Contacts of the helix formed by residues 542 - 556 (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 ASN 542 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510f GLU* 3.6 16.2 + - - -
539f SER* 3.8 5.1 + - - +
541f SER* 1.3 89.3 + - - +
543f PRO* 1.3 66.3 - - - +
544f ARG* 3.2 5.8 + - + +
545f LEU* 5.2 9.9 - - + +
546f ASN* 3.7 32.8 + - - +
547f ILE* 5.0 0.3 - - - +
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Residues in contact with PRO 543 (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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539f SER 3.4 15.4 - - - +
540f VAL* 4.3 5.2 - - - +
541f SER 3.4 9.4 - - - +
542f ASN* 1.3 87.3 - - - +
544f ARG* 1.3 63.5 + - + +
547f ILE* 3.1 33.7 - - + +
548f LEU* 4.6 1.2 + - - +
573f VAL* 3.6 25.8 - - + +
574f GLY* 4.7 5.5 - - - -
576f GLY* 6.5 0.4 - - - -
577f THR* 4.2 22.7 - - + +
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Residues in contact with ARG 544 (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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542f ASN* 3.2 4.2 - - + -
543f PRO* 1.3 84.9 - - + +
545f LEU* 1.3 78.7 + - + +
546f ASN 3.6 0.2 + - - -
548f LEU* 3.3 34.9 + - + +
577f THR* 3.2 26.3 + - - -
578f ASN 2.6 24.6 + - - -
579f ASN* 2.5 50.0 + - - +
582f LEU* 5.4 1.2 - - - +
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Residues in contact with LEU 545 (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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542f ASN* 4.1 9.3 + - + +
544f ARG* 1.3 92.4 - - + +
546f ASN* 1.3 70.3 + - - +
548f LEU* 4.9 3.4 - - + +
549f ASP* 3.2 25.5 + - - +
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Residues in contact with ASN 546 (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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510f GLU* 3.8 29.1 + - - +
513f LEU* 5.2 15.5 - - + +
535f LEU* 5.4 0.5 - - - +
539f SER* 5.3 8.6 + - - +
541f SER* 5.1 0.4 + - - -
542f ASN* 3.7 24.1 + - - +
544f ARG 3.4 0.4 - - - -
545f LEU* 1.3 84.5 - - - +
547f ILE* 1.3 65.6 + - + +
549f ASP* 5.1 0.2 - - - -
550f THR* 3.0 32.0 + - - +
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Residues in contact with ILE 547 (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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535f LEU* 3.7 26.5 - - + +
539f SER* 3.4 31.6 - - - +
543f PRO* 3.1 36.6 + - + +
545f LEU 3.4 0.6 - - - -
546f ASN* 1.3 80.2 - - + +
548f LEU* 1.3 69.4 + - + +
549f ASP 3.2 0.3 + - - -
550f THR* 3.4 1.1 + - - -
551f LEU* 3.1 44.6 + - + +
569f ALA 4.5 4.5 - - - +
570f MET* 3.6 30.5 - - + -
573f VAL* 4.9 5.2 - - + -
574f GLY* 5.2 2.5 - - - -
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Residues in contact with LEU 548 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543f PRO 5.4 0.9 - - - +
544f ARG* 3.3 29.6 - - + +
545f LEU* 4.9 2.9 - - + +
547f ILE* 1.3 78.8 - - - +
549f ASP* 1.3 82.0 + - + +
551f LEU* 4.6 0.4 - - - -
552f SER* 3.0 26.3 + - - -
570f MET* 4.0 21.8 - - + -
579f ASN* 3.9 24.5 - - - +
581f ARG* 4.1 24.0 - - + +
582f LEU* 4.0 16.2 - - + -
585f MET* 6.4 1.8 - - - -
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Residues in contact with ASP 549 (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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545f LEU 3.2 20.9 + - - +
546f ASN* 4.5 1.6 - - - +
547f ILE 3.2 0.8 - - - -
548f LEU* 1.3 92.9 - - + +
550f THR* 1.3 70.3 + - + +
