Contacts of the strand formed by residues 434 - 439 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.9 4.3 - - - -
25E PHE* 4.3 4.7 - - + -
363E LEU* 4.9 2.8 - - - +
423E GLY* 3.2 22.9 - - - -
424E ALA 3.6 3.8 + - - -
425E VAL 2.9 14.0 + - - +
427E ILE* 2.7 45.2 + - + +
432E TYR 3.4 1.6 - - - +
433E PRO* 1.3 72.9 - - - +
435E LEU* 1.3 62.8 + - - +
447E VAL* 5.2 1.6 - - + -
448E TYR 3.4 10.3 - - - +
449E ARG* 3.3 8.6 - - - +
450E ALA 3.2 21.0 + - - -
1421E CA 2.4 32.1 - - - -
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Residues in contact with LEU 435 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 3.8 32.7 - - + +
25E PHE* 4.8 0.2 - - - -
361E ALA* 4.6 2.7 - - + -
363E LEU* 3.5 26.5 - - + -
375E ALA* 4.4 10.8 - - + -
389E VAL* 4.4 12.3 - - + -
391E VAL* 5.6 0.7 - - + -
407E LEU* 3.9 13.5 - - + -
421E LEU* 4.4 6.3 - - + -
422E ARG 3.3 22.9 - - - +
434E ASP* 1.3 79.4 - - - +
436E ILE* 1.3 65.5 + - - +
437E VAL* 3.8 21.5 - - + -
447E VAL* 3.6 1.7 - - - +
448E TYR* 2.7 42.1 + - + +
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Residues in contact with ILE 436 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.7 26.9 - - + +
24E ASP 4.3 5.6 - - - +
25E PHE* 3.5 33.4 - - + -
35E ILE* 3.8 37.5 - - + -
421E LEU* 3.8 2.3 - - - -
422E ARG* 2.8 55.2 + - + +
434E ASP* 6.2 0.2 - - + -
435E LEU* 1.3 76.4 - - - +
437E VAL* 1.3 64.4 + - - +
445E VAL* 4.6 3.6 - - + -
446E ALA 3.6 4.9 - - - +
447E VAL* 4.0 15.7 - - + -
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Residues in contact with VAL 437 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 4.2 0.4 - - - -
389E VAL* 4.0 6.1 - - + -
411E PHE* 5.2 1.0 - - - -
417E PHE* 3.6 25.1 - - + -
418E GLY* 3.5 32.1 - - - +
420E SER 3.7 2.5 - - - -
421E LEU* 3.8 11.9 - - + -
435E LEU* 3.8 20.2 - - + -
436E ILE* 1.3 80.2 - - - +
438E GLY* 1.3 62.4 + - - +
439E ALA 4.0 0.3 + - - -
445E VAL* 3.4 6.0 - - - -
446E ALA* 2.8 40.4 + - - +
448E TYR* 3.7 23.3 - - + -
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Residues in contact with GLY 438 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY* 3.6 19.7 - - - -
23E LEU* 3.9 11.3 - - - +
416E ALA 3.7 1.2 - - - +
418E GLY 3.0 21.3 + - - -
419E PHE* 3.7 9.0 + - - +
420E SER 2.9 18.4 + - - -
437E VAL* 1.3 73.8 - - - +
439E ALA* 1.3 61.3 + - - -
440E TYR 3.7 3.4 + - - -
444E GLN 4.0 3.4 - - - -
445E VAL* 4.5 1.6 - - - -
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Residues in contact with ALA 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY 4.4 0.2 + - - -
411E PHE* 3.5 36.8 - - + -
415E SER* 3.2 19.1 - - - +
416E ALA 4.3 0.2 - - - -
417E PHE* 3.9 9.0 - - + +
437E VAL 4.0 0.4 + - - -
438E GLY* 1.3 72.6 - - - +
440E TYR* 1.3 66.4 + - - +
441E GLY 3.0 2.9 - - - -
442E ALA* 2.9 12.4 + - + -
443E ASN 3.1 7.4 + - - -
444E GLN 2.8 21.7 + - - +
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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