Contacts of the strand formed by residues 418 - 429 (chain B) in PDB entry 2Y1X
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 GLN 418 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B VAL 3.6 0.4 - - - +
341B VAL* 3.2 8.0 - - - +
342B ASP 3.1 31.5 + - - +
343B THR* 2.7 37.4 + - - -
344B PHE* 3.9 18.4 + - + -
390B PHE 3.5 7.2 - - - +
391B TRP* 3.9 14.8 - - + +
407B THR 3.0 25.2 + - - +
408B ALA 3.6 3.6 + - - -
409B PRO* 3.5 32.4 - - + +
411B GLU 5.2 1.4 + - - -
413B LEU* 4.8 6.5 - - - +
414B THR 5.8 1.0 - - - +
416B TRP 3.9 1.1 - - - -
417B TYR* 1.3 85.6 + - - +
419B VAL* 1.3 68.1 + - - +
420B ARG* 5.8 0.2 - - - -
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 4.2 13.5 - - + -
263B MET* 3.7 50.9 - - + +
339B PRO* 3.6 28.7 - - + -
340B VAL 3.4 5.6 - - - +
341B VAL* 4.3 9.4 - - + -
389B ALA* 3.3 2.3 - - - +
390B PHE* 2.6 40.5 + - - +
416B TRP 4.9 4.3 - - - +
418B GLN* 1.3 84.5 - - - +
420B ARG* 1.3 67.0 + - - +
421B CYS* 4.8 1.8 - - - -
470B LEU* 5.1 1.8 - - + -
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Residues in contact with ARG 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.6 32.8 - - + -
300B ASP* 2.5 35.0 + - - +
303B LEU* 3.5 18.3 - - + +
338B GLN 4.5 0.2 - - - +
339B PRO* 3.5 1.9 - - - +
340B VAL* 2.7 50.2 + - + +
342B ASP* 3.1 25.7 + - - -
343B THR 4.1 0.2 + - - -
344B PHE* 3.4 34.2 - - + +
348B ILE* 3.5 14.5 - - - +
388B LEU 3.4 2.5 - - - -
389B ALA* 3.6 21.8 - - + -
418B GLN 5.8 0.2 - - - -
419B VAL* 1.3 74.7 - - - +
421B CYS* 1.3 63.3 + - - +
422B LEU* 3.8 2.8 + - + -
476B ARG* 3.6 19.0 - - - +
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Residues in contact with CYS 421 (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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263B MET* 4.5 3.6 - - - -
298B PHE* 4.7 1.1 - - - -
339B PRO* 4.4 9.2 - - - -
387B GLY* 3.3 2.5 - - - -
388B LEU 3.0 28.2 + - - -
390B PHE* 3.6 24.0 - - + -
419B VAL* 4.8 0.7 - - - -
420B ARG* 1.3 74.8 - - - +
422B LEU* 1.3 64.8 + - - +
423B PHE* 4.1 3.3 - - + -
451B ILE* 4.2 20.2 - - - -
453B ILE* 3.6 25.1 - - + -
468B LEU* 3.5 28.7 - - + -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PHE* 3.9 16.2 - - + -
303B LEU* 4.0 27.4 - - + -
304B TYR* 4.1 20.0 - - + +
307B GLN* 3.9 28.5 - - + -
335B TYR 6.1 0.2 - - - +
336B PHE* 3.7 39.5 + - + +
338B GLN 5.4 3.4 + - - +
340B VAL* 4.1 14.8 - - + -
386B HIS* 3.3 24.7 - - + +
387B GLY* 4.3 0.2 - - - -
420B ARG 3.8 2.3 + - - +
421B CYS* 1.3 75.6 - - - +
423B PHE* 1.3 64.1 + - - +
424B GLN 4.2 0.5 + - - -
466B ASN* 3.7 7.8 - - - +
468B LEU* 4.3 8.1 - - - +
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 3.5 17.5 - - - -
336B PHE* 3.7 4.4 - - - -
385B VAL* 4.0 24.2 - - + -
386B HIS 2.9 9.2 + - - +
387B GLY* 3.7 28.9 - - - -
388B LEU* 4.0 18.8 - - + -
421B CYS 4.1 5.2 - - - -
422B LEU* 1.3 78.1 - - - +
424B GLN* 1.3 65.3 + - - +
425B SER 3.7 13.1 - - - +
426B PRO* 4.2 1.7 - - - +
427B LEU* 4.8 7.2 - - + -
