Contacts of the strand formed by residues 485 - 491 (chain D) in PDB entry 4YFI
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 LYS 485 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481D ARG* 3.4 11.8 - - - +
482D CYS 3.0 31.0 + - - +
483D ARG* 3.5 24.1 + - + +
484D ASN* 1.3 82.2 - - - +
486D ILE* 1.3 65.7 + - - +
487D VAL* 3.6 8.8 + - + +
523D GLN* 5.8 3.6 - - - +
525D VAL* 4.8 16.8 - - + +
540D GLN* 6.0 3.4 - - + -
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Residues in contact with ILE 486 (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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479D LYS* 3.7 28.9 - - + +
480D GLY 3.6 11.9 - - - +
481D ARG* 4.4 16.8 - - + +
485D LYS* 1.3 75.6 - - - +
487D VAL* 1.3 63.3 + - - +
540D GLN* 3.8 3.1 - - - +
541D TYR* 2.8 43.0 + - + +
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Residues in contact with VAL 487 (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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479D LYS* 3.4 5.5 - - - +
480D GLY 2.9 50.1 + - - -
481D ARG 3.6 10.1 - - - +
482D CYS* 3.9 15.3 - - + +
485D LYS* 3.6 13.9 - - + +
486D ILE* 1.3 79.2 - - - +
488D ALA* 1.3 59.3 + - - +
489D ILE* 3.6 17.0 - - + -
525D VAL* 4.3 11.4 - - + -
538D VAL* 3.5 24.5 - - + -
539D THR 3.1 15.0 - - - +
540D GLN* 4.9 0.4 - - - -
541D TYR* 3.6 10.4 - - - +
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Residues in contact with ALA 488 (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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469D ILE* 4.4 7.6 - - + -
477D VAL* 4.7 1.1 - - + -
478D TYR 3.2 9.2 - - - +
487D VAL* 1.3 73.9 - - - +
489D ILE* 1.3 60.8 + - - +
537D ILE 3.6 1.0 - - - +
538D VAL* 3.3 4.2 - - - +
539D THR* 2.8 33.5 + - - +
541D TYR* 4.0 3.0 - - + +
801D 4CW 3.5 54.1 - - + +
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Residues in contact with ILE 489 (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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463D ILE* 3.8 22.7 - - + -
464D GLU 4.3 1.3 - - - +
465D PHE* 3.9 27.1 - - + -
476D LYS 3.6 0.2 - - - +
477D VAL* 3.3 6.4 - - - +
478D TYR* 2.9 41.8 + - + +
479D LYS 4.1 3.6 - - - +
480D GLY* 3.8 22.9 - - - +
487D VAL* 3.6 26.9 - - + -
488D ALA* 1.3 76.1 - - - +
490D LYS* 1.3 59.6 + - - +
491D ARG* 3.3 5.9 + - + +
536D ALA* 4.0 24.5 - - + -
537D ILE 3.3 5.4 - - - +
538D VAL* 4.2 11.4 - - + -
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Residues in contact with LYS 490 (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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474D PHE* 3.7 40.8 - - + +
476D LYS 3.7 2.5 - - - -
477D VAL* 4.2 13.5 - - + +
489D ILE* 1.3 70.3 - - - +
491D ARG* 1.3 58.3 + - - +
492D TYR* 2.9 40.2 + - + +
509D GLU* 3.1 26.7 + - - +
536D ALA* 3.3 4.7 - - - -
537D ILE* 2.8 43.4 + - + +
606D ASP* 5.0 3.5 + - - -
608D GLY* 4.4 9.5 - - - -
801D 4CW 3.9 26.6 - - + +
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Residues in contact with ARG 491 (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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460D LEU* 3.6 28.9 - - - +
465D PHE* 4.1 24.6 - - + -
474D PHE* 4.0 4.0 - - - +
475D GLY* 3.5 3.5 - - - -
476D LYS* 2.7 39.4 + - + +
478D TYR* 4.0 25.0 + - + +
489D ILE* 3.3 4.7 + - + +
490D LYS* 1.3 74.5 - - - +
492D TYR* 1.3 70.3 + - - +
533D SER 3.4 21.7 + - - -
534D GLN* 3.8 15.0 + - - +
535D PHE 3.6 15.9 + - - -
536D ALA* 4.1 11.2 - - - -
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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