Contacts of the helix formed by residues 530 - 542 (chain C) in PDB entry 6PUO
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 CYS 530 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C LEU* 4.0 13.0 - - - -
527C ASP* 3.4 22.7 + - - +
528C PRO 4.5 2.1 - - - +
529C SER* 1.3 83.6 + - - +
531C LEU* 1.3 63.1 + - - +
532C PHE* 3.6 13.0 - - - +
533C HIS* 3.2 38.0 + - - +
534C SER* 3.7 8.8 + - - -
631C VAL 4.5 12.3 - - - +
632C GLN* 4.8 8.3 - - - +
666C GLU* 6.0 0.7 - - - -
675C MET* 6.2 2.7 - - + -
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Residues in contact with LEU 531 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C SER 3.9 0.8 + - - -
530C CYS* 1.3 71.9 - - - +
532C PHE* 1.3 64.9 - - - +
534C SER* 2.4 33.0 + - - +
535C LYS* 3.0 25.7 + - + +
662C LEU* 4.1 31.9 - - + +
665C GLU* 3.4 42.6 - - + +
666C GLU* 4.1 22.5 + - + +
675C MET* 6.0 3.6 - - + +
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Residues in contact with PHE 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 4.3 17.3 - + - -
526C LEU* 3.6 20.0 - - + -
530C CYS* 3.3 9.8 - - - +
531C LEU* 1.3 79.0 - - - +
533C HIS* 1.3 56.1 + - - +
535C LYS* 3.4 10.4 + - + +
536C LEU* 2.9 41.9 + - + +
561C VAL* 4.3 12.1 - - + -
564C VAL* 3.6 36.8 - - + -
565C LEU* 4.7 10.5 - - + -
568C LEU* 4.4 25.1 - - + -
627C ILE* 6.3 0.7 - - + -
631C VAL* 3.9 41.5 + - + +
662C LEU* 5.1 8.3 - - + +
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Residues in contact with HIS 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C GLU 5.9 1.3 + - - -
526C LEU* 4.6 23.0 + - + -
527C ASP 4.0 7.2 - - - +
528C PRO* 3.5 35.7 + - + +
530C CYS* 3.2 26.2 - - - +
531C LEU 3.2 0.6 - - - -
532C PHE* 1.3 77.4 - - - +
534C SER* 1.3 57.2 + - - +
536C LEU* 3.3 11.2 + - + +
537C GLN* 2.9 58.6 + - + +
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Residues in contact with SER 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530C CYS 3.7 5.8 + - - -
531C LEU* 2.4 37.0 + - - +
533C HIS* 1.3 78.8 + - - +
535C LYS* 1.3 59.7 + - - +
537C GLN* 3.3 8.5 + - - +
538C LYS* 3.0 29.3 + - - +
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Residues in contact with LYS 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531C LEU* 3.0 37.3 + - + +
532C PHE* 3.9 12.3 - - + +
534C SER* 1.3 80.1 + - - +
536C LEU* 1.3 57.8 + - - +
538C LYS* 3.3 12.4 + - - +
539C VAL* 3.0 30.5 + - - +
564C VAL* 4.2 23.0 - - + +
567C GLU* 4.2 19.9 + - - -
568C LEU* 4.6 15.5 - - - -
662C LEU* 4.8 5.8 - - + -
665C GLU* 3.4 29.1 + - - +
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Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523C TYR* 4.5 14.8 - - + +
526C LEU* 5.1 6.5 - - + -
532C PHE* 2.9 34.4 + - + +
533C HIS* 3.7 12.8 - - + +
535C LYS* 1.3 74.6 - - - +
537C GLN* 1.3 64.6 + - - +
539C VAL* 3.3 17.8 - - + +
540C LEU* 2.9 32.6 + - + +
556C LEU* 4.2 30.1 - - + -
560C HIS* 4.3 13.9 - - + +
561C VAL* 4.5 9.2 - - + +
564C VAL* 4.3 16.5 - - + +
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Residues in contact with GLN 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C HIS* 2.9 50.7 + - + +
534C SER* 3.3 8.7 + - - +
536C LEU* 1.3 82.5 - - - +
538C LYS* 1.3 57.4 + - - +
540C LEU* 3.3 19.7 + - - +
541C VAL* 3.0 32.9 + - - +
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Residues in contact with LYS 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534C SER 3.0 15.3 + - - +
535C LYS* 3.6 14.1 - - - +
536C LEU 3.3 0.2 - - - -
537C GLN* 1.3 77.4 - - - +
539C VAL* 1.3 57.4 + - - +
541C VAL* 3.3 8.6 - - + +
542C GLU* 2.9 45.5 + - + +
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Residues in contact with VAL 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535C LYS 3.0 16.9 + - - +
536C LEU* 3.3 31.6 - - + +
538C LYS* 1.3 77.0 - - - +
540C LEU* 1.3 62.0 + - - +
542C GLU* 3.6 6.5 + - + -
543C ASP* 3.4 20.4 + - - +
560C HIS* 4.4 13.2 + - + +
563C GLN* 3.5 40.6 - - + +
564C VAL* 4.3 17.0 - - + -
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Residues in contact with LEU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 2.9 20.9 + - + +
537C GLN* 3.7 23.3 - - - +
538C LYS 3.2 0.2 - - - -
539C VAL* 1.3 80.3 - - + +
541C VAL* 1.3 60.3 + - - +
542C GLU 3.5 0.2 + - - -
543C ASP* 3.5 15.8 + - + +
546C ARG* 5.1 8.4 - - + +
547C PRO* 5.5 1.0 - - - +
554C PRO* 4.3 21.6 - - + +
555C ARG 3.5 26.0 - - - +
556C LEU* 4.3 27.8 - - + +
560C HIS* 3.6 26.0 - - + +
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Residues in contact with VAL 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C GLN 3.0 16.7 + - - +
538C LYS* 3.3 20.0 - - + +
540C LEU* 1.3 77.0 - - - +
542C GLU* 1.3 74.0 + - - +
543C ASP 3.2 7.0 + - - +
547C PRO* 4.8 10.5 - - + +
554C PRO* 6.0 2.7 - - - -
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Residues in contact with GLU 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538C LYS* 2.9 31.6 + - + +
539C VAL* 4.0 8.7 - - + +
540C LEU 3.3 0.6 - - - -
541C VAL* 1.3 88.8 - - - +
543C ASP* 1.3 64.4 + - - +
544C PRO* 3.6 6.1 - - - +
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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