Contacts of the helix formed by residues 455 - 466 (chain D) in PDB entry 5SUY
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 GLY 455 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453D PHE 3.7 1.0 + - - -
454D LEU* 1.3 71.5 - - - +
456D SER* 1.3 60.0 + - - +
458D VAL* 3.3 7.4 + - - +
459D VAL* 3.2 25.8 + - - +
497D PHE* 3.9 6.6 - - - -
498D SER 4.0 0.2 - - - -
499D GLU* 3.5 18.4 + - - -
501D CYS 3.0 13.9 + - - -
503D TYR* 3.7 23.5 - - - -
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Residues in contact with SER 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ARG* 5.3 0.7 + - - -
454D LEU* 3.5 17.8 - - - +
455D GLY* 1.3 72.9 - - - +
457D ASP* 1.3 60.8 + - - +
459D VAL* 3.4 0.7 + - - -
460D ASP* 2.9 36.9 + - - +
472D ARG* 3.7 6.1 + - - -
499D GLU* 2.9 46.3 + - - -
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Residues in contact with ASP 457 (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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440B ARG* 2.8 44.5 + - - -
437C LEU* 3.8 11.0 - - + +
438C GLU* 3.7 26.9 - - + +
454D LEU* 3.0 25.6 + - + +
456D SER* 1.3 77.5 + - - +
458D VAL* 1.3 63.7 + - - +
460D ASP* 3.6 12.5 + - - +
461D TRP* 3.1 24.4 + - - +
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Residues in contact with VAL 458 (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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430C MET* 4.1 18.7 - - + +
437C LEU* 4.0 12.8 - - + +
453D PHE* 3.4 39.3 - - + -
454D LEU 3.1 8.3 + - - +
455D GLY* 3.3 11.6 + - - +
457D ASP* 1.3 75.9 - - - +
459D VAL* 1.3 64.0 + - + +
461D TRP* 3.1 4.0 + - - +
462D LEU* 2.9 41.8 + - + +
479D ALA* 4.0 12.6 - - + -
482D LEU* 4.8 4.7 - - + -
488D ILE* 4.8 11.0 - - + -
497D PHE* 5.4 0.7 - - + -
503D TYR* 5.5 0.9 - - + -
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Residues in contact with VAL 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D GLY 3.2 15.8 + - - +
456D SER 3.4 6.3 + - - +
458D VAL* 1.3 76.9 - - - +
460D ASP* 1.3 61.6 + - - +
462D LEU* 3.3 9.0 + - - +
463D TYR* 3.0 22.2 + - - +
472D ARG* 3.6 34.5 - - + +
475D ALA* 3.9 6.5 - - + +
476D ARG* 3.8 28.3 - - + +
479D ALA* 4.1 10.5 - - + -
497D PHE* 4.0 16.2 - - + -
499D GLU* 3.9 18.2 - - + -
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Residues in contact with ASP 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D SER* 2.9 21.3 + - - +
457D ASP* 3.7 15.8 - - - +
458D VAL 3.4 0.2 - - - -
459D VAL* 1.3 73.8 - - - +
461D TRP* 1.3 61.0 + - - +
463D TYR* 3.3 6.5 + - - +
464D HIS* 3.0 41.8 + - + -
472D ARG* 2.9 34.8 + - - +
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Residues in contact with TRP 461 (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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417C LEU* 3.9 20.6 - - + -
426C VAL* 4.4 9.4 - - + -
429C ALA* 4.3 3.1 - - + -
430C MET* 3.5 54.5 - - + -
435C SER* 2.9 30.9 + - - -
436C GLY 3.9 2.9 - - - -
437C LEU* 3.6 33.6 - - + +
457D ASP 3.1 18.7 + - - +
458D VAL 3.1 3.8 + - - +
460D ASP* 1.3 73.3 - - - +
462D LEU* 1.3 65.0 + - + +
464D HIS 3.3 0.9 + - - -
465D HIS* 2.7 75.5 + + + +
466D VAL* 4.0 19.1 - - + -
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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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426C VAL* 4.0 19.5 - - + -
430C MET* 4.6 3.1 - - - -
458D VAL* 2.9 36.7 + - + +
459D VAL* 3.6 5.4 - - - +
461D TRP* 1.3 86.6 - - + +
463D TYR* 1.3 62.5 + - - +
466D VAL* 3.0 38.9 + - + +
469D PHE* 3.8 12.6 - - + -
475D ALA* 3.8 23.8 - - + +
478D TYR* 3.9 33.7 - - + -
479D ALA* 3.8 11.2 - - + -
482D LEU* 4.5 7.2 - - + -
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Residues in contact with TYR 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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459D VAL 3.0 18.0 + - - +
460D ASP* 3.3 6.9 + - - +
462D LEU* 1.3 77.4 - - - +
464D HIS* 1.3 77.6 + + - +
466D VAL 4.2 7.2 - - - +
469D PHE* 3.8 31.3 + - + -
470D PRO 4.0 5.9 + - - -
471D GLU* 3.4 29.1 - - - -
472D ARG* 3.8 35.3 + - + -
475D ALA* 4.0 10.0 - - + +
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Residues in contact with HIS 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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460D ASP* 3.0 35.1 + - + +
461D TRP* 5.5 0.2 - - - -
463D TYR* 1.3 99.3 + + + +
465D HIS* 1.3 74.1 + - + +
466D VAL 3.8 0.4 - - - -
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Residues in contact with HIS 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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415C SER 5.3 6.1 + - - +
417C LEU* 3.8 19.1 + - + +
435C SER 4.0 7.8 + - - -
436C GLY* 5.4 3.0 - - - -
461D TRP* 2.7 82.3 + + + +
464D HIS* 1.3 91.9 - - + +
466D VAL* 1.3 63.0 + - - +
467D GLU* 4.2 1.8 - - - -
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Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 3.6 9.9 - - + -
418C SER* 3.6 28.9 - - - +
419C VAL* 3.9 2.0 - - - +
426C VAL* 4.0 28.5 - - + -
461D TRP* 4.0 14.6 - - + -
462D LEU* 3.0 26.9 + - + +
463D TYR 4.2 5.9 - - - +
464D HIS 3.8 0.6 - - - -
465D HIS* 1.3 82.9 - - - +
467D GLU* 1.3 65.3 + - - +
468D GLY 3.9 0.5 + - - -
469D PHE* 3.7 31.8 + - + -
478D TYR* 5.4 2.9 - - + -
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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