Contacts of the helix formed by residues 452 - 469 (chain D) in PDB entry 1S77
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 ILE 452 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D LYS 3.0 4.4 + - - -
451D PRO* 1.3 69.6 - - - +
453D GLY* 1.3 77.5 + - - +
456D GLY* 3.2 34.4 + - - +
457D TYR* 3.5 16.2 - - - +
460D LEU* 3.5 33.2 - - + -
521D VAL* 3.9 20.0 - - + -
526D LEU* 3.5 22.8 + - + +
528D TYR* 2.4 29.9 + - + +
530D CYS* 4.0 13.7 - - + -
818D PRO* 3.5 16.2 - - + -
819D ALA* 4.0 12.0 - - - +
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Residues in contact with GLY 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451D PRO* 3.4 3.0 - - - -
452D ILE* 1.3 74.2 - - - +
454D LYS* 1.3 56.8 + - - -
455D GLU 3.4 1.6 - - - -
457D TYR* 2.7 37.4 + - - +
526D LEU* 2.8 33.1 + - - -
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Residues in contact with LYS 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D GLY* 1.3 71.5 - - - +
455D GLU* 1.3 68.6 + - + +
457D TYR* 3.6 4.5 - - - +
458D TYR* 3.1 21.0 + - - +
526D LEU* 3.6 21.7 - - + +
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Residues in contact with GLU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D GLY 3.4 0.2 - - - -
454D LYS* 1.3 80.8 - - + +
456D GLY* 1.3 68.2 + - - +
458D TYR* 3.0 10.7 + - + +
459D TRP* 2.9 40.9 + - + -
818D PRO 5.6 0.9 - - - +
819D ALA 6.2 0.7 - - - +
822D ALA* 3.2 31.9 - - + +
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Residues in contact with GLY 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D ILE* 3.2 25.3 + - - -
453D GLY 3.4 2.6 + - - -
455D GLU* 1.3 78.9 - - - +
457D TYR* 1.3 57.3 + - - +
459D TRP* 3.4 1.0 + - - +
460D LEU* 2.8 29.8 + - - +
818D PRO* 3.2 33.2 + - - +
819D ALA* 4.4 1.4 - - - +
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Residues in contact with TYR 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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452D ILE* 3.4 9.5 - - + +
453D GLY 2.7 21.2 + - - +
454D LYS 3.6 4.9 - - - +
456D GLY* 1.3 70.5 - - - +
458D TYR* 1.3 64.9 + - - +
460D LEU* 3.0 9.0 + - + +
461D LYS* 2.9 51.4 + - + +
518D TYR* 3.5 27.6 + + - -
521D VAL* 3.6 36.8 - - + -
522D GLN* 2.6 27.1 + - - -
526D LEU* 4.0 23.6 - - + -
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Residues in contact with TYR 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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454D LYS 3.1 10.9 + - - +
455D GLU* 3.0 13.4 + - + +
457D TYR* 1.3 79.5 - - - +
459D TRP* 1.3 95.1 + + - +
461D LYS* 2.9 33.2 + - - +
462D ILE* 2.9 24.0 + - + +
475D PHE* 3.5 28.0 - - + +
476D PRO* 5.3 0.7 - - - +
479D ILE* 3.7 29.5 - - + +
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Residues in contact with TRP 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D GLU* 2.9 34.5 + - + +
456D GLY 4.0 1.1 - - - +
458D TYR* 1.3 91.8 - + - +
460D LEU* 1.3 61.5 + - - +
462D ILE* 3.0 31.0 + - + +
463D HIS* 2.7 31.5 + - - +
475D PHE* 3.7 26.2 - + - -
534D LEU* 3.6 8.3 - - + +
536D PHE* 3.5 27.8 - + + -
818D PRO 5.0 0.2 - - - -
821D ALA* 3.7 31.0 - - + -
822D ALA* 3.8 24.1 - - + +
825D PHE* 3.4 40.8 - + - -
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Residues in contact with LEU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D ILE* 3.5 23.6 - - + -
456D GLY 2.8 15.3 + - - +
457D TYR* 3.0 16.6 + - + +
459D TRP* 1.3 77.3 - - - +
461D LYS* 1.3 57.4 + - + +
463D HIS* 3.2 2.9 + - - +
464D GLY 2.9 24.3 + - - -
514D PHE* 3.3 23.1 - - + -
517D GLU* 4.2 9.4 - - + -
518D TYR* 4.2 19.1 - - + +
521D VAL* 4.0 16.6 - - + -
530D CYS* 4.9 0.2 - - - -
532D LEU* 3.7 15.7 - - + -
534D LEU* 3.5 26.6 - - + +
818D PRO* 4.7 4.7 - - + -
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Residues in contact with LYS 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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457D TYR* 2.9 55.1 + - + +
458D TYR* 2.9 15.7 + - - +
460D LEU* 1.3 75.0 - - - +
