Contacts of the strand formed by residues 458 - 470 (chain A) 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 ALA 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A THR 4.2 0.2 - - - -
229A PRO* 3.3 30.0 - - + +
266A TYR 3.5 9.4 - - - +
267A SER* 4.3 2.7 - - - +
456A GLY 3.7 1.9 + - - +
457A ASP* 1.3 74.9 - - - +
459A LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 459 (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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226A THR* 3.7 21.8 - - - +
227A THR 3.3 5.2 - - - +
228A THR* 3.9 23.1 - - + +
229A PRO* 4.3 4.7 - - + -
234A LEU* 3.9 18.6 - - + -
236A LEU* 4.0 4.9 - - + -
266A TYR* 3.0 34.5 + - + +
268A VAL* 4.3 18.8 - - + -
415A VAL* 3.7 39.0 - - + -
453A VAL* 4.6 2.0 - - + -
457A ASP 4.7 0.7 - - - +
458A ALA* 1.3 83.6 - - - +
460A THR* 1.3 62.6 + - - +
461A LEU 4.1 0.7 + - - -
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Residues in contact with THR 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 3.0 7.1 - - - -
227A THR* 2.8 39.3 + - - -
228A THR 5.5 0.2 + - - -
459A LEU* 1.3 73.9 - - - +
461A LEU* 1.3 66.8 + - - +
462A VAL* 3.5 1.4 + - - +
294B SER 3.8 3.6 - - - +
295B THR 3.6 20.9 - - - +
296B ARG 4.2 1.2 + - - -
297B LEU* 3.4 24.3 + - - -
298B GLY* 3.6 23.2 - - - -
472B LYS* 3.8 13.5 - - - +
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Residues in contact with LEU 461 (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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224A ALA* 3.9 8.5 - - + -
225A SER 3.6 16.6 - - - +
226A THR* 4.1 6.7 - - + -
261A LEU 3.7 11.9 - - - +
262A GLU* 3.9 8.3 - - - +
266A TYR* 3.6 39.8 - - + +
459A LEU 4.1 2.2 + - - -
460A THR* 1.3 73.8 - - - +
462A VAL* 1.3 60.2 + - - +
463A GLU 3.6 14.8 - - - +
464A LEU* 3.8 22.7 - - + -
214B PHE* 3.4 39.3 - - + -
472B LYS* 3.9 17.2 + - - -
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A SER* 2.8 20.5 + - - +
226A THR* 4.8 1.6 - - - -
227A THR* 4.2 8.3 - - - +
460A THR* 3.5 3.5 + - + +
461A LEU* 1.3 77.9 - - - +
463A GLU* 1.3 72.7 + - + +
214B PHE* 3.9 4.7 - - - -
295B THR* 3.4 50.3 - - + +
471B THR* 3.7 4.2 - - + -
472B LYS* 3.1 29.6 + - + +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ALA* 3.3 3.8 - - - -
225A SER* 2.8 50.6 + - - +
461A LEU* 3.6 3.9 - - - +
462A VAL* 1.3 88.3 - - + +
464A LEU* 1.3 70.6 + - - +
465A THR* 4.0 5.4 - - - +
214B PHE* 4.0 2.8 - - - -
217B GLU* 5.0 1.0 - - - +
469B HIS* 2.8 38.2 + - - +
470B PHE 3.2 15.5 - - - +
471B THR* 3.8 15.4 - - + +
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Residues in contact with LEU 464 (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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222A VAL* 4.2 14.1 - - + -
223A ASP 3.4 4.5 - - - +
224A ALA* 3.6 26.7 - - + -
238A VAL* 5.3 0.4 - - + -
258A VAL* 3.6 43.1 - - + +
261A LEU* 3.6 25.6 - - + -
262A GLU* 3.8 15.9 - - + +
266A TYR* 4.2 1.6 - - - +
461A LEU* 3.8 18.2 - - + -
463A GLU* 1.3 74.5 - - - +
465A THR* 1.3 63.4 + - - +
466A PRO* 3.7 2.7 - - - +
214B PHE* 4.8 1.8 - - + -
469B HIS* 3.7 0.2 - - - -
470B PHE* 2.8 41.6 + - + +
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Residues in contact with THR 465 (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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221A GLU 3.8 1.0 - - - +
222A VAL* 3.5 2.4 - - - +
223A ASP* 2.8 46.5 + - + +
225A SER* 5.7 0.3 + - - -
463A GLU* 3.5 8.8 + - - +
464A LEU* 1.3 76.2 + - - +
466A PRO* 1.3 67.9 - - - +
467A ALA* 3.8 3.6 + - + +
467B ALA* 4.4 10.8 - - + -
468B GLN 3.5 7.2 - - - +
469B HIS* 2.8 39.9 + - + +
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Residues in contact with PRO 466 (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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220A TRP* 4.3 8.8 - - + -
221A GLU 3.3 6.7 - - - +
222A VAL* 4.0 7.0 - - + -
254A THR* 3.6 29.6 - - + -
255A GLN* 6.0 1.8 - - + -
258A VAL* 4.3 11.2 - - + -
464A LEU 3.7 5.8 - - - +
465A THR* 1.3 88.5 - - - +
467A ALA* 1.3 59.9 + - - +
467B ALA* 3.3 3.9 - - - +
468B GLN* 3.0 53.5 + - + +
470B PHE* 3.8 17.0 - - + -
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TRP* 3.2 11.6 - - - -
221A GLU* 2.8 33.4 + - + +
465A THR* 3.8 4.5 + - + +
466A PRO* 1.3 75.0 - - - +
468A GLN* 1.3 60.2 + - - +
469A HIS* 3.5 13.8 - - - +
465B THR* 3.7 19.5 - - + -
466B PRO 3.2 12.1 - - - +
467B ALA* 3.8 8.1 - - + +
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Residues in contact with GLN 468 (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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218A GLU* 2.7 34.8 + - - +
219A PHE 3.8 3.4 - - - +
220A TRP* 3.5 36.4 - - + +
467A ALA* 1.3 72.7 - - - +
469A HIS* 1.3 65.9 + - - +
470A PHE* 3.3 21.4 - - + -
251B LYS* 4.3 4.8 - - - +
255B GLN* 2.9 37.3 + - - +
464B LEU 4.1 1.0 - - - +
465B THR* 3.3 15.9 + - - -
466B PRO* 2.8 40.4 + - + +
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Residues in contact with HIS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLU* 3.2 7.6 - - - +
219A PHE* 2.8 58.2 + + + +
221A GLU* 3.2 50.2 + - + +
467A ALA* 3.5 21.3 - - + +
468A GLN* 1.3 81.0 - - - +
470A PHE* 1.3 65.3 + - - +
463B GLU* 3.2 26.1 + - - +
465B THR* 3.5 15.9 + - + -
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Residues in contact with PHE 470 (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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218A GLU* 3.5 35.2 - - + +
219A PHE* 4.4 5.4 - - - -
468A GLN* 3.3 37.9 - - + -
469A HIS* 1.3 74.2 - - - +
471A THR* 1.3 65.3 + - - +
472A LYS* 3.2 20.6 + - + +
255B GLN* 3.9 10.5 - - - -
258B VAL* 4.8 14.4 - - + -
262B GLU* 5.1 10.3 - - - +
463B GLU* 3.1 20.4 + - + +
464B LEU 4.5 11.2 - - - -
466B PRO* 4.6 9.0 - - + -
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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