Contacts of the strand formed by residues 543 - 549 (chain D) in PDB entry 1T9D
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484D ALA* 4.3 5.4 - - + -
487D THR* 4.3 9.6 - - + +
489D ARG* 3.7 30.2 - - + +
490D HIS 2.8 13.3 + - - +
491D VAL* 3.4 20.1 - - + +
492D ILE 2.9 24.3 + - - +
536D GLN* 5.2 0.2 - - - -
541D GLU 3.9 0.2 + - - -
542D SER* 1.3 71.4 - - - +
544D VAL* 1.3 58.6 + - - +
545D ILE* 4.0 22.4 - - + -
571D LYS* 3.5 43.3 - - + -
633D VAL* 3.8 30.3 - - + +
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Residues in contact with VAL 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D ILE* 3.4 22.0 - - + +
494D THR* 4.6 4.7 - - + -
532D ALA* 3.6 38.1 - - + +
535D ALA* 4.4 10.1 - - + -
536D GLN* 3.6 48.8 + - + +
542D SER* 3.4 8.3 + - - +
543D LEU* 1.3 76.8 - - - +
545D ILE* 1.3 61.9 + - - +
569D PRO 5.4 1.0 + - - -
570D VAL* 3.7 4.9 - - + +
571D LYS* 2.8 29.5 + - - +
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Residues in contact with ILE 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D LEU* 4.1 23.1 - - + -
484D ALA* 3.9 28.0 - - + -
491D VAL* 4.2 8.1 - - + -
492D ILE 2.9 12.2 + - - +
493D VAL* 3.3 9.7 - - + +
494D THR* 2.9 26.5 + - - +
508D TRP* 4.3 8.5 - - + -
543D LEU* 4.0 22.0 - - + +
544D VAL* 1.3 79.2 - - - +
546D ASP* 1.3 64.2 + - - +
547D ILE* 3.7 20.8 + - + -
571D LYS* 3.2 19.5 - - + +
573D LEU* 4.7 1.1 - - + -
632D PHE* 4.3 9.2 - - + -
633D VAL* 4.8 3.6 - - + -
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Residues in contact with ASP 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D THR* 3.2 16.3 + - - +
495D THR* 3.7 0.7 - - - -
528D GLY* 3.4 23.0 - - - +
529D LEU* 3.3 13.7 + - - +
532D ALA* 4.0 10.5 - - + +
544D VAL 4.2 0.4 + - - -
545D ILE* 1.3 71.2 - - - +
547D ILE* 1.3 68.9 + - - +
548D ASP* 2.7 29.4 - - - +
571D LYS 2.7 13.1 + - - +
572D ILE* 3.8 18.6 - - + +
573D LEU 2.9 28.5 + - - +
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Residues in contact with ILE 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D ILE* 3.8 33.0 - - + -
480D LEU* 4.5 2.7 - - + -
493D VAL* 3.9 18.4 - - + -
494D THR 2.8 11.6 + - - +
495D THR* 3.0 29.1 - - + -
500D HIS* 3.2 14.2 + - + +
504D ALA* 4.0 15.3 - - + -
508D TRP* 3.9 31.4 - - + -
545D ILE* 4.1 15.0 - - + -
546D ASP* 1.3 70.3 - - - +
548D ASP* 1.3 58.2 + - - +
573D LEU* 3.8 17.3 - - + -
575D LEU* 4.5 10.1 - - + -
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Residues in contact with ASP 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D GLY* 3.4 11.5 - - - -
500D HIS* 3.5 12.1 - - - +
526D GLY* 5.4 1.3 + - - -
528D GLY* 4.0 1.8 + - - -
529D LEU 3.9 8.1 + - - -
546D ASP* 2.7 32.0 + - - +
547D ILE* 1.3 72.9 - - - +
549D GLY* 1.3 72.1 + - - +
552D SER* 3.4 20.8 - - - -
553D PHE* 3.8 25.7 - - + -
572D ILE* 5.1 0.7 - - + -
573D LEU 2.7 17.8 + - - +
574D ILE* 4.4 3.6 - - + -
575D LEU* 3.0 28.0 + - - +
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Residues in contact with GLY 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D HIS* 3.3 26.9 + - - -
548D ASP* 1.3 81.1 + - - +
550D ASP* 1.3 60.5 + - - -
551D ALA 3.4 2.0 - - - -
553D PHE* 2.9 30.7 + - - +
574D ILE* 4.2 3.4 - - - -
575D LEU 4.3 6.3 - - - -
2702D P22 3.6 10.1 - - - -
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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