Contacts of the strand formed by residues 501 - 506 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E ILE* 4.5 3.6 - - + -
493E LEU* 4.0 29.2 - - + -
495E TYR* 3.5 53.8 - - + +
498E ARG* 3.0 19.6 + - - +
499E GLY* 4.0 1.4 - - - +
500E ASP* 1.3 78.9 - - - +
502E ALA* 1.3 58.4 - - - +
503E ILE* 4.7 7.0 - - + -
516E LEU* 4.1 15.0 - - + +
517E ALA 3.8 4.7 - - - +
518E ALA* 3.5 21.0 + - - -
528E PHE* 4.6 11.0 - - + -
551E ILE* 3.7 23.3 - - + -
552E GLU 3.4 7.2 - - - +
554E THR* 4.5 0.4 - - - -
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Residues in contact with ALA 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501E LEU* 1.3 74.5 - - - +
503E ILE* 1.3 61.6 + - - +
504E HIS* 4.0 9.6 - - + +
516E LEU 3.1 11.7 - - - +
517E ALA* 4.6 1.6 - - - -
518E ALA 4.4 6.5 - - - +
550E GLU 3.7 0.5 - - - +
551E ILE* 3.5 2.9 - - - -
552E GLU* 3.0 48.2 + - + +
554E THR* 3.5 24.0 - - + -
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Residues in contact with ILE 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491E LEU* 4.0 22.4 - - + -
493E LEU* 4.5 16.2 - - + -
501E LEU* 4.7 5.2 - - + -
502E ALA* 1.3 80.2 - - - +
504E HIS* 1.3 66.4 + - - +
514E THR* 3.5 3.1 - - - -
515E LEU* 2.8 38.5 + - + -
516E LEU* 2.7 46.5 + - + +
528E PHE* 4.6 2.7 - - + -
533E PHE* 4.3 9.4 - - + -
549E LEU* 3.8 23.8 - - + -
550E GLU 3.2 8.3 - - - +
551E ILE* 4.3 16.2 - - + -
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Residues in contact with HIS 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502E ALA* 4.0 12.9 - - + +
503E ILE* 1.3 77.4 - - - +
505E LEU* 1.3 61.9 + - - +
506E VAL 4.3 0.4 - - - -
512E ARG* 3.5 30.5 + - + +
513E SER 3.3 6.3 - - - +
514E THR* 2.9 40.3 + - + -
515E LEU* 4.6 0.9 - - - -
517E ALA* 6.0 0.2 - - - -
548E VAL 3.7 0.6 - - - +
549E LEU* 3.4 8.5 - - - +
550E GLU* 2.8 56.4 + - + +
552E GLU* 3.0 28.8 + - + -
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Residues in contact with LEU 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487E ALA* 5.4 2.5 - - + -
488E GLN 5.5 0.2 - - - -
489E ALA* 4.4 13.9 - - + +
504E HIS* 1.3 75.1 - - - +
506E VAL* 1.3 59.3 + - - +
511E THR 3.4 2.8 - - - +
513E SER* 2.7 42.3 + - - +
515E LEU* 3.8 23.6 - - + -
535E THR* 4.7 13.0 - - + -
547E TRP* 3.7 37.2 - - + -
548E VAL 3.4 15.9 - - - +
549E LEU* 4.0 8.5 - - + -
566E PHE* 3.9 28.0 - - + -
568E LEU* 4.3 12.1 - - + -
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Residues in contact with VAL 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505E LEU* 1.3 76.6 - - - +
507E SER* 1.3 73.9 + - - +
510E GLY* 3.9 18.2 - - - +
511E THR 3.3 9.2 - - - +
512E ARG* 4.0 26.5 - - + +
546E GLU 4.1 0.2 - - - +
547E TRP* 3.3 10.0 - - - -
548E VAL* 2.8 47.6 + - + +
550E GLU* 3.7 23.6 - - - +
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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