Contacts of the strand formed by residues 501 - 506 (chain D) in PDB entry 4RYD
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 LEU 501 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D ILE* 4.4 2.5 - - + -
493D LEU* 4.1 22.2 - - + -
495D TYR* 3.6 60.6 - - + +
498D ARG* 3.1 22.8 + - + +
499D GLY* 4.0 1.0 - - - +
500D ASP* 1.3 80.6 - - - +
502D ALA* 1.3 58.8 + - - +
503D ILE* 4.7 6.5 - - + -
516D LEU* 4.1 15.5 - - + +
517D ALA 3.7 4.5 - - - +
518D ALA* 3.5 20.6 + - - -
528D PHE* 4.9 5.2 - - + -
551D ILE* 3.7 26.2 - - + -
552D GLU 3.4 7.0 - - - +
554D THR* 4.5 0.2 - - - -
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Residues in contact with ALA 502 (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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501D LEU* 1.3 74.4 - - - +
503D ILE* 1.3 62.3 + - - +
504D HIS* 3.9 9.8 - - + +
516D LEU 3.1 12.1 - - - +
517D ALA* 4.7 1.3 - - - -
518D ALA 4.4 6.1 - - - +
550D GLU 3.7 1.0 - - - +
551D ILE* 3.5 2.6 - - - +
552D GLU* 3.0 47.7 + - + +
554D THR* 3.5 24.2 - - + -
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Residues in contact with ILE 503 (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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491D LEU* 4.0 27.1 - - + -
493D LEU* 4.3 16.6 - - + -
501D LEU* 4.7 4.7 - - + -
502D ALA* 1.3 80.2 - - - +
504D HIS* 1.3 66.4 + - - +
514D THR* 3.5 3.6 - - - -
515D LEU* 2.8 33.4 + - + -
516D LEU* 2.7 45.2 + - + +
528D PHE* 4.8 2.0 - - + -
533D PHE* 4.4 8.1 - - + -
549D LEU* 3.7 23.8 - - + -
550D GLU 3.2 7.9 - - - +
551D ILE* 4.1 17.7 - - + -
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Residues in contact with HIS 504 (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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502D ALA* 3.9 13.9 - - + +
503D ILE* 1.3 77.4 - - - +
505D LEU* 1.3 61.2 + - - +
506D VAL* 4.3 0.9 - - + -
512D ARG* 3.6 30.9 + - + +
513D SER 3.3 6.7 - - - +
514D THR* 2.8 41.7 + - + -
515D LEU* 4.5 1.6 - - - -
517D ALA* 6.0 0.2 - - - -
548D VAL 4.4 0.2 - - - -
549D LEU* 3.4 9.0 - - - +
550D GLU* 2.8 55.8 + - + +
552D GLU* 3.4 25.7 + - + -
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Residues in contact with LEU 505 (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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487D ALA* 5.2 2.5 - - + -
488D GLN 5.5 0.4 - - - -
489D ALA* 4.5 13.0 - - + +
504D HIS* 1.3 74.2 - - - +
506D VAL* 1.3 61.4 + - - +
507D SER 4.0 0.3 + - - -
511D THR 3.3 2.3 - - - +
513D SER* 2.7 41.1 + - - +
515D LEU* 3.9 19.3 - - + -
535D THR* 4.5 19.3 - - + -
547D TRP* 3.7 37.7 - - + -
548D VAL 3.4 13.0 - - - +
549D LEU* 4.1 8.3 - - + -
566D PHE* 4.1 26.9 - - + -
568D LEU* 4.3 12.3 - - + -
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Residues in contact with VAL 506 (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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505D LEU* 1.3 77.1 - - - +
507D SER* 1.3 74.1 + - - +
510D GLY* 3.9 17.9 - - - +
511D THR 3.2 9.2 - - - +
512D ARG* 3.8 35.7 - - + +
546D GLU 4.1 0.3 - - - +
547D TRP* 3.3 9.8 - - - -
548D VAL* 2.8 49.8 + - + +
550D GLU* 3.8 12.1 - - - +
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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