Contacts of the helix formed by residues 461 - 471 (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 PRO 461 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412D ARG* 5.4 3.4 - - - -
446D PRO 4.9 10.3 - - - +
448D SER* 5.4 6.5 - - - -
453D SER* 4.6 22.0 - - - +
457D TYR* 4.9 13.5 - - + -
459D HIS 3.9 1.3 - - - +
460D PRO* 1.4 85.4 - - + +
462D LEU* 1.3 64.9 - - - +
463D LEU* 3.3 5.8 - - + +
464D GLU* 3.1 46.5 + - + +
465D ARG* 3.1 11.4 + - - +
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Residues in contact with LEU 462 (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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58D ILE* 4.9 10.1 - - + -
59D MET* 6.3 0.2 - - + -
435D LEU* 3.4 46.0 - - + +
436D ILE* 4.3 9.0 - - + +
439D ASN* 3.6 39.0 - - + +
446D PRO* 5.1 18.8 + - + -
460D PRO 3.7 1.0 + - - -
461D PRO* 1.3 70.7 - - - +
463D LEU* 1.4 51.7 + - - +
465D ARG* 3.2 9.8 + - - +
466D LEU* 2.9 55.7 + - + +
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Residues in contact with LEU 463 (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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54D GLU* 6.3 3.1 - - + -
55D LEU* 6.1 5.8 - - + -
446D PRO* 5.3 11.8 + - + +
461D PRO* 3.3 4.1 - - + +
462D LEU* 1.4 77.8 - - - +
464D GLU* 1.4 58.3 + - + +
466D LEU* 4.1 9.2 - - - +
467D GLN* 3.0 43.0 + - - +
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Residues in contact with GLU 464 (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* 6.1 0.5 - - - -
416D PHE* 3.6 32.7 - - + -
450D TRP* 5.7 4.7 - - - -
460D PRO* 4.2 1.9 - - - +
461D PRO* 3.1 40.4 + - + +
463D LEU* 1.4 76.9 - - + +
465D ARG* 1.4 61.0 + - - +
467D GLN* 3.7 10.3 + - - +
468D ALA* 3.4 16.6 + - - +
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Residues in contact with ARG 465 (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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335D HIS* 3.6 17.6 + - - -
415D GLU* 3.8 8.3 + - - -
416D PHE* 4.0 8.7 - - + -
419D ASP* 2.9 41.2 + - - +
435D LEU* 3.6 40.7 - - + +
459D HIS* 4.2 20.6 - - - +
460D PRO* 3.6 43.5 + - + +
461D PRO 3.1 9.9 + - - +
462D LEU* 3.7 10.2 - - - +
464D GLU* 1.4 73.5 - - - +
466D LEU* 1.4 62.8 + - - +
468D ALA* 3.6 3.8 + - - +
469D LEU* 3.3 28.9 + - - +
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Residues in contact with LEU 466 (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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58D ILE* 4.8 7.4 - - + -
432D TYR* 3.3 68.8 - - + +
435D LEU* 4.3 14.1 - - + -
436D ILE* 3.8 26.7 - - + -
462D LEU* 2.9 38.3 + - + +
463D LEU* 4.1 8.5 - - - +
465D ARG* 1.4 74.0 - - - +
467D GLN* 1.4 59.8 + - + +
469D LEU* 3.3 3.4 + - + -
470D LYS* 3.0 24.7 + - - +
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Residues in contact with GLN 467 (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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54D GLU* 5.1 8.9 + - - -
463D LEU* 3.0 29.6 + - - +
464D GLU* 4.0 9.7 - - - +
465D ARG 3.4 0.2 - - - -
466D LEU* 1.4 76.9 - - + +
468D ALA* 1.4 54.8 + - - +
470D LYS* 3.4 8.4 + - + +
471D THR* 2.7 37.9 + - - +
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Residues in contact with ALA 468 (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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416D PHE* 4.1 21.3 - - + +
419D ASP* 6.1 3.4 - - + -
423D LYS* 6.0 0.9 - - - +
464D GLU 3.4 15.5 + - - +
465D ARG* 3.8 6.3 - - - +
466D LEU 3.3 0.6 - - - -
467D GLN* 1.4 76.2 - - - +
469D LEU* 1.4 61.1 + - + +
471D THR* 3.7 18.8 + - - -
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Residues in contact with LEU 469 (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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419D ASP* 3.8 25.6 - - + +
423D LYS* 4.4 8.1 - - + +
428D ALA* 4.0 40.8 - - + +
431D LEU* 3.7 36.8 - - + -
432D TYR* 4.3 21.3 - - + +
435D LEU* 4.2 17.7 - - + -
465D ARG 3.3 17.2 + - - +
466D LEU* 3.3 8.9 + - - +
468D ALA* 1.4 77.0 - - - +
470D LYS* 1.4 62.4 + - - +
471D THR 3.3 4.2 + - - -
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Residues in contact with LYS 470 (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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432D TYR* 3.7 29.8 - - + +
466D LEU 3.0 12.8 + - - +
467D GLN* 3.7 9.4 - - + +
469D LEU* 1.4 75.1 - - - +
471D THR* 1.4 63.1 + - - +
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Residues in contact with THR 471 (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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467D GLN* 2.7 22.9 + - - +
468D ALA* 3.8 15.5 - - - -
469D LEU 3.3 4.2 - - - -
470D LYS* 1.4 80.2 - - - +
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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