 21.8 + - - +
290A ILE* 3.5 7.8 - - - +
291A ASP* 1.3 82.7 + - - +
293A VAL* 1.3 63.5 + - - +
294A THR 3.8 0.2 + - - -
337A LYS* 4.6 2.2 - - - -
338A LYS* 3.4 18.4 - - - +
340A TRP* 3.2 49.3 + - - -
378A GLU* 4.6 0.3 + - - -
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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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265A GLY 3.3 9.0 - - - +
266A PRO* 4.3 1.6 - - + -
279A LEU* 4.0 30.1 - - + -
283A LEU* 3.9 20.9 - - + -
290A ILE* 3.9 1.3 - - + -
292A SER* 1.3 71.6 - - - +
294A THR* 1.3 64.9 - - - +
295A TRP* 5.5 1.1 - - + -
326A VAL* 5.5 2.2 - - + -
330A VAL* 4.4 21.5 - - + -
337A LYS* 3.5 28.3 - - + -
338A LYS 2.9 10.2 + - - +
339A VAL* 3.5 11.6 - - + +
340A TRP 2.8 26.9 + - - +
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Residues in contact with THR 294 (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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221A GLU* 4.1 10.5 - - - +
264A TYR* 4.0 23.8 - - + -
265A GLY* 3.0 12.8 + - - -
266A PRO* 3.7 7.3 - - - +
267A ASP* 2.9 61.8 + - - -
268A VAL* 3.5 4.0 + - - +
292A SER 4.5 0.4 - - - +
293A VAL* 1.3 77.9 - - - +
295A TRP* 1.3 62.2 + - - +
340A TRP* 3.3 27.4 - - + -
342A GLY* 4.2 10.3 - - - -
381A MET* 5.2 0.2 - - + -
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Residues in contact with TRP 295 (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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268A VAL* 3.2 24.0 - - + +
269A GLY 4.6 1.3 - - - +
270A GLN* 4.1 8.1 - - + -
271A PRO* 4.1 11.4 - - + -
279A LEU* 5.8 1.8 - - + -
293A VAL* 4.6 2.2 - - + -
294A THR* 1.3 76.7 - - - +
296A HIS* 1.3 89.0 + - - +
297A HIS* 3.8 11.0 - - + -
319A PHE* 4.0 19.3 - + - -
322A SER* 4.0 18.8 - - - -
323A VAL* 4.0 20.4 - - + -
326A VAL* 3.7 33.7 - - + +
339A VAL* 3.5 27.9 - - + +
340A TRP 3.2 16.0 + - - -
341A LEU* 3.4 24.4 - - + +
342A GLY 2.7 24.4 + - - -
377A ILE* 3.8 11.5 - - + +
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Residues in contact with HIS 296 (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 ASN* 3.2 28.0 - - - -
225A GLU* 2.7 30.2 + - + +
267A ASP* 2.6 41.8 + - - +
268A VAL 2.8 13.7 + - - +
269A GLY* 4.3 0.7 - - - -
270A GLN* 3.2 22.2 + - - +
295A TRP* 1.3 97.1 - - - +
297A HIS* 1.3 61.0 + - - +
298A TYR* 4.9 1.8 - - + -
341A LEU* 4.0 0.2 - - - -
342A GLY 3.9 0.2 - - - -
343A GLU* 3.2 42.1 + - + +
621A CL 4.1 8.1 - - + -
58B ARG* 3.9 0.8 + - - -
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Residues in contact with HIS 297 (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 GLN* 3.6 24.1 + - - -
295A TRP* 3.8 6.1 - + + -
296A HIS* 1.3 77.6 - - - +
298A TYR* 1.3 84.8 + - - +
299A TYR* 3.7 26.8 - + - -
318A ILE* 4.7 5.3 - - - +
319A PHE* 3.6 36.3 + + + -
322A SER* 4.0 17.3 + - - -
341A LEU* 3.8 13.7 - - + +
343A GLU 3.2 5.1 + - - -
344A THR* 2.6 37.9 + - - +
345A SER 3.2 2.9 + - - -
368A LYS* 3.3 16.1 + - - -
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Residues in contact with TYR 298 (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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225A GLU* 4.6 3.8 - - - -
270A GLN* 3.0 28.8 + - - +
296A HIS* 4.9 0.4 - - + -
297A HIS* 1.3 87.1 + - - +
299A TYR* 1.3 63.3 + - - +
300A LEU 4.0 5.4 - - - +
318A ILE* 5.5 0.2 - - - +
343A GLU* 2.6 38.7 + - + +
344A THR* 4.6 0.2 - - - -
345A SER* 3.4 41.1 - - - +
346A SER 4.1 0.7 - - - +
347A ALA 3.5 25.1 - - - -
348A TYR* 3.6 31.5 - + + +
383A GLN* 3.3 19.5 + - + +
391A TYR* 4.0 9.1 + + - -
608A EDO 4.3 2.5 - - - -
613A EDO 3.9 17.0 - - - -
621A CL 4.2 8.7 - - + -
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Residues in contact with TYR 299 (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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297A HIS* 3.9 8.5 - + - -
298A TYR* 1.3 74.5 - - - +
300A LEU* 1.3 66.4 - - + +
315A VAL* 3.6 19.5 - - + +
316A LEU* 3.8 32.4 + - + +
318A ILE* 4.0 19.8 - - + +
319A PHE* 3.9 15.0 - - + +
345A SER 3.9 10.5 - - - -
346A SER* 3.0 11.2 + - - +
348A TYR* 5.9 0.4 - - - -
364A MET* 3.5 57.0 + - + -
367A ASP* 4.7 2.6 + - - -
368A LYS* 3.4 50.8 + - - +
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Residues in contact with LEU 300 (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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298A TYR* 3.4 0.9 - - - +
299A TYR* 1.3 89.7 - - + +
301A ASN* 1.3 68.5 + - - +
305A ALA* 3.7 22.4 - - + -
309A ASP* 3.7 36.1 - - + +
310A PHE* 3.9 15.0 - - + -
315A VAL* 4.4 11.7 - - + -
346A SER 3.1 7.3 + - - +
347A ALA* 3.3 4.1 - - + -
348A TYR* 2.9 39.5 + - - -
364A MET* 3.9 15.7 - - + -
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Residues in contact with ASN 301 (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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300A LEU* 1.3 71.3 - - - +
302A GLY* 1.3 67.3 + - - +
303A ARG* 3.0 38.4 + - - +
304A THR* 3.5 23.3 + - - +
305A ALA* 3.2 24.1 + - - +
347A ALA* 4.0 1.3 - - - -
348A TYR* 3.4 40.7 + - - +
349A GLY* 5.6 0.7 - - - -
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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