Contacts of the strand formed by residues 501 - 506 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C ILE* 4.5 1.8 - - + -
493C LEU* 4.0 28.7 - - + -
495C TYR* 3.4 54.3 - - + +
498C ARG* 3.0 21.1 + - + +
499C GLY 4.1 1.0 - - - +
500C ASP* 1.3 78.7 - - - +
502C ALA* 1.3 59.9 + - - +
503C ILE* 4.7 6.7 - - + -
516C LEU* 4.1 14.7 - - + +
517C ALA 3.7 4.3 - - - +
518C ALA* 3.5 20.6 + - - -
519C ARG 4.8 0.2 + - - -
528C PHE* 4.6 11.2 - - + -
551C ILE* 3.8 22.9 - - + -
552C GLU 3.5 7.0 - - - +
554C THR* 4.4 0.2 - - - -
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501C LEU* 1.3 74.9 - - - +
503C ILE* 1.3 63.3 + - - +
504C HIS* 3.8 15.8 - - + +
516C LEU 3.1 9.9 - - - +
517C ALA* 4.7 1.1 - - - -
518C ALA 4.4 7.4 - - - +
550C GLU 3.7 0.9 - - - +
551C ILE* 3.5 2.4 - - - -
552C GLU* 3.0 41.9 + - + +
554C THR* 3.4 24.5 - - + -
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Residues in contact with ILE 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491C LEU* 3.9 26.2 - - + -
493C LEU* 4.4 16.6 - - + -
501C LEU* 4.7 4.7 - - + -
502C ALA* 1.3 81.4 - - - +
504C HIS* 1.3 61.3 + - - +
514C THR* 3.5 3.5 - - - -
515C LEU* 2.8 38.5 + - + -
516C LEU* 2.7 45.3 + - + +
528C PHE* 4.8 2.2 - - + -
533C PHE* 4.4 7.9 - - + -
549C LEU* 3.7 24.5 - - + -
550C GLU 3.2 9.0 - - - +
551C ILE* 4.1 15.9 - - + -
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Residues in contact with HIS 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ALA* 3.8 15.4 - - + +
503C ILE* 1.3 79.5 - - - +
505C LEU* 1.3 60.7 + - - +
506C VAL 4.3 0.2 - - - -
512C ARG* 3.3 38.5 + - + +
513C SER 3.3 7.0 - - - +
514C THR* 2.9 40.5 + - + -
515C LEU* 4.7 0.9 - - - -
517C ALA* 6.0 0.2 - - - -
548C VAL 3.8 0.4 - - - +
549C LEU* 3.4 7.9 - - - +
550C GLU* 2.8 49.2 + - + +
552C GLU* 3.3 27.1 + - + -
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Residues in contact with LEU 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487C ALA* 5.3 2.7 - - + -
489C ALA* 4.3 14.6 - - + +
504C HIS* 1.3 73.8 - - - +
506C VAL* 1.3 60.1 + - - +
507C SER 4.0 0.3 + - - -
511C THR 3.3 2.8 - - - +
513C SER* 2.7 45.4 + - - +
515C LEU* 4.0 16.2 - - + -
535C THR* 4.6 18.2 - - + -
547C TRP* 3.7 36.6 - - + -
548C VAL 3.4 16.8 - - - +
549C LEU* 4.3 6.7 - - + -
566C PHE* 4.1 24.9 - - + -
568C LEU* 4.3 12.3 - - + -
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Residues in contact with VAL 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A HIS* 4.3 12.8 - - + +
505C LEU* 1.3 77.2 - - - +
507C SER* 1.3 75.4 + - - +
510C GLY* 3.9 23.1 - - - +
511C THR 3.3 4.0 - - - +
512C ARG* 4.2 23.6 - - + +
546C GLU 4.1 0.5 - - - +
547C TRP* 3.3 9.1 - - - -
548C VAL* 2.8 49.7 + - + +
550C GLU* 3.9 23.1 - - - +
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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