Contacts of the strand formed by residues 348 - 356 (chain B) in PDB entry 1YQZ
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 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B LEU* 3.4 50.2 - - + +
344B LYS* 4.3 4.9 + - - -
346B PHE 3.4 7.2 - - - +
347B ASP* 1.3 73.9 - - - +
349B LYS* 1.3 74.8 + - - +
350B MET* 5.2 2.0 - - + -
373B TYR* 3.7 33.8 - + - -
374B TYR 3.2 15.0 - - - +
376B THR* 3.9 3.9 - - - +
382B LEU* 3.7 15.9 - - + -
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Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B TYR* 1.3 79.6 - - - +
350B MET* 1.3 62.6 + - - +
373B TYR* 3.3 4.5 - - - +
374B TYR* 2.9 68.7 + - + +
376B THR* 3.5 23.8 - - + -
379B ARG* 5.1 1.8 - - - +
438B LYS* 4.7 10.5 - - - +
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Residues in contact with MET 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B TYR* 4.7 3.1 - - + -
349B LYS* 1.3 75.9 - - - +
351B VAL* 1.3 83.6 + - - +
352B GLU* 3.5 31.4 - - + +
371B ARG* 3.6 35.7 - - + +
372B VAL 3.5 4.7 - - - +
373B TYR* 3.8 22.4 - - + -
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B LYS* 5.6 0.2 - - + -
350B MET* 1.3 82.5 - - - +
352B GLU* 1.3 66.6 + - - +
371B ARG* 3.5 0.5 - - - -
372B VAL 2.9 32.3 + - - +
374B TYR* 3.5 31.6 - - + +
409B VAL* 5.0 1.8 - - + -
433B ILE* 3.7 27.2 - - + +
436B LYS* 3.6 36.6 - - + +
437B ALA* 3.8 16.2 - - + +
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Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B MET* 3.5 27.2 - - - +
351B VAL* 1.3 79.2 - - - +
353B VAL* 1.3 59.6 + - - +
369B HIS* 2.7 32.0 + - + +
370B LEU 3.2 13.0 - - - +
371B ARG* 2.9 24.1 + - - -
433B ILE* 3.8 2.0 - - - -
436B LYS* 2.7 32.9 + - - +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B GLU* 1.3 83.8 - - - +
354B THR* 1.3 63.3 + - - +
355B GLN* 5.4 3.6 - - + +
368B LEU 3.6 1.2 - - - +
369B HIS* 3.6 2.6 - - - -
370B LEU* 2.9 40.6 + - + +
429B LEU* 3.9 39.7 - - + +
432B MET* 3.9 21.1 - - + -
433B ILE* 4.1 8.3 - - + -
436B LYS* 3.2 28.7 - - + +
3004B CL 3.7 8.3 - - + -
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B VAL* 1.3 70.8 - - - +
355B GLN* 1.3 64.8 + - - +
367B PRO* 4.1 21.5 - - + -
368B LEU 3.3 11.9 - - - +
369B HIS* 3.5 27.7 - - + +
2003B MG 3.9 13.7 - - - -
3004B CL 3.3 20.9 - - - +
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Residues in contact with GLN 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B VAL* 4.1 4.1 - - + +
354B THR* 1.3 78.0 - - - +
356B GLY* 1.3 70.6 + - - +
360B ASN* 4.6 6.0 + - - +
367B PRO* 4.2 4.0 - - - -
368B LEU* 2.8 31.2 + - - +
425B HIS* 2.4 40.5 + - + +
427B LYS 4.3 4.9 + - - +
429B LEU* 3.9 27.2 - - + +
432B MET* 4.0 23.7 - - - +
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Residues in contact with GLY 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN* 1.3 86.6 - - - +
357B ALA* 1.3 66.2 + - - -
358B HIS 3.1 8.3 + - - +
360B ASN* 3.9 8.3 + - - -
365B ASN* 3.3 25.4 - - - -
366B SER 3.7 6.5 - - - -
367B PRO* 4.3 3.3 - - - +
425B HIS* 4.0 3.3 + - - -
429B LEU* 3.7 12.6 - - - +
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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