Contacts of the strand formed by residues 536 - 542 (chain C) in PDB entry 1RR8
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 ARG 536 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528C ASP* 3.0 38.3 + - - +
529C PHE 3.4 13.2 - - - +
530C LEU* 4.0 15.3 - - + -
534C SER 3.5 4.2 + - - +
535C ILE* 1.3 73.6 - - - +
537C TYR* 1.3 64.5 + - - +
538C TYR* 4.1 22.7 + - + +
631C ASN* 3.2 15.9 + - - +
633C GLN* 3.9 14.0 + - - +
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Residues in contact with TYR 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485C LEU* 3.4 31.9 + - + +
487C LEU* 3.8 22.0 - - + -
527C PHE* 3.4 24.0 - + + +
528C ASP* 3.5 3.8 - - - +
529C PHE* 2.9 68.3 + + + +
531C GLY* 5.3 1.1 - - - +
535C ILE 3.7 3.0 + - - +
536C ARG* 1.3 71.5 - - - +
538C TYR* 1.3 63.7 + - - +
539C ASN* 3.8 32.0 + - + -
628C ILE 5.8 1.6 - - - -
629C LEU 4.9 6.0 + - - -
630C CYS 6.0 0.2 - - - -
631C ASN* 3.8 32.8 - - + +
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Residues in contact with TYR 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C GLU* 2.8 42.3 + - + +
527C PHE 3.4 12.6 - - - -
528C ASP* 3.8 24.7 - - - +
536C ARG* 4.1 22.5 + - - +
537C TYR* 1.3 76.0 - - - +
539C ASN* 1.3 65.6 + - - +
540C LYS* 4.0 33.4 + - + +
631C ASN* 5.6 1.4 - - - +
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Residues in contact with ASN 539 (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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485C LEU* 3.7 27.7 - - - +
525C VAL 3.1 5.4 - - - +
526C GLU* 4.7 0.2 - - - -
527C PHE* 3.1 36.4 + - + +
537C TYR* 3.8 26.2 + - + -
538C TYR* 1.3 79.1 - - - +
540C LYS* 1.3 72.1 + - - +
541C VAL* 3.6 12.5 + - - +
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Residues in contact with LYS 540 (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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518C LEU* 5.6 6.7 - - + -
519C ASP* 3.7 23.3 - - - +
521C GLN* 5.0 7.7 - - - +
524C VAL* 3.9 20.6 - - + -
525C VAL 3.7 5.4 - - - -
526C GLU* 4.1 21.8 - - + -
538C TYR* 4.0 30.1 + - + +
539C ASN* 1.3 80.0 + - - +
541C VAL* 1.3 58.7 + - - +
542C PRO* 3.8 7.1 - - - +
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Residues in contact with VAL 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C LYS* 3.7 29.4 - - + +
485C LEU* 3.9 21.3 - - + -
523C TYR 3.7 0.2 - - - +
524C VAL* 4.4 1.6 - - - -
525C VAL* 3.1 33.6 + - + +
527C PHE* 3.7 33.4 - - + -
539C ASN* 3.9 13.9 - - - +
540C LYS* 1.3 73.6 - - - +
542C PRO* 1.4 73.9 - - + +
543C VAL* 3.5 10.4 + - + +
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Residues in contact with PRO 542 (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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480C TYR* 4.5 0.2 + - - -
484C LYS* 4.2 11.3 + - - +
521C GLN* 3.8 39.3 - - + +
522C GLU* 3.7 16.6 - - - +
523C TYR 3.5 9.0 - - - +
524C VAL* 4.5 3.8 - - + -
540C LYS 3.8 7.4 - - - +
541C VAL* 1.4 94.7 - - + +
543C VAL* 1.3 62.7 + - - +
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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