552f SER* 3.2 14.3 + - - -
553f LYS* 3.8 10.7 + - - -
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Residues in contact with THR 550 (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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516f PHE* 6.5 1.1 - - + -
535f LEU* 4.5 7.8 - - - +
546f ASN* 3.0 20.7 + - - +
547f ILE* 3.4 3.7 + - - -
549f ASP* 1.3 84.0 - - + +
551f LEU* 1.3 67.4 + - - +
552f SER 3.3 1.1 + - - -
553f LYS* 3.8 20.8 + - - +
554f PHE* 3.8 22.1 - - - -
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Residues in contact with LEU 551 (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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532f PRO* 4.5 6.5 - - + -
535f LEU* 3.8 20.6 - - + -
547f ILE* 3.1 35.8 + - + +
548f LEU* 3.7 4.3 - - - +
550f THR* 1.3 77.6 - - - +
552f SER* 1.3 62.3 + - - +
553f LYS 3.4 1.1 - - - -
554f PHE* 4.0 19.0 - - + +
555f SER* 3.2 25.5 + - - -
566f SER* 3.3 38.0 - - - +
569f ALA* 3.7 9.9 - - + -
570f MET* 3.6 27.8 - - + +
585f MET* 6.1 0.2 - - - +
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Residues in contact with SER 552 (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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548f LEU 3.0 18.6 + - - -
549f ASP* 3.2 10.4 + - - -
551f LEU* 1.3 79.5 - - - +
553f LYS* 1.3 59.8 + - - +
555f SER* 3.0 6.2 + - - -
556f HIS* 2.6 41.5 + - - -
581f ARG* 4.4 15.8 + - - -
585f MET* 6.1 3.6 - - - -
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Residues in contact with LYS 553 (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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549f ASP* 3.8 22.2 + - - -
550f THR* 3.8 16.9 + - - +
551f LEU 3.4 0.2 - - - -
552f SER* 1.3 81.7 - - - +
554f PHE* 1.3 77.1 + - + +
555f SER 3.3 0.7 + - - -
556f HIS* 3.7 10.9 + - - +
557f ASP* 4.0 9.0 + - - +
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Residues in contact with PHE 554 (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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520f LEU* 6.4 3.4 - - + -
528f ARG* 4.1 35.9 - - + -
531f VAL* 6.3 2.0 - - + -
532f PRO* 4.7 15.7 - - + -
550f THR* 3.8 20.0 - - - -
551f LEU* 3.7 17.3 + - + +
552f SER 3.4 0.2 - - - -
553f LYS* 1.3 93.3 - - + +
555f SER* 1.3 62.3 + - - +
556f HIS 3.4 0.4 - - - -
557f ASP* 3.7 20.8 + - + +
562f VAL* 3.7 24.1 - - + +
563f SER* 4.0 3.1 - - - -
566f SER* 3.8 14.4 + - - -
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Residues in contact with SER 555 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551f LEU* 3.2 16.4 + - - -
552f SER* 3.0 19.1 + - - -
554f PHE* 1.3 79.4 - - - +
556f HIS* 1.3 70.7 + - - +
557f ASP 3.3 1.4 + - - +
563f SER* 3.8 14.1 + - - -
566f SER* 3.7 15.2 - - - -
585f MET* 4.9 6.0 - - - -
589f LEU* 5.7 1.4 - - - +
592f TYR* 5.6 5.0 - - - -
602f MET* 3.7 31.9 - - - +
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Residues in contact with HIS 556 (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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552f SER* 2.6 37.5 + - - +
553f LYS* 3.7 6.3 + - - +
554f PHE 3.4 0.4 - - - -
555f SER* 1.3 89.3 + - - +
557f ASP* 1.3 63.4 + - - +
558f ALA* 3.6 1.4 + - - -
581f ARG* 6.1 2.5 - - - -
585f MET* 5.7 10.2 - - + +
588f GLN* 5.9 2.8 + - - -
589f LEU* 5.6 6.1 - - + +
592f TYR* 3.7 26.3 + - - +
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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