435B LEU* 5.4 0.7 - - + -
453B ILE* 3.8 23.6 - - + -
455B ALA* 4.3 21.1 - - + -
464B SER* 3.6 24.9 - - - +
466B ASN* 3.1 25.1 - - - -
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 2.6 29.8 + - - -
308B PHE* 5.3 1.6 - - - -
332B VAL* 3.5 20.2 - - + +
333B ASP* 2.7 39.4 + - - +
336B PHE* 3.7 34.8 - - + +
337B ARG* 6.1 0.8 - - - +
422B LEU 4.1 0.4 + - - -
423B PHE* 1.3 72.3 - - - +
425B SER* 1.3 62.0 + - - +
465B SER 5.7 3.5 + - - -
466B ASN* 3.5 11.4 + - - +
315C TYR* 4.2 14.9 + - - +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 4.5 0.2 - - - -
423B PHE* 3.7 4.3 - - - +
424B GLN* 1.3 84.5 + - - +
426B PRO* 1.3 72.9 - - - +
427B LEU* 3.9 1.6 + - - +
463B LYS 6.1 0.7 - - - -
464B SER* 3.5 24.2 + - - -
315C TYR* 3.9 13.9 + - - -
316C GLN* 5.3 1.8 - - - -
317C PRO* 3.1 44.1 - - - +
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Residues in contact with PRO 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 3.7 21.8 - - + +
384B LEU* 4.3 21.5 - - + +
385B VAL 3.1 20.9 - - - +
386B HIS* 3.6 29.4 - - + +
423B PHE* 4.2 6.0 - - + +
424B GLN 3.6 7.4 - - - +
425B SER* 1.3 91.7 - - - +
427B LEU* 1.3 63.0 + - - +
428B PHE 4.1 1.2 + - - -
462B SER* 5.3 0.2 + - - -
316C GLN* 5.3 8.5 + - - +
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Residues in contact with LEU 427 (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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383B GLY 3.7 0.5 - - - +
384B LEU* 3.4 3.2 - - - -
385B VAL* 2.6 48.6 + - + +
423B PHE* 4.8 6.7 - - + -
425B SER 4.7 1.3 - - - +
426B PRO* 1.3 78.8 - - - +
428B PHE* 1.3 60.9 + - - +
429B ALA 3.7 0.3 + - - -
435B LEU* 3.7 24.9 - - + -
455B ALA* 3.6 27.4 - - + +
457B VAL* 3.9 11.0 - - + -
462B SER* 2.9 42.2 - - - +
463B LYS 3.8 14.6 - - - +
464B SER* 3.9 15.0 - - - -
318C SER* 5.4 0.2 - - - -
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Residues in contact with PHE 428 (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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165A GLN 5.9 1.6 - - - -
167A TYR* 4.7 26.0 - + + -
382B SER* 4.9 2.2 - - - -
383B GLY* 3.7 18.6 - - - -
384B LEU* 4.4 15.5 - - + +
426B PRO 4.1 1.8 + - - -
427B LEU* 1.3 73.1 - - - +
429B ALA* 1.3 87.8 + - - +
430B LYS* 3.9 28.7 - - + -
433B ASP* 4.8 0.3 - - - +
457B VAL* 3.7 18.5 - - - +
460B THR* 4.9 6.9 + - - +
462B SER* 5.0 4.4 + - - -
316C GLN* 5.9 5.4 - - - +
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Residues in contact with ALA 429 (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* 5.0 2.0 - - + -
379B MET* 4.0 25.8 - - + -
381B HIS 5.1 0.2 - - - +
382B SER* 3.2 0.9 - - - -
383B GLY 2.8 37.9 + - - +
385B VAL* 4.3 15.3 - - + -
427B LEU 3.7 0.2 + - - -
428B PHE* 1.3 84.1 - - - +
430B LYS* 1.3 62.4 + - - +
433B ASP* 3.7 7.4 - - - +
435B LEU* 6.1 2.0 - - + -
457B VAL* 4.6 11.9 - - + -
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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