Contacts of the strand formed by residues 434 - 439 (chain C) in PDB entry 1TYE
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 ASP 434 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.9 2.7 - - - -
25C PHE* 4.7 4.3 - - + -
363C LEU* 4.4 3.7 - - - +
366C LEU* 5.9 1.3 - - - +
423C GLY* 3.2 22.7 - - - -
424C ALA 3.5 3.6 + - - -
425C VAL 3.1 14.0 + - - +
427C ILE* 2.9 45.2 + - + +
428C ASP* 3.3 1.6 - - - +
433C PRO* 1.3 73.6 - - - +
435C LEU* 1.3 64.2 + - - +
447C VAL* 5.2 1.8 - - + -
448C TYR 3.6 10.3 - - - +
449C ARG* 3.4 9.1 - - - +
450C ALA 3.1 22.8 + - - +
1414C CA 2.7 28.3 - - - -
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Residues in contact with LEU 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.8 20.0 - - + -
25C PHE* 4.7 1.1 - - - -
361C ALA* 4.8 1.3 - - + -
363C LEU* 3.6 26.7 - - + -
375C ALA* 4.5 10.1 - - + -
389C VAL* 4.5 9.2 - - + -
391C VAL* 5.5 2.5 - - + -
407C LEU* 3.9 24.0 - - + -
421C LEU* 4.6 5.4 - - + -
422C ARG 3.3 26.0 - - - +
434C ASP* 1.3 81.2 - - - +
436C ILE* 1.3 67.7 + - - +
437C VAL* 3.9 22.0 - - + -
446C ALA 3.8 0.3 - - - +
447C VAL* 3.5 2.6 - - - +
448C TYR* 2.7 39.0 + - + +
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Residues in contact with ILE 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU* 3.9 20.1 - - + +
24C ASP 4.2 11.0 - - - -
25C PHE* 3.6 24.9 - - + -
35C ILE* 3.5 48.9 - - + -
420C SER 4.1 0.2 - - - +
421C LEU* 3.7 2.8 - - - -
422C ARG* 2.9 56.3 + - + +
435C LEU* 1.3 77.2 - - - +
437C VAL* 1.3 64.6 + - - +
445C VAL* 4.5 2.7 - - + -
446C ALA 3.4 3.6 - - - +
447C VAL* 4.0 18.2 - - + -
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Residues in contact with VAL 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C VAL* 4.1 7.0 - - + -
411C PHE* 5.6 0.2 - - - -
417C PHE* 3.7 27.3 - - + -
418C GLY* 3.7 24.0 - - - +
420C SER 3.6 2.5 - - - -
421C LEU* 3.5 23.8 - - + -
435C LEU* 3.9 20.6 - - + -
436C ILE* 1.3 80.2 - - - +
438C GLY* 1.3 63.6 + - - +
439C ALA* 5.2 0.9 - - - +
445C VAL* 3.4 5.3 - - - -
446C ALA* 2.7 43.1 + - + +
448C TYR* 4.1 15.5 - - + -
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Residues in contact with GLY 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY 3.6 9.2 - - - -
23C LEU* 3.9 8.7 - - - +
416C ALA 3.8 1.7 - - - +
417C PHE* 3.7 0.5 - - - -
418C GLY 3.0 25.5 + - - -
419C PHE* 3.9 4.5 + - - -
420C SER* 2.9 30.2 + - - -
437C VAL* 1.3 74.4 - - - +
439C ALA* 1.3 60.9 + - - +
440C TYR 4.0 1.6 - - - -
444C GLN 4.0 4.3 - - - -
445C VAL* 4.3 2.2 - - - -
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Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE 4.1 0.4 - - - -
20C GLY 4.1 1.0 + - - -
411C PHE* 4.1 22.2 - - + -
415C SER* 3.3 20.2 - - - +
416C ALA 4.3 0.4 - - - -
417C PHE* 3.8 15.3 - - + +
437C VAL 5.2 0.7 - - - +
438C GLY* 1.3 74.3 - - - +
440C TYR* 1.3 60.1 + - - +
441C GLY 3.1 3.4 - - - -
442C ALA* 2.8 22.4 + - + -
443C ASN 3.0 8.7 + - - -
444C GLN 2.8 20.8 + - - +
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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