Contacts of the strand formed by residues 536 - 542 (chain A) in PDB entry 1TF4
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 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A TRP* 3.9 25.1 - - + +
503A PHE 3.8 11.9 - - - +
504A THR* 4.8 8.3 - - - +
531A HIS* 3.4 8.3 - - - -
532A VAL* 2.9 54.3 + - + +
533A SER* 2.9 15.7 + - - +
535A ASP* 1.3 77.6 + - - +
537A TYR* 1.3 62.8 + - - +
576A TRP* 5.3 3.8 - - + -
605A PRO* 4.2 26.2 - - + +
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Residues in contact with TYR 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A TRP* 3.3 9.5 - - - +
503A PHE* 2.9 55.1 + + + -
505A LEU* 3.8 32.3 - - + +
511A PRO* 3.7 33.8 - - + +
529A VAL* 4.1 16.6 - - + -
530A HIS 3.1 20.0 - - - +
531A HIS* 3.5 39.0 + + + +
532A VAL 4.4 0.7 - - - +
534A GLY 4.3 0.9 - - - -
535A ASP* 3.6 15.5 - - - -
536A LEU* 1.3 77.7 - - - +
538A TYR* 1.3 63.6 + - - +
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ARG* 3.4 54.2 + - + -
501A TYR 3.3 12.6 - - - +
502A TRP* 3.5 24.0 - - + +
503A PHE* 4.4 2.0 - - - -
529A VAL* 3.6 3.1 - - - -
530A HIS* 2.7 80.2 + + + +
531A HIS 5.3 2.0 - - - -
532A VAL* 3.6 28.5 - - + -
537A TYR* 1.3 76.9 - - - +
539A VAL* 1.3 67.7 + - - +
540A GLU* 4.0 10.1 + - + -
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Residues in contact with VAL 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PHE* 3.8 0.7 - - - +
500A ARG* 3.3 5.0 - - - +
501A TYR* 3.0 39.9 + - + +
503A PHE* 4.0 9.0 - - + -
516A VAL* 4.1 18.2 - - + -
526A PRO* 4.0 22.4 - - + -
528A ASP 5.1 1.1 - - - +
529A VAL* 3.9 26.0 - - + +
530A HIS* 5.0 0.2 - - - -
538A TYR* 1.3 76.0 - - - +
540A GLU* 1.3 63.5 + - - +
541A ILE* 4.2 13.0 + - + +
562A PHE* 4.8 8.5 - - + -
564A ILE* 3.9 23.8 - - + -
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Residues in contact with GLU 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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498A THR* 4.4 21.6 + - - +
499A PHE 3.3 9.9 - - - +
500A ARG* 3.1 35.3 + - + +
526A PRO* 3.8 23.5 - - - +
528A ASP 5.4 0.2 + - - -
530A HIS* 4.5 17.4 + - - +
538A TYR* 4.0 17.6 + - + -
539A VAL* 1.3 76.3 - - - +
541A ILE* 1.3 71.1 + - - +
542A ASP* 3.9 9.2 + - - +
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Residues in contact with ILE 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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498A THR* 3.1 7.3 - - - -
499A PHE* 2.9 75.3 + - + -
501A TYR* 6.6 0.2 - - + -
521A ASN* 4.7 1.3 - - - +
523A CYS* 3.8 19.7 - - + -
524A ALA 3.8 13.0 - - - +
526A PRO* 3.7 29.4 - - + -
539A VAL* 4.4 11.2 - - + +
540A GLU* 1.3 75.3 - - - +
542A ASP* 1.3 61.5 + - - +
543A CYS* 3.8 2.5 + - - -
560A VAL* 3.9 17.7 - - + -
562A PHE* 4.5 16.8 - - + -
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Residues in contact with ASP 542 (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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498A THR* 3.6 11.1 - - + +
523A CYS* 3.9 0.4 - - - -
524A ALA* 3.0 42.0 + - + +
540A GLU* 3.9 10.9 + - - +
541A ILE* 1.3 72.0 - - - +
543A CYS* 1.3 61.5 + - - +
544A THR* 2.9 39.8 + - - +
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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