Contacts of the strand formed by residues 536 - 542 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B TRP* 3.9 25.4 - - + +
503B PHE* 3.7 11.4 - - - +
504B THR* 4.8 7.0 - - - +
531B HIS* 3.4 8.7 - - - -
532B VAL* 2.9 53.1 + - + -
533B SER* 2.9 16.2 + - - +
535B ASP* 1.3 77.3 - - - +
537B TYR* 1.3 62.8 + - - +
576B TRP* 5.2 4.3 - - + +
605B PRO* 4.1 25.8 - - + -
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Residues in contact with TYR 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B TRP* 3.2 10.0 - - - -
503B PHE* 2.8 54.5 + + + -
505B LEU* 3.8 30.6 - - + +
511B PRO* 3.7 35.0 - - + +
514B ILE* 6.0 0.2 - - + -
529B VAL* 4.1 16.8 - - + -
530B HIS 3.1 20.9 - - - -
531B HIS* 3.5 39.9 + + + -
532B VAL* 4.4 1.1 - - - +
534B GLY 4.2 4.2 + - - -
535B ASP 3.4 16.8 - - - -
536B LEU* 1.3 75.1 - - - +
538B TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ARG* 3.4 55.1 + - + -
501B TYR 3.2 13.0 - - - +
502B TRP* 3.5 22.7 - - + +
503B PHE* 4.4 2.5 - - - -
529B VAL* 3.7 3.5 - - - -
530B HIS* 2.8 74.1 + + + +
531B HIS 5.3 2.0 - - - -
532B VAL* 3.4 30.5 - - + -
537B TYR* 1.3 76.4 - - - +
539B VAL* 1.3 68.2 + - - +
540B GLU* 3.9 10.6 + - + -
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Residues in contact with VAL 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B PHE* 3.7 1.0 - - - +
500B ARG* 3.3 4.7 - - - +
501B TYR* 2.9 38.5 + - + +
503B PHE* 3.9 20.4 - - + -
516B VAL* 4.1 17.9 - - + -
526B PRO* 4.0 22.4 - - + -
528B ASP 5.2 1.3 - - - +
529B VAL* 3.9 17.0 - - + +
530B HIS* 5.1 1.3 - - - -
538B TYR* 1.3 76.4 - - - +
540B GLU* 1.3 64.1 + - - +
541B ILE* 4.2 13.5 + - + +
562B PHE* 4.8 7.9 - - + -
564B ILE* 4.0 19.1 - - + -
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Residues in contact with GLU 540 (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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498B THR* 4.4 21.0 + - - +
499B PHE 3.3 10.3 - - - +
500B ARG* 3.2 35.0 + - + -
526B PRO* 3.8 22.9 - - - +
528B ASP 5.5 0.2 + - - -
530B HIS* 4.5 18.1 + - - +
538B TYR* 3.9 17.3 + - + -
539B VAL* 1.3 77.0 - - - +
541B ILE* 1.3 70.4 - - - +
542B ASP* 3.9 9.2 + - - +
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Residues in contact with ILE 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B THR* 3.1 7.3 - - - -
499B PHE* 2.9 69.5 + - + -
521B ASN* 4.7 1.6 - - - +
523B CYS* 3.9 20.0 - - + -
524B ALA 3.8 13.5 - - - +
526B PRO* 3.7 29.2 - - + -
539B VAL* 4.4 12.1 - - + +
540B GLU* 1.3 75.0 - - - +
542B ASP* 1.3 62.1 + - - +
543B CYS* 3.8 2.8 + - - -
560B VAL* 4.0 22.7 - - + -
562B PHE* 4.6 15.7 - - + -
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Residues in contact with ASP 542 (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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498B THR* 3.6 11.1 - - + +
523B CYS* 3.9 0.4 - - - -
524B ALA* 3.0 42.2 + - + +
540B GLU* 3.9 11.5 + - - +
541B ILE* 1.3 72.5 - - - +
543B CYS* 1.3 62.1 + - - +
544B THR* 2.8 39.6 + - - +
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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
------------------------------------------------------------
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