Contacts of the strand formed by residues 344 - 351 (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 LEU 344 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B LEU* 4.1 19.3 - - + -
337B LEU 4.2 2.5 - - - +
338B LYS* 4.2 21.8 - - + +
342B GLY 3.7 0.9 + - - +
343B THR* 1.3 72.5 - - - +
345B ILE* 1.3 61.8 + - - +
346B ALA 4.0 0.4 - - - -
367B ARG* 3.3 4.9 - - - -
368B SER* 2.7 41.5 + - - -
371B ASN* 3.7 11.9 - - - +
372B GLY* 3.6 20.6 - - - +
375B TRP* 3.3 17.4 - - + -
741B GLN* 5.0 0.7 - - + -
743B LEU* 3.7 26.2 - - + -
766B PHE* 3.6 35.0 - - + -
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Residues in contact with ILE 345 (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 ALA 3.5 1.6 - - - +
336B LEU* 3.4 6.7 - - - +
337B LEU* 2.8 47.3 + - + +
339B THR* 3.8 15.9 - - + -
343B THR* 4.4 5.2 - - + -
344B LEU* 1.3 75.2 - - - +
346B ALA* 1.3 61.8 + - - +
365B ILE* 3.8 37.0 - - + -
366B ARG 3.6 2.7 - - - -
367B ARG* 4.5 4.3 - - + -
405B LEU* 4.1 13.0 - - + +
414B ILE* 3.8 30.7 - - + -
529B ASP 3.5 25.1 - - - +
530B GLY* 3.8 10.3 - - - -
533B TRP* 5.1 2.0 - - + -
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Residues in contact with ALA 346 (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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314B ILE* 4.1 8.1 - - + -
315B PHE* 3.4 15.0 - - + -
335B ALA 3.4 4.7 - - - -
336B LEU* 4.5 2.5 - - + -
344B LEU 3.9 0.4 + - - -
345B ILE* 1.3 72.9 - - - +
347B GLY* 1.3 58.2 + - - +
365B ILE* 3.1 5.5 - - - -
366B ARG 2.8 36.5 + - - +
375B TRP* 3.6 26.2 - - + -
751B LEU* 3.5 21.8 - - + -
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Residues in contact with GLY 347 (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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333B ILE 4.3 1.1 - - - -
334B PRO* 3.4 5.9 - - - +
335B ALA 2.7 36.5 + - - -
345B ILE 4.0 0.8 - - - -
346B ALA* 1.3 74.3 - - - +
348B ALA* 1.3 63.3 + - - +
364B VAL 3.2 9.6 - - - -
365B ILE* 3.8 10.1 - - - -
403B MET* 4.1 13.7 - - - -
405B LEU* 4.2 3.0 - - - +
751B LEU* 3.9 4.3 - - - +
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Residues in contact with ALA 348 (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* 3.6 28.0 - - + -
331B TYR* 4.1 2.0 - - + -
332B ARG 3.6 4.9 - - - +
333B ILE 3.7 4.5 - - - -
347B GLY* 1.3 75.5 - - - +
349B ASP* 1.3 68.4 + - - +
350B GLU 3.6 0.2 + - - -
362B GLY 3.6 1.2 - - - +
363B MET* 3.8 0.5 - - - -
364B VAL* 2.8 37.0 + - + +
403B MET* 3.7 11.4 - - - +
764B LEU* 3.7 17.9 - - + -
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Residues in contact with ASP 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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331B TYR* 3.4 10.6 - - - -
332B ARG 2.7 33.1 + - - +
333B ILE* 3.6 13.9 + - - +
348B ALA* 1.3 71.9 - - - +
350B GLU* 1.3 59.9 + - - +
351B ARG* 2.8 44.7 + - + +
361B ILE* 3.9 4.1 - - + +
362B GLY 3.7 4.9 - - - -
363B MET* 3.4 15.0 - - - +
401B ILE* 3.4 14.2 - - - +
402B ASP* 3.0 24.7 + - - -
403B MET* 4.4 1.2 + - - +
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Residues in contact with GLU 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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328B ILE* 3.8 27.3 - - + +
331B TYR* 2.6 40.6 + - + +
348B ALA 3.6 1.4 + - - -
349B ASP* 1.3 69.4 - - - +
351B ARG* 1.3 60.4 + - - +
352B ARG* 3.3 14.6 + - - +
360B ASP 3.6 0.5 - - - +
361B ILE* 3.3 4.7 - - - +
362B GLY* 2.8 39.0 + - - +
364B VAL* 3.7 19.4 - - + +
378B ARG* 2.9 26.5 + - - -
380B THR* 5.0 3.3 + - - +
383B ASN* 5.0 9.0 + - - -
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Residues in contact with ARG 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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328B ILE* 4.0 1.1 - - - -
330B SER* 2.9 47.2 + - - +
332B ARG* 3.7 19.0 - - + +
333B ILE* 3.5 9.5 - - - +
349B ASP* 2.8 42.1 + - + +
350B GLU* 1.3 70.6 - - - +
352B ARG* 1.3 65.0 + - - +
353B LEU 3.5 2.4 + - - -
354B HIS 3.3 16.9 + - - +
355B SER 3.1 22.5 + - - -
356B SER 3.2 18.0 + - - +
357B ASP* 2.8 22.4 + - - -
358B TRP 5.7 0.4 - - - +
360B ASP 4.1 4.0 - - - -
361B ILE* 4.0 15.4 - - + +
401B ILE* 3.4 12.4 - - - +
1777B DAN 2.9 26.1 + - - -
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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