Contacts of the strand formed by residues 414 - 419 (chain D) in PDB entry 5Y7K
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 414 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409D ALA 4.4 0.3 - - - +
410D LEU* 3.9 0.9 - - - +
411D THR* 2.9 36.0 + - - +
413D ASP* 1.3 93.6 - - + +
415D LEU* 1.3 59.4 + - - +
416D TYR* 4.2 16.1 - - + -
433D LYS* 3.4 55.9 + - + -
434D ILE 3.4 13.9 - - - -
435D GLN* 3.7 34.4 + - + -
436D LEU* 3.9 5.4 - - - -
441D LYS* 5.3 1.3 - - + -
443D THR* 6.0 0.7 - - - -
485D SER 6.1 0.4 - - - -
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Residues in contact with LEU 415 (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 HIS* 5.9 0.2 - - + -
372D TYR* 3.5 45.5 - - + -
384D ILE* 3.7 30.1 - - + -
397D ILE* 4.5 2.0 - - + -
407D ILE* 4.2 13.9 - - + -
409D ALA 3.7 7.4 - - - +
410D LEU* 3.9 15.5 - - + -
414D TYR* 1.3 74.1 - - - +
416D TYR* 1.3 76.8 + - - +
417D TYR* 3.9 5.6 + - + -
432D TYR 3.9 0.3 - - - +
433D LYS* 3.7 1.5 - - - -
434D ILE* 3.1 46.0 + - + +
436D LEU* 3.8 9.2 - - + -
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Residues in contact with TYR 416 (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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407D ILE* 4.0 0.2 - - - +
408D GLU* 2.9 25.3 + - - -
409D ALA* 3.0 31.8 + - + +
411D THR* 4.3 20.5 + - + +
414D TYR* 4.2 18.5 - - + +
415D LEU* 1.3 77.7 - - - +
417D TYR* 1.3 61.1 + - - +
431D LEU* 4.0 5.2 - - + -
432D TYR 3.3 7.0 - - - +
433D LYS* 3.5 36.6 - - + +
445D LEU* 3.7 22.0 - - + -
461D PHE* 3.4 41.3 - + + -
465D ALA* 4.6 3.4 - - + -
468D TYR* 5.1 1.6 - + - -
485D SER* 3.9 25.1 + - - -
488D ASP* 4.6 3.5 + - - -
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Residues in contact with TYR 417 (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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384D ILE* 3.8 25.6 - - + -
398D THR* 4.2 13.9 - - + +
402D TRP* 3.8 21.3 - + - -
404D VAL* 3.6 18.6 - - + -
406D GLY 3.3 13.7 - - - +
407D ILE* 4.4 1.8 - - - -
408D GLU* 4.4 1.1 - - - +
415D LEU* 4.0 11.7 - - + -
416D TYR* 1.3 75.0 - - - +
418D ILE* 1.3 69.7 + - - +
419D SER* 3.6 23.8 - - - -
421D GLU* 4.0 0.9 + - - -
431D LEU* 3.3 5.5 - - - +
432D TYR* 2.8 63.0 + - + +
434D ILE* 4.2 21.3 - - + -
442D VAL* 3.6 16.4 - - + +
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Residues in contact with ILE 418 (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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404D VAL* 3.3 7.1 - - - +
405D ILE* 2.6 38.4 + - + -
406D GLY 2.9 9.4 + - - +
408D GLU* 3.6 26.9 - - + +
417D TYR* 1.3 74.3 - - - +
419D SER* 1.3 62.3 + - - +
429D ARG* 4.1 24.0 - - - -
430D ASN 3.3 12.3 - - - +
431D LEU* 3.6 40.2 - - + +
457D TYR 4.2 19.1 - - - +
458D SER* 5.1 2.9 - - - -
459D VAL* 4.3 9.9 - - + +
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Residues in contact with SER 419 (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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402D TRP* 3.6 21.2 - - - -
403D GLU 3.2 18.4 - - - -
404D VAL* 3.9 0.9 - - - -
405D ILE* 3.9 7.9 - - - -
417D TYR* 3.6 9.2 - - - -
418D ILE* 1.3 77.0 - - - +
420D ASN* 1.3 59.6 + - - +
421D GLU* 3.4 6.3 + - - +
422D TYR* 5.2 0.5 + - - +
428D GLY 4.2 2.0 - - - -
429D ARG* 3.6 2.8 - - - -
430D ASN* 3.1 29.3 + - - +
432D TYR* 3.1 27.5 - - - -
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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