Contacts of the helix formed by residues 481 - 495 (chain D) in PDB entry 5YD6
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 GLU 481 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476D VAL* 5.2 3.8 - - - +
480D GLY* 1.3 69.3 - - - -
482D TRP* 1.3 60.3 + - - +
483D ILE* 3.4 0.9 - - - -
484D ASP* 3.2 31.3 + - + +
485D SER* 3.6 5.7 + - - -
568D GLN* 3.0 25.9 + - - -
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Residues in contact with TRP 482 (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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406D PHE* 3.8 29.8 - + - -
410D LEU* 5.2 0.2 - - + -
444D LEU* 4.0 24.0 - - + -
447D PHE* 4.8 6.3 - + - -
448D VAL* 3.4 29.6 - - + -
479D PHE* 3.4 31.0 - + - +
480D GLY 2.8 2.2 + - - -
481D GLU* 1.3 75.7 - - - +
483D ILE* 1.3 57.8 + - - +
485D SER* 2.9 8.5 + - - -
486D ILE* 2.8 43.7 + - + +
565D LEU* 2.8 27.8 + - + +
568D GLN* 3.6 39.6 - - + +
569D GLY* 3.4 30.7 - - - -
572D ARG* 5.0 3.1 - - + -
573D ILE* 5.8 0.2 - - + -
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Residues in contact with ILE 483 (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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462D LEU* 3.8 27.8 - - + -
472D ARG* 3.4 22.9 - - + +
475D CYS* 3.8 27.1 - - + +
476D VAL* 3.7 14.4 - - + -
479D PHE* 3.7 32.6 - - + +
480D GLY 3.5 18.6 - - - +
482D TRP* 1.3 75.4 - - - +
484D ASP* 1.3 80.2 + - - +
486D ILE* 3.4 9.6 - - + +
487D VAL* 2.7 39.5 + - + +
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Residues in contact with ASP 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D ARG* 4.0 25.7 + - - +
476D VAL* 4.6 6.4 - - - +
481D GLU* 3.2 22.9 + - + +
483D ILE* 1.3 92.7 - - - +
485D SER* 1.3 58.5 + - - +
487D VAL* 3.9 6.6 - - - +
488D GLU* 3.0 28.9 + - - +
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Residues in contact with SER 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D GLU* 3.6 4.8 + - - -
482D TRP 2.9 9.1 + - - -
484D ASP* 1.3 75.6 - - - +
486D ILE* 1.3 59.0 - - - +
488D GLU* 3.6 12.1 + - - +
489D PHE* 3.1 22.7 + - - +
565D LEU* 3.5 19.8 - - - +
568D GLN* 2.9 39.5 + - - -
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Residues in contact with ILE 486 (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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447D PHE* 5.6 0.2 - - + -
448D VAL* 4.3 27.1 - - + +
451D LEU* 4.0 27.6 - - + -
452D ALA* 5.2 4.9 - - + +
462D LEU* 4.2 10.1 - - + -
479D PHE* 4.4 6.7 - - + -
482D TRP* 2.8 60.4 + - + +
483D ILE* 3.4 22.7 - - + +
485D SER* 1.3 73.8 - - - +
487D VAL* 1.3 55.8 + - - +
489D PHE* 3.1 7.3 + - - +
490D SER* 2.8 32.9 + - - -
565D LEU* 4.2 5.2 - - + -
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Residues in contact with VAL 487 (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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457D PRO* 3.9 26.3 - - + +
460D GLY* 5.6 3.4 - - - +
461D LYS 6.3 0.2 - - - -
462D LEU* 4.4 22.4 - - + -
472D ARG* 4.0 39.0 - - + +
483D ILE 2.7 21.5 + - - +
484D ASP* 3.9 4.5 - - - +
486D ILE* 1.3 70.8 - - - +
488D GLU* 1.3 58.5 + - - +
490D SER* 3.2 9.4 + - - -
491D SER* 2.8 31.8 + - - +
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Residues in contact with GLU 488 (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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484D ASP 3.0 18.5 + - - +
485D SER* 3.7 11.3 + - - +
