Contacts of the strand formed by residues 361 - 368 (chain B) in PDB entry 2YA6
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 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B ASP* 3.9 18.8 - - + +
350B GLU 3.3 8.5 - - - +
351B ARG* 4.0 28.5 - - + +
358B TRP* 3.5 35.7 - - - +
359B GLY 3.3 9.8 + - - +
360B ASP* 1.3 80.7 + - - +
362B GLY* 1.3 71.8 + - - +
363B MET* 3.8 8.5 - - + -
382B THR 4.5 1.2 - - - +
383B ASN* 3.8 12.1 + - - +
384B LEU 5.0 1.2 + - - -
397B SER* 4.9 0.8 + - - -
398B PRO 5.1 1.8 + - - -
399B VAL* 4.2 5.2 - - + -
400B ASN* 3.1 42.2 + - - +
401B ILE* 4.3 4.7 - - + -
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Residues in contact with GLY 362 (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 ALA 3.6 0.3 - - - +
350B GLU* 2.8 43.9 + - - +
361B ILE* 1.3 74.3 - - - +
363B MET* 1.3 70.9 + - - +
364B VAL* 3.8 6.3 - - - -
380B THR* 4.9 0.9 - - - -
382B THR 3.4 9.4 - - - -
383B ASN* 3.8 19.5 - - - +
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Residues in contact with MET 363 (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 ALA 3.8 2.5 - - - +
349B ASP* 3.4 26.0 - - - +
361B ILE* 3.8 3.1 - - + -
362B GLY* 1.3 81.8 - - - +
364B VAL* 1.3 55.0 + - - +
380B THR* 3.6 2.3 - - - -
381B ILE* 2.7 47.2 + - + +
382B THR* 2.9 16.8 + - - +
400B ASN* 3.7 33.9 - - + +
401B ILE 3.9 2.5 - - - +
402B ASP 4.5 1.3 - - - -
403B MET* 3.9 22.9 - - + -
418B TYR* 3.6 48.9 - - + -
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Residues in contact with VAL 364 (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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315B PHE* 3.7 24.0 - - + -
331B TYR* 4.1 4.3 - - + -
346B ALA 4.0 0.2 - - - +
347B GLY* 3.2 3.1 - - - -
348B ALA* 2.8 50.4 + - + +
350B GLU* 3.7 42.2 - - + +
362B GLY 4.1 4.0 - - - +
363B MET* 1.3 76.0 - - - +
365B ILE* 1.3 65.0 + - - +
378B ARG* 4.6 7.0 - - + -
379B VAL 3.3 7.0 - - - +
380B THR* 3.7 23.6 - - + +
381B ILE* 4.8 0.2 - - - -
403B MET* 3.9 1.9 - - - +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PHE* 4.3 1.8 - - - -
345B ILE* 3.8 24.2 - - + -
346B ALA 3.1 6.7 - - - +
347B GLY* 3.8 11.2 - - - -
364B VAL* 1.3 79.6 - - - +
366B ARG* 1.3 62.1 + - - +
367B ARG* 3.7 22.4 - - + -
378B ARG* 3.4 4.9 - - - +
379B VAL* 2.7 58.6 + - + +
381B ILE* 3.7 20.4 - - + +
403B MET* 4.7 1.6 - - - -
405B LEU* 4.7 5.8 - - + -
530B GLY* 3.1 26.5 - - - +
533B TRP* 3.9 20.4 - - + +
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Residues in contact with ARG 366 (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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313B ASP 4.8 2.6 + - - -
314B ILE* 2.8 48.7 + - + +
315B PHE* 3.7 12.8 - - + -
344B LEU 3.5 0.2 - - - +
345B ILE* 3.6 1.4 - - - -
346B ALA 2.8 32.3 + - - +
365B ILE* 1.3 80.0 - - - +
367B ARG* 1.3 63.4 + - - +
375B TRP* 3.1 45.4 + - + +
376B GLY 2.7 28.8 + - - +
377B ASP* 4.4 7.6 + - - +
378B ARG* 3.7 33.2 - - + +
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Residues in contact with ARG 367 (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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343B THR* 3.8 11.0 - - + +
344B LEU 3.3 4.5 - - - -
345B ILE* 4.5 7.4 - - + -
365B ILE* 3.7 17.0 - - + -
366B ARG* 1.3 74.1 - - - +
368B SER* 1.3 58.2 + - - +
369B GLU* 3.0 36.6 + - - +
375B TRP* 3.4 3.9 - - - -
376B GLY* 2.8 35.2 + - - +
377B ASP 4.9 3.2 + - - +
379B VAL* 5.2 4.9 - - + -
529B ASP* 2.7 45.3 + - - +
530B GLY 3.7 20.0 - - - +
531B LYS* 3.5 32.4 - - - +
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.5 6.1 - - - -
344B LEU* 2.7 37.8 + - - +
367B ARG* 1.3 71.9 - - - +
369B GLU* 1.3 57.8 + - - +
370B ASP* 2.7 29.1 + - - -
371B ASN 4.0 2.9 + - - -
372B GLY* 2.8 20.4 + - - -
374B THR 2.8 14.1 + - - -
375B TRP* 3.5 27.6 - - - -
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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