Contacts of the strand formed by residues 542 - 548 (chain A) in PDB entry 2YT4
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 PHE 542 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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533A PHE 4.4 1.6 - - - -
535A CYS* 5.2 0.2 - - - -
540A GLU 3.5 0.2 - - - -
541A PRO* 1.3 96.6 - - + +
543A GLY* 1.3 61.1 + - - +
557A THR* 3.2 7.2 + - - -
558A ALA 3.1 29.6 + - - +
559A SER 2.9 37.9 - - - -
560A SER* 3.3 6.7 - - - +
561A LYS* 3.4 36.8 - - + +
564A ALA* 3.6 2.3 - - - +
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Residues in contact with GLY 543 (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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532A PHE* 3.4 12.5 - - - +
533A PHE* 3.0 53.0 + - - +
535A CYS* 4.9 0.4 - - - -
541A PRO 3.6 1.4 + - - -
542A PHE* 1.3 76.6 - - - +
544A ALA* 1.3 61.9 + - - +
556A GLY 3.3 9.6 - - - -
557A THR* 4.3 1.6 - - - -
564A ALA* 4.1 1.8 - - - -
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Residues in contact with ALA 544 (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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530A TYR* 5.2 2.7 - - + -
531A ASN 3.2 8.7 - - - +
532A PHE* 4.0 17.7 - - + -
533A PHE* 3.5 5.4 - - - -
543A GLY* 1.3 74.1 - - - +
545A SER* 1.3 58.8 + - - +
555A SER* 3.4 1.0 - - - -
556A GLY 2.6 37.7 + - - +
564A ALA* 3.5 31.4 - - + +
565A LYS* 3.8 9.9 - - + +
568A ALA* 3.8 4.5 - - + -
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Residues in contact with SER 545 (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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530A TYR* 3.4 6.9 - - - -
531A ASN* 2.7 39.3 + - - -
533A PHE* 3.6 16.6 - - - -
544A ALA* 1.3 76.9 - - - +
546A VAL* 1.3 67.1 + - - +
547A THR* 4.1 3.7 - - - +
552A THR* 3.0 30.1 + - - +
554A GLY 3.4 7.2 - - - -
555A SER* 3.9 9.0 - - - -
568A ALA* 4.0 1.6 - - - -
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Residues in contact with VAL 546 (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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516A LEU* 5.1 2.7 - - + -
520A MET* 5.2 0.2 - - - -
528A PRO* 4.3 14.1 - - + -
529A VAL 3.5 7.4 - - - +
530A TYR* 3.3 34.8 - - + +
545A SER* 1.3 73.2 + - - +
547A THR* 1.3 73.6 + - - +
548A ILE* 4.2 15.5 - - + -
552A THR* 3.4 1.9 - - - -
553A TYR* 2.7 29.3 + - + +
554A GLY 2.9 8.3 + - - +
568A ALA 3.9 13.9 - - - +
569A ALA* 4.4 2.0 - - - +
572A THR* 3.5 31.4 - - + +
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Residues in contact with THR 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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529A VAL* 2.6 59.5 + - - +
531A ASN* 4.4 21.4 - - + +
545A SER* 4.3 5.4 - - - +
546A VAL* 1.3 79.0 - - - +
548A ILE* 1.3 71.5 + - - +
550A GLY* 4.5 14.9 + - - +
551A VAL 3.0 10.5 - - - -
552A THR* 3.8 20.2 - - - +
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Residues in contact with ILE 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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520A MET* 3.2 41.7 - - + -
524A LEU* 6.2 2.2 - - + -
526A VAL* 5.2 2.5 - - + -
527A ARG 4.6 2.2 - - - +
528A PRO* 4.1 5.4 - - + -
529A VAL* 4.7 0.9 - - - -
546A VAL* 4.2 6.5 - - + -
547A THR* 1.3 84.4 - - - +
549A ASP* 1.3 72.5 + - + +
551A VAL* 2.8 21.0 + - - +
553A TYR* 3.4 38.3 + - + +
572A THR* 5.9 2.0 - - + -
576A LEU* 5.9 3.6 - - + -
684A LEU 4.6 2.1 - - - +
686A PRO* 5.4 2.3 - - + +
687A HIS* 3.7 32.8 - - + +
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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