Contacts of the strand formed by residues 436 - 442 (chain D) in PDB entry 1YKN
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 TYR 436 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381D ALA* 6.3 0.7 - - + -
382D GLY* 3.3 16.6 - - - -
383D ARG* 3.5 40.9 + - + -
429D CME 3.6 5.9 + - - +
431D THR* 3.1 5.2 - - - -
432D ASP* 2.8 40.3 + - - +
434D ASP* 3.8 24.2 - - + -
435D GLY* 1.3 75.2 - - - +
437D TYR* 1.3 63.5 + - - +
522D ARG* 3.8 28.5 + - - -
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Residues in contact with TYR 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D VAL* 3.9 16.4 - - - +
381D ALA* 3.6 5.8 + - - +
382D GLY 3.0 43.8 + - - +
383D ARG 4.0 1.6 - - - -
384D VAL* 4.1 17.7 - - + -
397D VAL* 4.3 8.1 - - + -
429D CME 3.4 25.4 - - - -
431D THR* 4.1 9.2 - - + -
436D TYR* 1.3 79.1 - - - +
438D SER* 1.3 72.8 + - - +
439D PHE* 3.6 29.6 - + - -
463D PHE* 3.9 15.4 - + - -
523D PHE* 2.7 42.9 + - - +
525D ILE* 4.1 16.2 - - + -
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Residues in contact with SER 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D HIS* 3.7 9.7 + - - +
379D ILE* 4.7 7.6 - - - -
380D VAL 3.5 5.6 - - - -
381D ALA* 3.8 15.3 - - - -
429D CME 3.1 36.2 - - - +
437D TYR* 1.3 85.2 - - - +
439D PHE* 1.4 67.9 + - - +
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Residues in contact with PHE 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D HIS* 3.3 23.8 - - - +
363D LEU* 4.7 1.3 - - + -
379D ILE* 3.4 6.9 - - - +
380D VAL* 2.9 35.5 + - + +
397D VAL* 3.7 26.7 - - + -
399D MET* 3.7 45.8 - - + -
427D GLY* 4.5 2.2 - - - -
428D ARG 3.6 20.6 - - - -
429D CME 3.5 27.8 - - + -
437D TYR* 3.6 32.3 - + - -
438D SER* 1.4 74.5 - - - +
440D ARG* 1.3 62.7 + - - +
441D THR* 5.3 0.2 - - - -
463D PHE* 4.0 7.2 - + - -
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Residues in contact with ARG 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D HIS* 3.2 5.9 + - - -
362D ASP* 2.7 46.8 + - + +
363D LEU* 2.8 32.4 + - - +
364D LEU* 3.5 29.9 + - + +
365D LEU* 4.1 13.5 - - - +
377D ARG* 3.7 20.0 - - - +
378D ILE 3.2 15.3 - - - +
379D ILE* 4.3 13.0 - - + +
439D PHE* 1.3 75.6 - - - +
441D THR* 1.3 65.1 + - - +
514D ASN* 6.1 0.8 - - - +
517D ASP* 5.0 6.5 + - - -
518D CYS* 5.4 7.2 - - + +
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Residues in contact with THR 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LEU* 3.4 22.3 - - - +
364D LEU* 3.7 18.8 - - - +
377D ARG 3.6 1.2 - - - -
378D ILE* 2.7 61.2 + - + +
380D VAL* 3.9 15.7 - - + -
399D MET* 4.4 7.6 - - + -
401D GLN* 2.8 30.6 + - - +
423D PHE* 4.0 1.6 - - - -
439D PHE 5.1 0.2 - - - +
440D ARG* 1.3 79.6 - - - +
442D ILE* 1.4 61.3 + - - +
461D ILE* 4.4 1.6 - - + -
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Residues in contact with ILE 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D LEU* 3.8 20.1 - - + +
373D PRO* 4.0 18.2 - - + +
374D ILE 4.1 10.5 - - - +
375D GLY* 4.0 22.0 - - - +
376D GLU 3.1 12.6 - - - +
377D ARG* 4.6 3.8 - - + -
378D ILE* 4.1 3.6 - - - -
401D GLN* 2.9 26.4 + - - +
403D ASN* 4.1 7.0 - - + -
404D ALA* 3.7 28.0 - - + +
420D ASP* 5.5 0.7 - - - +
423D PHE* 3.5 29.6 - - + -
441D THR* 1.4 78.5 + - - +
443D LYS* 1.3 64.0 + - - +
444D PRO* 3.5 1.2 - - - +
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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