Contacts of the strand formed by residues 543 - 549 (chain B) in PDB entry 1T9A
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 543 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484B ALA* 4.5 3.4 - - + -
487B THR* 4.2 25.1 - - + +
489B ARG* 3.8 32.0 - - + +
490B HIS 2.7 15.5 + - - +
491B VAL* 3.4 22.0 - - + +
492B ILE 3.0 23.4 + - - +
536B GLN* 5.0 0.2 - - - -
542B SER* 1.3 68.9 - - - +
544B VAL* 1.3 61.4 + - - +
545B ILE* 4.1 20.4 - - + -
569B PRO 5.5 0.4 - - - +
571B LYS* 4.0 35.0 - - + +
633B VAL* 4.4 15.7 - - + +
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Residues in contact with VAL 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 3.4 19.5 - - + +
494B THR* 4.5 5.4 - - + -
532B ALA* 3.6 39.3 - - + +
535B ALA* 4.3 10.5 - - + +
536B GLN* 3.4 48.7 + - + +
542B SER* 3.5 9.0 + - - +
543B LEU* 1.3 75.0 - - - +
545B ILE* 1.3 62.0 + - - +
546B ASP 4.3 0.2 - - - -
569B PRO 5.5 0.4 + - - -
570B VAL* 3.8 3.8 - - + +
571B LYS* 3.0 28.4 + - - +
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Residues in contact with ILE 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480B LEU* 4.2 20.4 - - + -
484B ALA* 4.1 26.2 - - + -
491B VAL* 4.3 8.7 - - + -
492B ILE 2.9 11.4 + - - +
493B VAL* 3.3 9.0 - - + +
494B THR* 2.8 28.1 + - - +
508B TRP* 4.3 9.2 - - + -
543B LEU* 4.1 22.4 - - + +
544B VAL* 1.3 80.1 - - - +
546B ASP* 1.3 63.8 + - - +
547B ILE* 3.8 22.3 + - + -
571B LYS* 3.3 16.8 - - + +
573B LEU* 4.7 1.1 - - + -
632B PHE* 4.5 8.3 - - + -
633B VAL* 4.7 4.5 - - + -
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Residues in contact with ASP 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B THR* 3.1 16.8 + - - +
495B THR* 3.7 0.2 - - - -
528B GLY* 3.1 31.3 - - - +
529B LEU* 3.4 9.2 + - - +
532B ALA* 4.0 5.3 - - + +
545B ILE* 1.3 72.0 - - - +
547B ILE* 1.3 62.9 + - - +
548B ASP* 2.8 30.1 - - - +
571B LYS 2.8 8.7 + - - -
572B ILE* 3.6 29.2 - - + +
573B LEU 2.8 30.9 + - - +
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Residues in contact with ILE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ILE* 3.8 31.0 - - + -
480B LEU* 4.4 3.6 - - + -
493B VAL* 4.0 17.3 - - + -
494B THR 2.8 11.5 + - - +
495B THR* 3.0 26.2 - - + -
500B HIS* 3.2 16.5 - - + +
504B ALA* 4.1 14.6 - - + -
508B TRP* 3.8 33.4 - - + -
545B ILE* 4.0 14.4 - - + -
546B ASP* 1.3 71.0 - - - +
548B ASP* 1.3 60.6 + - - +
573B LEU* 3.7 19.5 - - + -
575B LEU* 4.4 9.4 - - + -
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Residues in contact with ASP 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B GLY* 3.3 11.6 - - - -
500B HIS* 3.4 10.0 - - - +
526B GLY 5.3 1.6 + - - -
528B GLY* 3.8 8.7 + - - -
529B LEU* 3.9 3.5 + - - +
546B ASP* 2.8 31.0 - - - +
547B ILE* 1.3 72.9 - - - +
549B GLY* 1.3 73.3 + - - +
552B SER* 3.1 22.3 - - - -
553B PHE* 4.1 22.5 - - + -
572B ILE* 5.1 0.4 - - + -
573B LEU 2.7 16.0 + - - +
574B ILE* 4.4 5.4 - - + -
575B LEU* 3.0 30.7 + - - +
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Residues in contact with GLY 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B HIS* 3.3 17.4 + - - -
548B ASP* 1.3 81.1 + - - +
550B ASP* 1.3 59.8 + - - -
551B ALA 3.4 2.9 - - - -
552B SER 3.4 0.3 + - - -
553B PHE* 2.9 29.6 + - - +
574B ILE* 4.3 3.1 - - - -
575B LEU 4.1 7.6 - - - -
698B P23 3.4 19.7 - - - -
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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