Contacts of the helix formed by residues 471 - 485 (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 GLU 471 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463D TYR* 3.4 15.8 - - - -
469D PHE* 3.4 1.6 - - - +
470D PRO* 1.3 92.9 - - + +
472D ARG* 1.3 66.7 + - - +
473D ARG* 3.2 36.5 + - + +
474D GLU* 3.1 20.2 + - + +
475D ALA 3.8 2.1 + - - -
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Residues in contact with ARG 472 (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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456D SER* 3.7 14.8 + - - -
459D VAL* 3.6 17.6 - - + +
460D ASP* 2.9 30.7 + - - +
463D TYR* 3.5 38.0 + - + -
471D GLU* 1.3 72.4 - - - +
473D ARG* 1.3 63.7 + - - +
475D ALA* 2.9 13.9 + - - +
476D ARG* 3.0 12.2 + - - +
499D GLU* 2.9 38.4 + - - -
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Residues in contact with ARG 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D GLU* 3.8 29.3 + - + +
472D ARG* 1.3 77.0 - - - +
474D GLU* 1.3 78.0 + - - +
476D ARG* 3.4 13.3 + - + +
477D LYS* 3.2 25.5 + - - +
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Residues in contact with GLU 474 (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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469D PHE* 3.7 24.4 - - + -
470D PRO* 3.7 32.1 - - + -
471D GLU* 3.1 12.7 + - + +
472D ARG 3.1 1.0 - - - -
473D ARG* 1.3 109.2 + - + +
475D ALA* 1.3 65.3 + - - +
477D LYS* 3.4 27.1 + - - +
478D TYR* 3.1 17.0 + - - +
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Residues in contact with ALA 475 (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* 3.9 25.2 - - + +
462D LEU* 3.8 6.7 - - + +
463D TYR* 4.0 23.8 - - + +
469D PHE* 3.7 23.4 - - + -
471D GLU 3.8 1.0 + - - -
472D ARG 2.9 11.4 + - - +
474D GLU* 1.3 76.5 - - - +
476D ARG* 1.3 64.0 + - - +
478D TYR* 3.3 3.6 + - - +
479D ALA* 3.1 21.7 + - - +
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Residues in contact with ARG 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D VAL* 3.8 16.9 - - + +
472D ARG* 3.0 11.3 + - - +
473D ARG* 3.6 14.6 - - - +
474D GLU 3.3 0.4 - - - -
475D ALA* 1.3 75.6 - - - +
477D LYS* 1.3 63.6 + - - +
479D ALA* 3.2 4.9 + - - +
480D SER* 3.0 28.6 + - - -
497D PHE* 3.4 51.4 + - + +
498D SER* 4.2 6.5 - - - +
499D GLU* 3.7 26.3 + - - +
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Residues in contact with LYS 477 (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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473D ARG* 3.2 11.2 + - - +
474D GLU* 3.6 31.0 - - - +
475D ALA 3.3 0.2 - - - -
476D ARG* 1.3 82.3 - - - +
478D TYR* 1.3 60.9 + - - +
480D SER* 3.3 8.8 + - - -
481D GLY* 3.1 17.7 + - - -
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Residues in contact with TYR 478 (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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418C SER 4.9 1.0 + - - -
419C VAL* 4.8 20.4 - - + -
421C THR 4.3 5.3 + - - -
423C MET* 3.6 33.8 - - + +
426C VAL* 3.4 30.9 - - + +
462D LEU* 3.9 26.2 - - + -
466D VAL* 5.4 3.1 - - + -
469D PHE* 3.8 26.7 - + + -
474D GLU 3.1 14.2 + - - +
475D ALA 3.6 8.1 - - - +
476D ARG 3.2 0.4 - - - -
477D LYS* 1.3 74.1 - - - +
479D ALA* 1.3 61.6 + - - +
481D GLY* 3.1 3.6 + - - +
482D LEU* 2.9 48.5 + - + +
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Residues in contact with ALA 479 (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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458D VAL* 4.0 12.3 - - + -
459D VAL* 4.1 6.5 - - + -
462D LEU* 3.8 17.5 - - + +
475D ALA 3.1 10.9 + - - +
476D ARG 3.6 7.9 - - - +
478D TYR* 1.3 78.3 - - - +
480D SER* 1.3 61.5 + - - +
482D LEU* 3.2 11.5 + - - +
483D LEU* 3.1 19.1 + - - +
488D ILE* 4.0 7.2 - - + +
497D PHE* 3.9 24.3 - - + -
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Residues in contact with SER 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476D ARG* 3.0 18.8 + - - -
477D LYS* 3.6 12.6 - - - -
478D TYR 3.2 0.4 - - - -
479D ALA* 1.3 74.7 - - - +
481D GLY* 1.3 56.3 - - - +
483D LEU* 3.4 5.5 + - - +
484D LYS* 3.0 26.6 + - - +
497D PHE* 3.7 31.3 + - - +
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Residues in contact with GLY 481 (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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423C MET* 4.1 15.4 - - - +
477D LYS 3.1 10.4 + - - -
478D TYR* 3.1 8.1 + - - -
480D SER* 1.3 73.4 - - - +
482D LEU* 1.3 63.1 + - - +
484D LYS* 3.2 8.6 + - - +
485D ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 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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423C MET* 4.0 19.5 - - + +
426C VAL* 5.7 0.9 - - + -
427C THR* 3.5 26.9 - - - +
430C MET* 4.6 16.2 - - + -
458D VAL* 4.8 4.3 - - + -
462D LEU* 4.5 12.1 - - + -
478D TYR* 2.9 46.6 + - + +
479D ALA* 3.2 15.0 + - - +
481D GLY* 1.3 77.4 - - - +
483D LEU* 1.3 58.4 + - - +
485D ALA* 3.5 2.3 + - - -
486D GLY 3.3 3.1 + - - -
487D LEU* 3.1 40.1 + - + +
488D ILE* 3.4 17.2 + - + -
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Residues in contact with LEU 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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479D ALA 3.1 11.8 + - - +
480D SER* 3.6 8.1 - - - +
481D GLY 3.3 0.2 - - - -
482D LEU* 1.3 73.3 - - - +
484D LYS* 1.3 65.7 + - - +
486D GLY* 3.0 14.2 + - - -
488D ILE* 3.6 29.9 - - + +
489D ARG* 4.0 2.0 - - - -
490D HIS* 3.7 43.1 - - + +
495D ILE 3.5 24.9 - - - +
497D PHE* 3.8 25.6 - - + +
503D TYR* 4.1 10.3 - - + -
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Residues in contact with LYS 484 (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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480D SER 3.0 14.1 + - - +
481D GLY* 3.2 10.7 + - - +
483D LEU* 1.3 75.9 - - - +
485D ALA* 1.3 59.4 + - - +
486D GLY 3.5 0.5 + - - -
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Residues in contact with ALA 485 (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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423C MET* 5.0 7.0 - - - -
481D GLY 3.1 16.4 + - - +
482D LEU* 3.9 4.7 - - - +
483D LEU 3.2 0.2 - - - -
484D LYS* 1.3 75.0 - - - +
486D GLY* 1.3 61.1 + - - +
487D LEU* 3.4 20.7 + - + +
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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