Contacts of the strand formed by residues 420 - 431 (chain B) in PDB entry 1CYY
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 PHE 420 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238B VAL* 3.8 15.0 - - + -
240B HIS 3.1 17.5 - - - +
241B GLN* 3.2 44.6 - - + -
246B PHE* 4.3 3.1 - + - -
257B ALA* 3.9 27.8 - - + -
260B LEU* 3.7 33.9 - - + -
261B LEU* 3.6 29.6 - - + -
416B GLY* 3.8 0.9 - - - -
417B ALA 2.7 39.9 + - - +
418B GLY* 4.1 2.4 - - - +
419B ASP* 1.3 88.4 - - + +
421B ARG* 1.3 72.5 + - - +
422B LEU* 4.5 2.5 - - + -
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Residues in contact with ARG 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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238B VAL* 3.7 1.0 - - - +
239B THR* 2.8 27.6 + - - +
240B HIS* 3.0 69.1 + - + +
243B ASP* 4.9 14.5 + - - +
269B LEU* 4.0 22.2 - - + -
414B THR* 4.1 17.1 - - + +
415B VAL 3.2 10.1 - - - +
416B GLY* 4.9 0.2 - - - -
420B PHE* 1.3 80.2 - - - +
422B LEU* 1.3 66.6 + - - +
423B LYS* 6.1 0.6 - - - +
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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
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224B ALA* 4.0 25.6 - - + +
236B LEU* 4.0 21.1 - - + -
237B GLN 3.1 11.4 - - - +
238B VAL* 3.7 29.4 - - + +
239B THR* 4.0 4.3 - - - -
261B LEU* 4.8 3.6 - - + -
266B TYR* 4.3 8.3 - - + -
414B THR* 3.4 7.1 - - - +
415B VAL* 2.7 53.3 + - + +
417B ALA* 4.0 26.2 - - + -
420B PHE* 4.5 3.6 - - + -
421B ARG* 1.3 85.7 - - - +
423B LYS* 1.3 61.1 + - - +
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Residues in contact with LYS 423 (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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236B LEU* 3.5 6.2 - - - -
237B GLN* 2.9 35.6 + - + +
239B THR* 3.5 26.7 + - + +
240B HIS* 6.4 1.1 - - - -
412B THR* 3.7 18.6 - - - +
413B LEU 2.9 11.0 - - - +
414B THR* 4.1 11.1 + - - +
421B ARG* 6.1 0.6 - - - +
422B LEU* 1.3 76.2 - - - +
424B ALA* 1.3 60.0 + - - +
425B ARG* 3.0 51.0 - - + +
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Residues in contact with ALA 424 (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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234B LEU* 3.8 14.1 - - + -
235B ALA 3.3 24.2 - - - +
236B LEU* 3.4 13.5 - - + -
412B THR* 3.4 4.7 - - - +
413B LEU* 2.9 35.6 + - + +
423B LYS* 1.3 73.2 - - - +
425B ARG* 1.3 64.4 + - - +
448B ARG* 4.6 0.9 - - - +
450B LEU* 3.8 15.2 - - + +
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Residues in contact with ARG 425 (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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411B THR 3.5 4.7 - - - +
412B THR* 3.4 26.3 + - + +
423B LYS* 3.0 43.3 - - + +
424B ALA* 1.3 78.8 - - - +
426B GLY* 1.3 58.8 + - - +
447B ASP* 4.1 13.2 - - - +
448B ARG* 3.1 22.6 + - - +
450B LEU* 3.9 2.9 - - - -
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Residues in contact with GLY 426 (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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410B SER* 3.3 3.1 - - - -
411B THR* 2.8 34.4 + - - +
425B ARG* 1.3 75.6 - - - +
427B ARG* 1.3 64.9 + - - +
447B ASP* 3.6 6.3 - - - -
448B ARG* 3.5 14.6 - - - -
450B LEU* 3.7 15.2 - - - +
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Residues in contact with ARG 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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276B THR* 5.2 2.5 + - - -
278B SER* 4.9 7.9 - - - -
408B TYR* 3.5 61.1 + - + -
409B ASP 3.3 6.3 - - - +
410B SER* 3.9 18.2 - - - +
426B GLY* 1.3 76.3 - - - +
428B ILE* 1.3 63.5 + - - +
429B LEU 4.1 1.2 + - - -
440B ALA* 5.6 6.5 - - - +
447B ASP* 3.0 38.8 + - - +
448B ARG 3.3 10.1 + - - +
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Residues in contact with ILE 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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295A THR* 3.1 33.2 - - + +
296A ARG* 3.7 26.9 - - + +
441A LEU* 4.2 22.4 - - + -
408B TYR* 3.2 5.9 - - - -
409B ASP* 2.9 42.7 + - + +
411B THR* 5.9 2.9 - - - +
427B ARG* 1.3 76.2 - - - +
429B LEU* 1.3 76.0 + - - +
430B ARG* 3.4 1.5 + - + +
448B ARG 5.7 0.4 - - - -
449B ILE* 3.7 28.5 - - + -
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Residues in contact with LEU 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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296A ARG* 4.8 2.3 + - - -
439A PRO* 3.5 32.0 - - + +
407B LYS 3.9 3.8 - - - +
408B TYR* 3.6 30.5 - - + +
427B ARG 4.1 1.8 + - - -
428B ILE* 1.3 80.4 - - - +
430B ARG* 1.3 58.8 + - - +
431B PHE 3.4 35.4 - - - +
432B ASP* 3.7 18.6 - - + +
435B THR* 5.3 0.9 - - - +
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Residues in contact with ARG 430 (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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297A LEU* 5.4 2.7 - - - -
389A LYS* 3.4 29.3 - - - +
392A GLN* 3.3 25.4 + - - +
396A ARG* 2.8 49.3 + - - +
439A PRO* 3.7 9.3 - - - +
275B PRO* 4.4 5.1 - - - +
276B THR 5.5 0.2 + - - -
407B LYS* 2.8 52.2 + - + +
408B TYR 3.5 13.7 + - - -
409B ASP* 2.9 43.0 + - - +
428B ILE* 3.4 2.4 + - + +
429B LEU* 1.3 74.0 - - - +
431B PHE* 1.3 62.0 + - - +
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Residues in contact with PHE 431 (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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396A ARG* 4.7 9.0 - - - +
439A PRO* 5.4 0.9 - - - -
346B LYS* 3.4 42.8 - - + -
347B TYR* 3.5 34.5 - + - -
404B THR* 3.3 21.3 - - - -
405B PRO 3.4 18.8 - - - -
406B ALA* 3.1 6.8 - - - +
407B LYS* 2.8 48.6 + - + +
429B LEU* 3.4 7.4 - - - +
430B ARG* 1.3 82.5 - - + +
432B ASP* 1.3 61.8 + - - +
433B GLY* 3.4 20.6 - - - -
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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