Contacts of the strand formed by residues 322 - 330 (chain D) in PDB entry 5Y7K
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 TYR 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292D SER* 4.5 8.9 - - - -
293D MET* 3.7 6.5 - - + +
316D LEU* 3.2 15.4 - - - +
317D ARG* 3.3 60.6 + - - +
319D ILE 3.8 0.4 + - - -
320D GLN 3.6 1.8 - - - -
321D ASN* 1.3 88.1 - - - +
323D SER* 1.3 60.5 + - - +
324D VAL* 3.5 21.3 - - + +
346D ILE* 3.0 36.6 - - + +
347D GLU 3.9 3.1 - - - -
348D MET* 3.5 36.6 - - + +
354D VAL* 4.4 1.0 - - - +
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D MET* 3.9 0.7 - - - -
301D CYS* 5.0 0.2 - - - -
314D GLN* 5.2 2.5 + - - -
315D TRP 3.1 15.3 - - - -
316D LEU* 4.2 7.9 - - - -
322D TYR* 1.3 74.3 - - - +
324D VAL* 1.3 68.1 + - - +
325D MET 4.3 0.2 - - - -
346D ILE* 3.6 2.6 - - - +
347D GLU* 2.8 59.6 + - - +
354D VAL* 4.0 5.3 - - - +
359D PRO* 3.7 31.5 - - - +
373D LYS* 5.7 0.2 + - - -
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D PRO* 4.0 20.9 - - + -
292D SER* 3.8 13.2 - - - +
293D MET* 3.5 11.6 - - + +
313D LEU 3.7 1.0 - - - +
314D GLN* 3.4 2.7 - - - -
315D TRP* 2.8 38.0 + - - +
322D TYR* 3.5 25.6 - - + +
323D SER* 1.3 79.5 - - - +
325D MET* 1.3 65.8 + - - +
344D GLN* 3.6 33.7 - - + +
345D HIS 3.5 3.1 - - - +
346D ILE* 3.9 13.9 - - + -
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Residues in contact with MET 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D SER* 3.0 27.1 - - - +
313D LEU 3.4 3.1 - - - -
314D GLN* 3.8 20.2 - - + -
324D VAL* 1.3 73.2 - - - +
326D ASP* 1.3 64.6 + - - +
327D ILE* 3.6 18.4 - - + -
343D ARG 4.2 0.7 - - - +
344D GLN* 3.6 10.0 - - - +
345D HIS* 2.7 46.7 + - + +
362D PRO* 4.1 11.9 - - + -
364D PHE* 3.5 24.9 - - + -
371D PHE* 3.6 33.7 - - + -
373D LYS* 4.7 11.0 - - - +
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Residues in contact with ASP 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ILE* 5.5 0.5 - - - +
288D THR 4.6 5.9 - - - +
290D PRO* 3.9 28.4 - - + +
311D ILE 3.9 0.9 - - - +
312D SER* 3.3 4.2 + - - -
313D LEU* 2.5 53.7 + - + +
315D TRP* 4.7 5.3 + - + +
325D MET* 1.3 75.1 - - - +
327D ILE* 1.3 63.7 + - - +
328D CYS* 4.0 3.3 - - - -
339D CYS* 3.2 35.0 - - - +
340D LEU 4.5 5.4 - - - +
341D VAL* 5.9 0.2 - - - -
343D ARG 4.7 0.2 - - - -
344D GLN* 4.4 16.5 - - - +
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Residues in contact with ILE 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D ARG* 3.7 34.1 - - + +
311D ILE 3.7 4.7 - - - +
312D SER* 4.6 2.5 - - - +
325D MET* 3.6 29.6 - - + -
326D ASP* 1.3 79.5 + - - +
328D CYS* 1.3 60.2 + - - +
329D ASP* 4.4 2.9 - - - +
339D CYS* 3.5 15.1 - - - -
340D LEU 4.0 1.6 + - - +
343D ARG* 3.6 43.1 + - + +
345D HIS* 3.8 13.9 - - + -
364D PHE* 4.5 3.4 - - + -
371D PHE* 4.2 0.2 - - + -
389D ILE* 3.5 36.6 - - + +
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Residues in contact with CYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D ILE* 3.9 24.0 - - + -
310D ARG* 3.4 2.9 - - - +
311D ILE* 2.9 49.9 + - + +
313D LEU* 5.2 4.7 - - - -
326D ASP* 4.0 11.4 - - - -
327D ILE* 1.3 73.2 - - - +
329D ASP* 1.3 63.0 + - - +
337D TRP* 3.9 6.0 - - + -
338D ASN 3.2 7.4 - - - +
339D CYS* 2.0 44.4 - - - -
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Residues in contact with ASP 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D GLU* 3.3 6.3 - - + +
310D ARG* 2.7 54.9 + - - +
327D ILE* 4.4 0.7 - - - +
328D CYS* 1.3 75.2 - - - +
330D TYR* 1.3 68.2 + - - +
331D ASP* 3.7 0.9 + - - +
337D TRP* 3.5 5.0 - - - -
338D ASN* 2.9 31.5 + - + +
343D ARG* 3.2 27.2 + - - +
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Residues in contact with TYR 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D PHE* 3.7 28.3 - + - -
272D ASN* 4.6 9.3 + - + -
309D GLU* 2.7 49.2 + - + +
329D ASP* 1.3 77.1 - - - +
331D ASP* 1.3 78.7 + - - +
332D GLU* 3.8 21.3 + - - +
335D GLY* 3.6 32.4 + - - -
336D ARG 3.7 3.4 - - - -
337D TRP* 3.5 40.9 - + + -
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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