Contacts of the strand formed by residues 546 - 552 (chain A) in PDB entry 3PE3
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 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A LEU* 4.2 8.8 - - + +
544A GLY 4.0 1.4 + - - -
545A ARG* 1.3 71.6 - - - +
547A ARG* 1.3 60.3 + - - +
548A VAL* 3.6 9.1 + - + -
575A LYS 2.8 16.2 + - - +
576A PHE* 3.4 33.2 - - + -
577A GLU 3.0 20.8 + - - -
624A HIS* 3.5 31.2 - - + -
625A ILE* 3.8 12.6 - - + -
1010A TYR* 3.7 22.4 - - + -
1011A LEU* 3.9 17.0 - - + -
1014A TRP* 3.8 28.7 - - + -
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Residues in contact with ARG 547 (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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541A LEU* 3.6 27.1 + - - +
542A SER* 3.5 27.7 + - - +
546A LEU* 1.3 70.3 - - - +
548A VAL* 1.3 61.5 + - - +
577A GLU* 2.9 41.2 + - + +
579A PHE* 3.5 17.2 - - + -
621A ASP 3.5 21.8 + - - -
622A GLY* 3.3 25.8 + - - +
623A ILE* 3.4 7.5 - - - +
624A HIS* 2.8 45.5 + - + +
625A ILE 3.2 7.4 + - - -
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Residues in contact with VAL 548 (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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546A LEU* 3.6 11.6 + - + +
547A ARG* 1.3 75.2 - - - +
549A GLY* 1.3 60.3 + - - +
550A TYR* 3.8 33.4 + - + -
571A HIS* 5.4 1.3 - - + +
576A PHE* 4.0 20.0 - - + -
577A GLU 3.1 9.5 + - - +
578A VAL* 3.7 6.6 - - + -
579A PHE* 2.9 29.1 + - - +
623A ILE* 4.3 0.7 - - - -
625A ILE* 3.4 14.8 - - + +
627A VAL* 4.2 7.4 - - + -
1010A TYR* 3.9 35.0 - - + +
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Residues in contact with GLY 549 (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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548A VAL* 1.3 72.1 - - - +
550A TYR* 1.3 60.2 + - - -
579A PHE* 3.1 9.6 - - - -
581A TYR* 3.9 17.3 - - - -
623A ILE* 3.5 5.9 - - - +
625A ILE 2.9 13.1 + - - +
626A LEU* 3.5 11.8 - - - +
627A VAL* 2.7 34.5 + - - +
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Residues in contact with TYR 550 (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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548A VAL* 3.8 15.5 - - + -
549A GLY* 1.3 70.3 - - - -
551A VAL* 1.3 58.5 + - - +
552A SER 4.0 0.2 - - - -
555A PHE* 3.7 13.0 - - + -
564A MET* 5.3 3.8 - - + -
567A ILE* 4.3 3.8 - - + +
568A PRO* 5.0 7.4 - - + -
571A HIS* 2.8 36.2 + + - -
578A VAL* 4.0 25.1 - - + -
579A PHE 2.8 10.3 + - - +
580A CYS* 3.6 10.5 - - - -
581A TYR 2.7 31.2 + - - +
627A VAL* 3.8 17.9 - - + -
629A MET* 4.0 10.8 - - - -
652A TRP* 3.6 34.1 - + - -
1006A LEU* 3.5 7.7 - - + +
1010A TYR* 2.9 29.0 + - - -
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Residues in contact with VAL 551 (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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550A TYR* 1.3 74.3 - - - +
552A SER* 1.3 62.2 + - - +
581A TYR* 3.5 20.2 - - + +
583A LEU* 3.8 31.4 - - + -
618A ILE* 4.7 4.9 - - + -
626A LEU* 3.9 24.2 - - + -
627A VAL 2.9 14.7 + - - +
628A ASN* 4.3 0.9 - - - +
629A MET* 3.2 26.4 + - - +
630A ASN* 4.0 3.3 - - - +
640A LEU* 4.5 9.0 - - + -
641A PHE* 3.8 32.1 - - + -
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Residues in contact with SER 552 (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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551A VAL* 1.3 76.2 - - - +
553A SER* 1.3 58.5 + - - +
554A ASP* 3.1 32.5 + - - +
555A PHE* 3.6 28.9 - - - -
560A THR* 4.1 5.0 - - - +
581A TYR 3.2 9.1 + - - +
582A ALA* 3.5 4.5 - - - -
583A LEU* 2.8 26.0 + - - -
629A MET* 3.9 18.6 - - - +
630A ASN* 3.3 7.7 + - - -
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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