462D ILE* 1.3 66.0 + - - +
464D GLY 3.2 0.3 + - - -
465D ALA* 2.9 21.3 + - - +
478D ARG 5.4 0.4 - - - -
479D ILE* 3.6 23.8 - - + +
482D ILE* 3.4 37.4 - - + +
483D GLU* 3.6 28.5 + - + -
514D PHE* 4.0 7.0 - - - -
518D TYR* 4.0 13.5 - - + +
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Residues in contact with ILE 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D TYR* 2.9 21.8 + - + +
459D TRP* 3.0 42.6 + - + +
461D LYS* 1.3 75.0 - - - +
463D HIS* 1.3 65.5 + - - +
465D ALA* 3.1 5.9 + - - +
466D ASN* 2.8 36.6 + - - +
475D PHE* 3.8 23.1 - - + +
478D ARG* 3.7 34.5 - - + +
479D ILE* 3.5 22.4 - - + -
536D PHE* 5.3 2.5 - - + -
882D PHE* 5.1 2.2 - - + -
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Residues in contact with HIS 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D TRP 2.7 12.9 + - - +
460D LEU 3.4 8.0 + - - +
462D ILE* 1.3 74.5 - - - +
464D GLY* 1.3 52.7 + - - +
466D ASN* 3.0 15.2 + - + +
467D CYS* 2.7 62.6 + - - -
510D CYS* 4.3 11.0 - - + +
514D PHE* 4.4 3.4 - - - +
532D LEU* 3.7 19.3 - - + +
533D PRO 3.6 18.4 + - - -
534D LEU* 3.4 27.4 - - + +
535D ALA* 3.4 36.3 + - + +
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Residues in contact with GLY 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D LEU 2.9 11.5 + - - -
461D LYS 3.2 0.4 + - - -
463D HIS* 1.3 74.9 - - - +
465D ALA* 1.3 61.8 + - - +
467D CYS* 3.2 3.0 + - - -
468D ALA 3.0 17.3 + - - -
482D ILE* 3.8 6.7 - - - -
511D PHE* 3.1 14.3 - - - -
514D PHE* 3.5 39.0 - - - -
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Residues in contact with ALA 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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461D LYS 2.9 12.7 + - - +
462D ILE 3.3 8.5 - - - +
464D GLY* 1.3 74.3 - - - +
466D ASN* 1.3 63.7 + - - +
468D ALA* 3.0 4.0 + - - +
469D GLY 3.0 4.5 + - - -
470D VAL* 3.0 34.1 + - + +
478D ARG* 3.4 42.6 - - + +
481D PHE* 4.2 7.0 - - + -
482D ILE* 3.7 7.9 - - + +
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Residues in contact with ASN 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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462D ILE* 2.8 24.7 + - - +
463D HIS* 3.1 14.7 - - + +
465D ALA* 1.3 76.9 - - - +
467D CYS* 1.3 61.4 + - - +
469D GLY* 3.0 14.6 + - - -
471D ASP* 3.4 25.4 - - + +
478D ARG* 2.7 34.4 + - - +
506D ASP* 5.4 1.0 - - - +
507D SER* 5.0 0.9 + - - -
535D ALA 4.0 17.6 + - - -
536D PHE* 5.8 0.4 - - - -
882D PHE* 4.1 13.9 - - - -
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Residues in contact with CYS 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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463D HIS* 2.7 57.2 + - - -
464D GLY* 3.2 8.3 + - - +
466D ASN* 1.3 72.7 - - - +
468D ALA* 1.3 60.0 + - - +
469D GLY 3.6 0.2 + - - -
505D GLN* 4.0 1.0 - - - +
506D ASP* 3.7 2.1 + - - +
507D SER* 3.0 40.8 + - - +
510D CYS* 3.8 21.8 - - - -
511D PHE* 3.6 24.5 - - + +
514D PHE* 5.0 0.2 - - - -
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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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464D GLY 3.0 12.9 + - - +
465D ALA 3.0 9.6 + - - +
467D CYS* 1.3 78.6 - - - +
469D GLY* 1.3 58.5 + - - +
470D VAL* 3.4 4.0 + - + +
481D PHE* 3.5 29.2 - - + -
505D GLN* 3.6 24.9 - - - +
506D ASP* 2.8 17.3 + - - +
511D PHE* 3.6 14.1 - - + -
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Residues in contact with GLY 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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465D ALA 3.8 0.2 - - - -
466D ASN 3.0 13.1 + - - -
467D CYS 3.3 0.4 - - - -
468D ALA* 1.3 79.9 - - - +
470D VAL* 1.3 55.2 + - - +
471D ASP* 2.7 32.5 + - - +
472D LYS* 4.5 0.5 + - - +
506D ASP* 3.8 18.8 - - - -
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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
------------------------------------------------------------
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