Contacts of the helix formed by residues 426 - 438 (chain f) in PDB entry 5T0J
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 426 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393f ASP* 5.2 8.1 - - - +
424f VAL* 2.9 32.8 + - + +
425f SER* 1.3 74.7 - - - +
427f PRO* 1.3 65.2 - - + +
428f PHE* 3.3 8.9 - - + +
429f ARG* 4.8 13.7 - - + +
430f SER* 2.7 33.7 + - - +
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Residues in contact with PRO 427 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425f SER 3.1 9.6 - - - +
426f GLU* 1.3 88.7 - - + +
428f PHE* 1.3 83.2 + - + +
430f SER* 3.0 14.0 + - - +
431f PHE 3.7 1.4 + - - -
462f ASP* 5.2 7.0 - - - +
464f LYS* 2.8 42.7 + - + +
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Residues in contact with PHE 428 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426f GLU* 3.3 6.2 - - + -
427f PRO* 1.3 95.0 - - + +
429f ARG* 1.3 67.1 + - - +
431f PHE* 3.1 21.1 + - - +
432f ALA* 4.4 0.9 + - - +
464f LYS* 3.6 12.3 + - - +
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Residues in contact with ARG 429 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393f ASP* 3.6 39.5 - - + +
397f ARG* 3.4 31.2 + - - +
426f GLU* 4.4 10.6 + - + +
428f PHE* 1.3 79.4 - - - +
430f SER* 1.3 61.7 + - - +
431f PHE 3.3 0.7 + - - -
432f ALA* 3.7 2.3 + - - -
433f ASN* 3.3 18.1 + - - +
684f SER* 6.4 0.2 - - - -
685f VAL* 6.3 1.0 - - - +
686f ARG* 4.1 27.0 - - - +
687f VAL* 5.3 8.3 - - - +
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Residues in contact with SER 430 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393f ASP* 5.0 4.8 + - - -
424f VAL* 6.4 2.0 - - - -
426f GLU* 2.7 26.2 + - - +
427f PRO* 3.0 14.4 + - - +
429f ARG* 1.3 77.2 - - - +
431f PHE* 1.3 55.9 + - - +
433f ASN* 3.6 10.8 - - - +
434f THR* 2.5 55.2 + - - -
462f ASP* 4.9 6.8 + - - -
464f LYS* 5.2 1.2 - - - +
465f GLU* 5.5 3.3 - - - +
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Residues in contact with PHE 431 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427f PRO 3.7 1.3 + - - -
428f PHE 3.1 15.0 + - - +
430f SER* 1.3 80.9 + - - +
432f ALA* 1.3 69.3 + - + +
433f ASN 3.2 0.2 + - - -
434f THR* 4.6 0.2 - - - -
435f LEU* 3.3 10.0 - - + +
464f LYS* 3.6 39.7 - - + +
467f GLU* 5.8 3.4 - - + -
468f GLU* 3.0 50.5 - - + +
493f VAL* 5.9 2.5 - - + -
495f VAL* 4.7 28.0 - - + -
682f PRO* 5.8 10.1 - - + -
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Residues in contact with ALA 432 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397f ARG* 3.5 27.4 + - - +
428f PHE 4.4 1.4 + - - +
429f ARG 3.7 2.2 + - - +
431f PHE* 1.3 86.3 - - + +
433f ASN* 1.3 58.5 + - - +
435f LEU* 4.2 14.2 - - - +
679f ARG* 3.1 41.3 + - + -
682f PRO* 6.2 4.0 - - + -
687f VAL* 6.3 1.1 - - + -
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Residues in contact with ASN 433 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392f LYS* 2.4 32.3 + - - +
393f ASP* 2.9 33.1 + - - +
396f ALA* 3.3 17.2 - - - +
397f ARG* 3.4 15.9 - - - +
429f ARG 3.3 20.3 + - - +
430f SER* 3.8 4.2 - - - +
431f PHE 3.1 1.0 - - - -
432f ALA* 1.3 77.7 - - - +
434f THR* 1.3 73.1 + - - +
435f LEU 3.0 9.0 + - - -
436f VAL* 3.6 4.7 + - - +
437f ASP* 3.2 24.0 + - - +
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Residues in contact with THR 434 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392f LYS* 5.2 9.4 - - + -
422f GLU* 6.1 4.7 - - + -
430f SER* 2.5 44.4 + - - +
431f PHE* 4.6 0.3 - - - -
433f ASN* 1.3 79.5 - - - +
435f LEU* 1.3 66.0 + - - +
437f ASP* 3.7 19.8 + - - +
438f VAL* 3.7 17.7 + - - +
465f GLU* 3.4 32.6 - - + +
468f GLU* 3.5 10.0 + - - +
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Residues in contact with LEU 435 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431f PHE* 3.3 20.4 + - + +
432f ALA* 4.2 13.0 - - - +
433f ASN 3.0 0.6 + - - -
434f THR* 1.3 80.9 - - - +
436f VAL* 1.3 72.5 + - + +
438f VAL* 4.4 0.5 - - - +
439f CYS* 3.1 29.7 + - - +
468f GLU* 3.2 43.2 + - + +
471f ASP* 5.4 6.3 - - + +
495f VAL* 6.3 1.1 - - + -
675f ASP 5.5 1.6 - - - +
678f LEU* 3.8 35.4 - - + -
679f ARG* 6.1 2.5 - - + +
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Residues in contact with VAL 436 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397f ARG* 4.0 15.5 - - - +
400f PRO* 4.0 2.0 - - - +
401f LEU* 4.8 1.6 - - + -
433f ASN 3.6 3.1 + - - +
435f LEU* 1.3 90.6 - - + +
437f ASP* 1.3 61.4 - - - +
438f VAL 3.5 0.9 - - - -
439f CYS* 3.7 10.1 - - + -
440f ALA* 3.0 35.9 + - + +
674f PHE 5.5 0.2 - - - +
675f ASP* 3.1 49.1 - - + +
678f LEU* 5.9 1.8 - - + -
679f ARG* 3.5 17.0 - - - +
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Residues in contact with ASP 437 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392f LYS* 3.8 20.8 + - - -
396f ALA* 3.1 32.8 - - - +
400f PRO* 3.3 12.1 - - - +
418f LEU* 4.2 2.4 - - - +
433f ASN* 3.2 24.2 + - - +
434f THR* 3.7 13.0 - - - +
435f LEU 3.4 0.6 - - - -
436f VAL* 1.3 80.8 - - - +
438f VAL* 1.3 61.4 + - + +
439f CYS 3.5 0.2 + - - -
441f TYR* 2.6 58.7 + - - -
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Residues in contact with VAL 438 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415f GLU* 4.8 4.0 - - + +
434f THR* 3.7 16.2 + - - +
435f LEU 4.4 0.2 - - - +
437f ASP* 1.3 80.0 - - + +
439f CYS* 1.3 70.9 + - - +
441f TYR* 3.5 24.9 + - + +
442f ALA 5.1 1.6 + - - +
449f LYS* 5.8 1.9 - - - +
453f LEU* 3.7 32.3 - - + +
465f GLU* 4.5 14.4 - - - +
468f GLU 5.3 1.3 - - - +
469f ASP* 4.8 7.4 - - - +
472f LYS* 3.3 29.7 - - + +
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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