Contacts of the strand formed by residues 381 - 388 (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 ILE 381 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B HIS* 3.4 20.1 - - - +
372B VAL* 3.9 23.8 - - + -
373B TYR 3.7 4.3 - - - +
374B TYR* 4.3 1.6 - - - -
380B GLN* 1.3 75.2 - - - +
382B LEU* 1.3 61.1 + - - +
383B ARG 4.0 6.5 - - - +
384B ALA* 5.1 2.9 - - + -
399B LEU* 4.5 6.7 - - + -
402B ALA* 4.4 15.7 - - + -
403B MET* 3.8 33.2 - - + +
407B LEU* 3.7 19.9 + - + +
408B THR 4.3 3.8 - - - +
409B VAL* 4.0 15.9 - - + +
412B LEU* 4.0 33.9 - - + -
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B HIS* 3.0 21.9 + - - -
286B VAL* 3.8 16.6 - - + -
337B GLY* 3.4 1.0 - - - -
338B VAL* 3.1 18.6 + - + +
343B LEU* 4.5 13.7 - - + -
346B PHE* 3.7 47.6 - - + -
348B TYR* 3.7 21.1 - - + -
373B TYR 2.8 13.7 + - - +
374B TYR 3.7 5.8 - - - +
375B ASP* 3.5 38.8 - - + +
380B GLN* 4.0 3.4 - - + +
381B ILE* 1.3 76.3 - - - +
383B ARG* 1.3 57.2 + - - +
403B MET* 3.7 3.6 - - - -
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU 2.9 26.7 + - - -
187B MET* 3.9 1.0 - - - +
188B ASP* 2.8 36.1 + - - +
335B SER* 3.9 19.0 + - - -
336B VAL 3.2 11.4 + - - +
337B GLY* 4.2 3.4 + - - -
338B VAL* 2.9 34.4 + - + +
339B LYS* 3.9 2.2 - - - +
340B PRO* 3.4 23.9 - - - +
343B LEU* 4.1 13.9 - - + -
372B VAL* 3.5 4.2 - - - +
373B TYR* 2.8 55.0 + - + +
381B ILE* 3.8 3.9 - - - +
382B LEU* 1.3 81.2 - - - +
384B ALA* 1.3 66.8 + - - +
385B ALA* 4.5 3.0 - - - +
403B MET* 4.0 2.6 - - - +
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Residues in contact with ALA 384 (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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335B SER* 3.2 5.7 - - - -
336B VAL* 2.9 42.6 + - + +
371B ARG 3.2 11.4 - - - +
372B VAL* 4.0 5.2 - - + -
373B TYR* 5.3 0.7 - - - -
381B ILE* 5.1 3.6 - - + -
383B ARG* 1.3 79.0 - - - +
385B ALA* 1.3 62.2 + - - +
396B ILE* 3.9 9.0 - - + -
399B LEU* 3.6 32.8 - - + -
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B MET* 3.8 24.9 - - + -
188B ASP* 4.4 14.1 - - - +
191B MET* 3.7 16.6 - - + +
334B ALA 3.4 6.7 - - - +
335B SER* 4.1 5.2 - - - -
370B LEU* 3.5 3.1 - - - +
371B ARG* 2.8 36.0 + - + +
373B TYR* 5.7 0.9 - - + -
383B ARG* 4.5 2.5 - - + +
384B ALA* 1.3 76.7 - - - +
386B ALA* 1.3 60.8 + - - +
396B ILE* 3.9 2.9 - - - -
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Residues in contact with ALA 386 (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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332B THR 3.8 1.0 - - - +
333B PHE* 3.7 0.7 - - - -
334B ALA 2.9 32.7 + - - +
368B LEU* 4.3 4.9 - - + -
369B HIS 3.1 10.8 - - - +
370B LEU* 4.0 11.2 - - + -
385B ALA* 1.3 75.6 - - - +
387B VAL* 1.3 64.3 + - - +
392B ALA* 3.8 21.8 - - + +
395B ARG* 4.8 2.7 - - + -
396B ILE* 3.7 22.7 - - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B MET* 3.7 22.4 - - + -
191B MET* 3.5 33.0 - - + +
194B PRO* 4.1 15.3 - - + -
331B TYR* 4.2 5.8 - - + -
332B THR 3.3 4.5 - - - +
333B PHE* 3.7 33.4 - - + -
367B PRO 4.2 1.0 - - - +
368B LEU* 3.8 4.5 - - - -
369B HIS* 2.9 36.6 + - + +
386B ALA* 1.3 80.1 - - - +
388B GLY* 1.3 62.0 + - - +
392B ALA* 4.5 0.2 - - - -
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR* 3.8 15.3 - - - -
332B THR* 3.0 31.4 + - - +
367B PRO 3.9 13.5 - - - -
368B LEU* 4.0 9.9 - - - +
387B VAL* 1.3 77.9 - - - +
389B LYS* 1.3 63.7 - - - -
390B GLU* 3.2 3.9 + - - -
392B ALA* 4.3 1.7 - - - +
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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
------------------------------------------------------------
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