Contacts of the strand formed by residues 535 - 541 (chain A) in PDB entry 3RFU
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 SER 535 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ILE* 6.0 5.8 - - - -
466A LEU* 5.3 2.3 - - - +
530A ARG* 3.6 13.6 + - - +
533A GLY 3.3 4.1 + - - -
534A ALA* 1.3 68.3 - - - +
536A VAL* 1.3 64.2 + - - +
537A MET* 4.7 9.4 - - - +
549A LEU 3.8 1.2 - - - +
550A VAL* 3.7 1.7 - - - -
551A VAL* 3.0 53.5 + - - +
552A GLU* 5.0 1.3 - - - +
582A ARG* 4.5 7.2 - - - +
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A ALA* 3.5 32.1 - - + +
529A LEU* 4.1 5.8 - - + -
530A ARG* 3.0 34.2 + - + +
534A ALA 3.3 14.8 - - - +
535A SER* 1.3 73.5 + - - +
537A MET* 1.3 84.4 + - - +
538A PHE* 5.8 4.4 - - + -
548A LEU* 3.8 33.0 - - + -
549A LEU 3.7 2.2 - - - +
550A VAL* 3.8 17.7 - - + +
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU* 5.4 15.5 - - + -
506A ILE* 3.8 20.2 - - + -
507A GLY* 4.0 28.0 - - - -
508A ASN* 4.1 11.7 - - + +
530A ARG* 5.2 7.6 - - - +
535A SER* 4.7 13.2 - - - +
536A VAL* 1.3 93.3 - - - +
538A PHE* 1.3 65.3 + - + +
548A LEU* 3.6 3.3 - - - +
549A LEU* 3.0 41.6 + - + +
551A VAL* 6.1 2.0 - - + -
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Residues in contact with PHE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A ILE* 2.9 17.8 - - - +
507A GLY 3.0 26.2 + - - +
508A ASN* 3.5 2.2 - - - -
509A ALA* 3.4 42.6 - - + -
512A MET* 3.3 24.9 - - + +
522A LEU* 4.3 4.7 - - + -
523A PHE* 3.8 29.2 - + - -
526A ALA* 3.4 34.3 - - + -
536A VAL* 5.9 3.4 - - + -
537A MET* 1.3 75.7 - - + +
539A MET* 1.3 60.3 + - - +
545A THR* 4.8 10.8 - - + -
547A ALA 4.0 3.1 - - - +
548A LEU* 3.3 16.2 - - + -
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Residues in contact with MET 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 4.8 0.2 - - + -
451A ALA* 3.4 50.7 - - + +
454A LEU* 4.7 2.0 - - - -
455A ALA* 3.5 19.5 - - - -
504A VAL* 3.4 27.4 - - + -
505A ALA 3.1 7.6 - - - +
506A ILE* 4.0 13.7 - - + -
512A MET* 4.0 1.8 - - - -
538A PHE* 1.3 77.6 - - - +
540A ALA* 1.3 63.3 + - - +
541A VAL* 4.8 1.8 - - + -
545A THR* 3.8 2.3 - - - +
546A VAL* 2.9 32.3 + - + +
547A ALA* 3.0 37.5 + - + +
549A LEU* 4.8 8.7 - - + -
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A HIS 3.1 5.2 - - - +
504A VAL* 3.0 2.9 - - - -
505A ALA* 3.0 30.0 + - - +
512A MET* 3.6 17.2 - - + -
515A HIS 3.8 17.2 - - - +
516A GLY* 4.2 1.8 - - - -
539A MET* 1.3 74.7 - - - +
541A VAL* 1.3 61.7 + - - +
544A LYS 3.1 28.3 - - - +
545A THR* 3.4 7.2 - - - +
546A VAL* 3.8 0.4 - - - -
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 3.8 18.4 - - + -
454A LEU* 3.7 23.6 - - + -
501A GLY* 5.4 5.2 - - - -
502A HIS 5.8 0.2 - - - +
503A HIS 3.5 4.9 - - - +
504A VAL* 3.7 24.2 - - + +
539A MET* 4.8 4.0 - - + -
540A ALA* 1.3 76.2 - - - +
542A ASP* 1.3 83.1 + - + +
544A LYS* 3.2 20.7 + - + +
546A VAL* 3.5 29.2 - - + +
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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