Contacts of the helix formed by residues 449 - 456 (chain D) in PDB entry 2YPT
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 449 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LEU* 5.7 0.2 - - - +
40D ARG* 3.4 37.1 + - - +
41D GLN* 3.6 24.4 - - + +
44D ILE* 3.9 25.7 - - + +
448D SER* 1.4 72.2 + - - +
450D TRP* 1.3 64.0 + - - +
451D LEU* 3.3 29.9 + - - +
452D PHE* 3.1 8.3 + - + +
453D SER* 3.0 28.1 + - - -
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Residues in contact with TRP 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D SER 3.4 4.7 + - - -
449D ASP* 1.3 73.1 + - - +
451D LEU* 1.3 79.5 + - + +
453D SER* 3.2 8.8 + - - -
454D MET* 3.1 43.3 + - + +
464D GLU* 5.7 4.3 - - - -
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Residues in contact with LEU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D TRP* 5.2 7.1 - - + -
36D PHE* 5.9 1.6 - - + -
37D LEU* 3.8 18.2 - - + +
40D ARG* 4.5 14.4 - - - +
449D ASP* 3.3 12.4 + - - +
450D TRP* 1.3 94.3 - - + +
452D PHE* 1.4 60.4 - - - +
454D MET* 4.1 3.5 - - - +
455D TRP* 3.6 22.3 + - - +
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Residues in contact with PHE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 3.2 33.4 - - + +
38D ALA* 3.8 21.5 - - + -
41D GLN* 3.3 43.5 - - + -
448D SER* 4.5 0.4 - - - -
449D ASP* 3.1 15.4 + - + +
451D LEU* 1.4 75.9 - - - +
453D SER* 1.4 59.8 + - - +
455D TRP* 3.4 1.4 + - - -
456D HIS* 2.9 63.8 + + + +
457D TYR* 3.5 26.0 - + - -
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Residues in contact with SER 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D ARG* 3.0 20.3 + - - -
448D SER* 3.8 11.7 + - - -
449D ASP 3.0 13.4 + - - -
450D TRP* 3.2 20.1 + - - -
452D PHE* 1.4 73.4 - - - +
454D MET* 1.3 59.0 + - - +
455D TRP 3.3 0.2 - - - -
457D TYR* 3.1 49.0 + - - +
461D PRO* 4.6 15.7 - - - +
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Residues in contact with MET 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D PHE* 3.3 18.6 - - + -
408D THR* 4.5 1.0 - - - +
409D VAL* 4.6 0.2 - - - +
412D ARG* 2.8 36.2 + - - +
450D TRP* 3.1 39.5 + - + +
451D LEU* 4.1 7.2 - - - +
452D PHE 3.3 0.2 - - - -
453D SER* 1.3 77.1 + - - +
455D TRP* 1.3 58.3 + - - +
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Residues in contact with TRP 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL* 5.4 5.6 - - + -
33D TRP* 3.3 39.0 - + + -
34D GLU* 3.3 23.7 + - - +
37D LEU* 3.6 20.9 - - + -
401D GLU* 3.7 30.0 + - + -
405D PHE* 3.5 51.1 - + + -
408D THR* 3.9 13.3 + - - +
451D LEU 3.6 6.5 + - - +
452D PHE 3.4 1.5 + - - +
453D SER 3.3 0.2 - - - -
454D MET* 1.3 80.1 - - - +
456D HIS* 1.4 85.8 + + - +
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Residues in contact with HIS 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 4.0 23.3 - - + +
37D LEU* 3.9 16.6 - - + +
38D ALA* 6.1 0.2 - - + -
408D THR* 3.5 9.4 + - - +
452D PHE* 2.9 59.3 + + + +
455D TRP* 1.4 104.0 + + - +
457D TYR* 1.3 66.0 + - + +
458D SER* 3.2 5.5 + - - -
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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