Contacts of the strand formed by residues 335 - 342 (chain A) in PDB entry 1Y7V
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 MET 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LYS* 5.3 1.3 - - + -
228A TRP* 3.6 34.5 - - + -
279A LEU* 4.3 5.8 - - + -
306A HIS* 3.4 41.6 + - + +
307A GLY* 3.8 8.1 - - - -
308A ILE* 2.8 28.5 + - - +
333A ASN 3.9 2.6 + - - -
334A THR* 1.3 75.7 - - - +
336A LEU* 1.3 59.4 + - - +
337A PHE* 3.8 20.9 - - + -
376A VAL* 4.0 33.0 - - + -
504A SO4 5.6 1.6 - - - +
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Residues in contact with LEU 336 (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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288A LEU* 4.4 2.2 - - + -
308A ILE* 3.6 39.7 - - + +
310A VAL* 4.6 1.8 - - + -
324A LEU* 3.4 46.9 - - + +
327A THR* 4.1 8.7 - - + -
328A HIS* 4.6 13.2 - - + +
334A THR 4.4 5.4 - - - +
335A MET* 1.3 75.7 - - - +
337A PHE* 1.3 55.9 + - - +
373A TYR 4.1 11.4 - - - +
374A HIS* 4.3 14.3 + - + +
375A VAL* 3.2 19.4 - - + -
376A VAL* 2.7 35.4 + - - +
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Residues in contact with PHE 337 (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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79A LYS* 4.3 3.1 - - + -
118A ILE* 3.7 25.8 - - + -
175A LEU* 3.7 20.2 - - + -
228A TRP* 3.6 29.8 - + - -
279A LEU* 4.2 17.7 - - + -
308A ILE 3.2 8.6 + - - +
309A ALA* 3.3 3.1 - - - -
310A VAL* 2.7 36.6 + - - +
335A MET* 3.8 16.4 - - + -
336A LEU* 1.3 75.6 - - - +
338A ALA* 1.3 71.8 + - - +
339A SER* 4.0 5.2 - - - -
375A VAL* 3.9 2.7 - - - -
376A VAL* 4.2 8.3 - - + -
377A GLY* 3.8 25.1 - - - -
379A THR* 3.1 22.2 - - - -
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Residues in contact with ALA 338 (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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310A VAL* 3.3 12.6 - - + +
311A HIS 6.4 0.2 - - - -
337A PHE* 1.3 77.4 - - - +
339A SER* 1.3 56.6 + - - +
340A GLU 3.7 4.7 - - - +
370A ASN* 3.7 23.1 - - - +
375A VAL* 3.6 1.2 - - - +
377A GLY 2.9 20.8 + - - +
378A TRP* 3.5 22.0 - - + +
379A THR* 2.7 33.7 + - - +
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Residues in contact with SER 339 (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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120A ARG* 3.3 23.2 + - - -
175A LEU* 4.1 13.2 - - - -
231A THR* 5.2 0.2 - - - -
282A ASP* 2.5 29.6 + - - -
309A ALA* 3.6 11.0 - - - +
310A VAL 2.8 12.2 + - - -
311A HIS* 3.0 12.2 - - - -
337A PHE* 3.6 14.9 + - - -
338A ALA* 1.3 72.0 - - - +
340A GLU* 1.3 61.9 + - - +
379A THR* 3.6 17.0 - - - +
380A ASP 4.6 1.2 - - - +
381A TRP* 5.7 0.2 - - - -
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Residues in contact with GLU 340 (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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120A ARG* 3.0 23.1 + - - +
179A TRP* 3.9 3.6 - - - -
234A ASN* 3.4 2.8 - - - +
235A GLU* 3.9 0.3 - - - +
310A VAL 4.3 0.3 - - - +
311A HIS* 3.4 26.9 + - + +
312A TRP* 3.0 25.6 + - - +
313A TYR* 4.6 1.7 + - - -
338A ALA* 3.7 3.0 - - - +
339A SER* 1.3 83.0 + - - +
341A ALA* 1.3 65.8 + - - +
379A THR 3.3 7.6 + - - -
380A ASP 4.9 1.3 - - - -
381A TRP* 4.1 21.8 - - + -
507A INS 1.4 65.8 + - + +
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Residues in contact with ALA 341 (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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312A TRP* 3.3 7.2 - - + +
314A LEU* 4.8 5.4 - - + -
340A GLU* 1.3 76.7 - - - +
342A CYS* 1.3 64.4 + - - +
363A TYR* 4.0 6.4 + - + +
378A TRP* 3.3 45.5 - - + -
379A THR 3.5 6.0 + - - +
380A ASP* 3.8 8.4 - - - +
381A TRP* 3.3 26.2 - - - +
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Residues in contact with CYS 342 (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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312A TRP 3.2 6.2 + - - +
313A TYR* 3.7 17.0 - - + -
314A LEU* 2.9 37.5 + - - +
315A ASP* 4.0 0.5 - - - +
340A GLU* 5.0 0.2 - - - -
341A ALA* 1.3 79.1 - - - +
343A VAL* 1.3 65.7 + - - +
345A SER* 3.7 20.0 - - - +
363A TYR* 4.7 0.9 - - - -
381A TRP* 4.2 8.3 - - - -
398A VAL* 4.1 11.9 - - - -
507A INS 3.5 38.8 - - - -
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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