Contacts of the strand formed by residues 444 - 448 (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 GLN 444 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E PHE* 4.7 12.7 - - + +
11E TYR 3.2 12.6 + - - +
12E ALA* 3.9 17.9 - - + +
19E PHE* 3.4 2.8 + - - +
411E PHE* 3.7 38.9 - - + -
412E PRO* 5.5 1.6 - - - +
439E ALA* 2.8 32.6 + - - +
442E ALA* 3.1 22.6 - - + +
443E ASN* 1.3 81.3 - - + +
445E VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E THR 3.8 0.3 - - - +
10E PHE* 3.4 5.7 - - - -
11E TYR* 2.9 44.9 + - + +
19E PHE* 3.4 29.8 - - + -
20E GLY* 3.9 15.5 - - - -
23E LEU* 3.6 21.5 - - + -
35E ILE* 4.8 9.2 - - + -
37E VAL* 4.0 10.8 - - + -
411E PHE* 4.4 2.9 - - - -
436E ILE* 4.6 7.2 - - + -
437E VAL 3.4 15.5 - - - +
438E GLY* 4.6 0.4 - - - -
444E GLN* 1.3 77.4 - - - +
446E ALA* 1.3 66.5 + - - +
447E VAL* 4.2 1.6 - - + -
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Residues in contact with ALA 446 (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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8E LEU* 5.1 1.3 - - + -
9E THR 3.3 4.3 - - - +
10E PHE* 3.8 25.1 - - + -
410E PRO* 4.8 0.4 - - + -
411E PHE* 3.8 14.8 - - + -
417E PHE* 4.8 3.1 - - + -
436E ILE* 3.6 0.5 - - - -
437E VAL* 2.8 41.8 + - - +
445E VAL* 1.3 74.1 - - - +
447E VAL* 1.3 63.4 + - - +
448E TYR* 3.9 22.3 - - + +
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Residues in contact with VAL 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 3.2 25.5 - - - +
9E THR* 2.8 32.4 + - - +
11E TYR* 3.9 17.5 - - + -
35E ILE* 3.7 26.5 - - + -
58E TRP* 4.2 16.4 - - + -
427E ILE* 4.3 20.4 - - + -
434E ASP* 5.2 0.7 - - + -
435E LEU 3.6 8.5 - - - +
436E ILE* 4.0 14.1 - - + +
445E VAL* 5.1 2.0 - - + -
446E ALA* 1.3 75.4 - - - +
448E TYR* 1.3 69.7 + - - +
449E ARG* 4.4 2.6 + - + +
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Residues in contact with TYR 448 (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* 4.1 22.1 - - + +
4E ASP 3.8 17.3 - - - -
5E PRO* 4.3 11.0 - - + -
8E LEU* 3.3 33.4 - - + +
407E LEU* 3.7 35.0 - - + +
408E ASP 4.0 5.9 + - - -
410E PRO* 3.8 11.6 - - - +
417E PHE* 3.6 20.2 - + - -
434E ASP* 3.4 5.9 - - - +
435E LEU* 2.7 40.4 + - + +
437E VAL* 3.7 29.6 - - + -
446E ALA* 3.9 14.1 - - + -
447E VAL* 1.3 75.8 - - - +
449E ARG* 1.3 63.2 + - - +
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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