486D ILE 3.3 0.2 - - - -
487D VAL* 1.3 77.0 - - - +
489D PHE* 1.3 56.0 + - - +
491D SER* 3.3 9.6 + - - -
492D ASN* 3.0 47.1 + - - +
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Residues in contact with PHE 489 (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 VAL* 4.5 2.7 - - + -
449D LEU* 3.9 31.2 - - + -
452D ALA* 3.6 26.9 - - + -
485D SER 3.1 12.2 + - - +
486D ILE 3.5 3.6 - - - +
488D GLU* 1.3 72.7 - - - +
490D SER* 1.3 55.9 + - - +
492D ASN* 3.6 8.0 - - - +
493D LEU* 2.7 51.1 + - + +
558D LYS* 3.8 39.3 - - + -
561D GLU* 4.0 22.0 - - + -
562D LEU* 4.3 12.6 - - + -
565D LEU* 3.4 33.7 - - + -
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Residues in contact with SER 490 (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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452D ALA* 2.6 42.3 + - - -
455D SER* 4.3 6.1 - - - -
457D PRO* 3.4 22.5 - - - +
486D ILE* 2.8 15.0 + - - -
487D VAL* 3.4 13.5 - - - -
489D PHE* 1.3 73.9 - - - +
491D SER* 1.3 55.5 + - - +
493D LEU* 3.8 0.8 - - - +
494D GLN* 2.8 38.6 + - - +
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Residues in contact with SER 491 (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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457D PRO* 3.5 26.1 + - - +
458D VAL* 5.8 0.2 - - - -
487D VAL* 2.8 18.0 + - - +
488D GLU* 3.4 12.9 - - - -
490D SER* 1.3 71.3 - - - +
492D ASN* 1.3 59.7 + - - +
494D GLN* 3.9 1.9 - - - +
495D ASN* 2.8 43.1 + - - +
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Residues in contact with ASN 492 (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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488D GLU* 3.0 43.5 + - - +
489D PHE* 3.7 6.0 - - - +
491D SER* 1.3 78.7 - - - +
493D LEU* 1.3 62.0 + - - +
495D ASN* 3.4 10.8 + - - +
496D MET* 3.4 18.2 + - - +
558D LYS* 3.5 24.0 + - - +
561D GLU* 5.2 3.0 + - - -
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Residues in contact with LEU 493 (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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449D LEU* 4.1 21.3 - - + -
452D ALA* 3.8 26.5 - - + +
453D TYR* 4.0 28.0 - - + +
489D PHE* 2.7 34.7 + - + +
490D SER 3.8 2.5 - - - +
492D ASN* 1.3 72.9 - - - +
494D GLN* 1.3 60.2 + - + +
496D MET* 3.3 22.3 + - - +
497D ASN 3.9 0.2 + - - -
498D ILE* 3.5 35.7 + - + +
503D PHE* 4.4 2.5 - - + -
506D ILE* 5.8 2.7 - - + -
558D LYS* 4.0 27.9 - - + +
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Residues in contact with GLN 494 (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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452D ALA 2.9 21.7 - - - +
453D TYR* 3.3 22.4 - - + +
455D SER 2.8 23.6 + - - +
456D ASN* 5.0 2.0 + - - +
457D PRO* 3.4 27.0 - - + +
458D VAL* 5.7 3.4 - - - +
490D SER 2.8 19.5 + - - +
491D SER 4.1 2.2 - - - +
493D LEU* 1.3 70.4 - - + +
495D ASN* 1.3 60.8 + - - +
496D MET 3.2 4.5 - - - -
497D ASN* 3.2 25.4 + - - +
498D ILE 5.8 0.9 - - - +
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Residues in contact with ASN 495 (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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491D SER* 2.8 29.4 + - - +
492D ASN* 3.4 7.5 + - - +
493D LEU 3.4 0.6 - - - -
494D GLN* 1.3 76.0 + - - +
496D MET* 1.3 59.9 + - - +
497D ASN* 3.2 15.4 + - - +
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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