Contacts of the strand formed by residues 405 - 411 (chain A) in PDB entry 4QYJ
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 VAL 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ILE* 3.7 15.5 - - - +
305A SER* 4.2 9.9 - - - +
352A VAL* 4.7 2.0 - - + -
355A HIS 5.8 0.2 - - - -
356A ILE* 3.9 29.4 - - + +
381A VAL* 5.7 0.2 - - + -
384A THR* 3.4 7.4 - - - +
386A PHE* 4.2 17.9 - - + -
396A LEU* 3.9 28.9 - - + -
401A VAL* 4.0 31.8 - - + +
403A GLY 2.9 7.1 + - - +
404A PRO* 1.3 86.7 - - + +
406A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 5.9 0.2 - - + -
289A ALA* 4.8 3.8 - - + -
293A ILE* 4.1 22.4 - - + -
294A PHE* 5.0 1.1 - - + -
304A GLY 3.5 21.3 - - - +
305A SER 3.4 18.8 - - - +
307A LEU* 3.8 26.9 - - + +
321A LEU* 4.0 31.0 - - + -
384A THR 3.0 11.6 + - - +
385A ILE* 3.5 14.9 - - + +
386A PHE* 2.7 36.0 + - - +
396A LEU* 5.7 0.7 - - - -
404A PRO 4.3 0.2 - - - -
405A VAL* 1.3 78.3 - - - +
407A VAL* 1.3 58.1 + - - +
408A ALA 4.7 0.2 - - - +
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Residues in contact with VAL 407 (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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305A SER 3.3 13.5 + - - +
306A ARG* 3.7 7.6 - - + -
307A LEU* 2.8 25.5 + - - +
364A ALA* 5.8 2.5 - - + -
386A PHE* 3.2 16.2 - - + +
388A ASN* 3.8 24.5 - - + +
394A ILE* 5.8 3.4 - - + -
396A LEU* 4.4 18.1 - - + +
397A LEU* 2.7 40.8 - - + -
406A LEU* 1.3 73.7 - - - +
408A ALA* 1.3 61.8 + - - +
409A THR* 4.0 3.2 + - - +
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Residues in contact with ALA 408 (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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307A LEU* 3.2 22.9 - - + +
309A VAL* 5.7 0.2 - - + -
314A TYR* 2.5 28.5 + - + +
318A ILE* 3.9 27.1 - - + -
385A ILE* 4.8 10.1 - - + -
386A PHE 2.8 14.3 + - - +
387A ALA* 3.7 2.2 - - - -
388A ASN 3.0 13.7 + - - -
406A LEU* 5.0 0.2 - - + -
407A VAL* 1.3 71.2 - - - +
409A THR* 1.3 57.0 + - - +
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Residues in contact with THR 409 (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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307A LEU 2.7 11.5 + - - +
308A TYR* 3.3 26.5 - - + -
309A VAL 3.2 21.1 + - - -
314A TYR* 3.7 3.9 - - - -
388A ASN* 3.4 38.4 + - + +
391A LYS* 4.5 11.7 - - + -
397A LEU* 4.4 8.2 - - + +
407A VAL* 4.3 8.0 + - - +
408A ALA* 1.3 74.7 - - - +
410A PRO* 1.3 74.9 - - + +
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Residues in contact with PRO 410 (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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308A TYR* 4.9 2.5 - - - -
309A VAL 3.3 8.7 - - - +
311A GLU* 4.8 9.2 - - + +
314A TYR* 3.7 36.3 - - + -
388A ASN 3.6 12.1 - - - +
389A ARG* 4.2 8.3 - - + -
390A GLU 5.2 2.9 - - - +
391A LYS* 5.8 3.6 - - + +
409A THR* 1.3 102.3 - - + +
411A PHE* 1.3 65.6 + - - +
416A GLU* 4.5 3.8 - - - +
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Residues in contact with PHE 411 (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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275A ILE* 4.2 3.4 - - + -
276A VAL 3.9 14.4 - - - -
277A LEU* 4.2 17.3 - - + -
308A TYR* 3.9 12.8 - - + -
309A VAL 3.3 24.6 + - - -
310A HIS* 3.2 35.8 - + + -
311A GLU* 3.1 22.9 + - - +
410A PRO* 1.3 79.2 - - - +
412A SER* 1.3 59.5 - - - +
413A ASP 2.9 29.4 - - - -
414A ILE* 4.5 4.0 - - + -
416A GLU* 3.9 16.6 - - + +
417A VAL* 3.8 39.0 - - + -
420A GLU* 6.4 0.9 - - + -
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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