Contacts of the helix formed by residues 534 - 546 (chain E) in PDB entry 4P0S
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 PRO 534 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517E GLU* 4.1 2.5 - - - +
518E THR* 4.7 15.5 - - + -
521E SER* 3.3 24.0 - - - +
531E ASN* 6.2 0.7 - - + -
533E GLY* 1.3 81.4 - - - -
535E ALA* 1.3 59.9 + - - +
536E LEU 3.6 0.4 - - - -
537E SER* 3.6 9.0 - - - -
538E ARG* 3.1 26.3 + - - +
10Q T 4.6 7.0 - - - +
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Residues in contact with ALA 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E GLY 3.0 0.6 - - - -
534E PRO* 1.3 80.0 - - - +
536E LEU* 1.3 64.3 + - + +
538E ARG* 3.3 12.2 + - - +
539E THR* 3.1 30.2 + - - -
9Q G 4.2 16.2 - - - +
10Q T 3.0 31.0 - - - +
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Residues in contact with LEU 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482E VAL* 5.5 2.5 - - + -
483E ARG 3.7 9.0 - - - +
484E GLY* 3.1 48.7 - - - +
485E VAL* 4.4 11.4 - - + +
489E LYS* 4.3 4.9 - - - -
532E LEU* 3.5 47.3 - - + +
533E GLY 4.0 1.4 - - - -
535E ALA* 1.3 81.0 - - + +
537E SER* 1.3 60.4 + - - +
538E ARG 3.1 0.4 - - - -
539E THR* 3.8 8.2 - - - +
540E LEU* 2.9 37.7 + - + +
9Q G 6.0 7.0 - - - +
10Q T 5.5 2.2 - - - +
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Residues in contact with SER 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507E TYR* 3.8 4.7 + - - -
516E GLN 4.3 0.9 + - - -
517E GLU 2.6 27.7 + - - +
519E LEU 3.8 0.2 + - - -
520E LEU* 3.2 33.8 + - - +
521E SER* 3.4 19.9 + - - -
532E LEU* 4.7 1.6 - - - +
533E GLY 3.9 2.6 - - - -
534E PRO* 3.6 14.7 - - - -
535E ALA 3.3 0.2 - - - -
536E LEU* 1.3 79.0 - - - +
538E ARG* 1.3 56.1 + - - +
540E LEU* 3.8 5.6 + - - -
541E SER* 3.2 24.6 + - - -
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Residues in contact with ARG 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517E GLU* 3.7 33.6 + - + +
534E PRO 3.1 21.3 + - - +
535E ALA* 3.4 11.6 + - - +
536E LEU 3.1 0.4 - - - -
537E SER* 1.3 74.3 - - - +
539E THR* 1.3 81.1 + - - +
540E LEU 3.2 1.6 - - - -
541E SER* 3.0 19.3 + - - -
542E GLN* 3.4 41.5 + - + +
473F LEU* 6.0 3.4 - - - +
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Residues in contact with THR 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482E VAL* 4.2 25.4 - - + -
483E ARG 5.7 0.7 - - - +
535E ALA 3.1 15.8 + - - -
536E LEU* 3.4 10.3 + - - +
538E ARG* 1.3 87.4 + - - +
540E LEU* 1.3 63.7 + - + +
542E GLN* 3.3 24.8 + - - +
543E LEU* 3.4 11.4 + - - +
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Residues in contact with LEU 540 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479E LEU* 4.7 12.8 - - + -
482E VAL* 4.6 13.7 - - + -
485E VAL* 4.5 19.7 - - + -
493E LEU* 3.8 26.0 - - + -
503E LEU* 5.6 2.0 - - + -
507E TYR* 3.8 10.6 + - - +
520E LEU* 3.6 26.0 - - + -
532E LEU* 4.4 7.4 - - + -
536E LEU 2.9 24.4 + - - +
537E SER* 3.9 2.2 - - - +
539E THR* 1.3 75.4 - - - +
541E SER* 1.3 63.0 + - - +
543E LEU* 3.4 5.5 + - + -
544E TYR* 3.2 46.3 + - + +
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Residues in contact with SER 541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507E TYR* 3.6 15.2 + - - -
516E GLN* 3.7 26.9 - - - -
517E GLU* 3.8 16.0 - - - +
537E SER 3.2 14.5 + - - -
538E ARG 3.0 18.9 + - - -
540E LEU* 1.3 75.9 - - - +
542E GLN* 1.3 55.6 + - - +
545E CYS* 2.7 47.1 + - - +
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Residues in contact with GLN 542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E ARG* 3.4 48.8 + - + +
539E THR* 3.3 17.3 + - - +
540E LEU 3.2 0.4 - - - -
541E SER* 1.3 82.2 + - - +
543E LEU* 1.3 63.4 + - - +
545E CYS 4.2 0.2 - - - -
546E SER* 3.0 29.8 + - - +
550E LEU* 4.2 4.2 - - - +
473F LEU 5.4 3.6 - - - +
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Residues in contact with LEU 543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539E THR 3.4 10.0 + - - +
540E LEU* 3.7 12.1 - - + +
541E SER 3.3 0.2 - - - -
542E GLN* 1.3 80.4 - - - +
544E TYR* 1.3 86.8 + - + +
545E CYS 3.9 0.2 + - - -
546E SER* 4.9 1.0 + - - +
550E LEU* 3.4 39.6 - - + +
478F LEU* 3.9 26.2 - - + -
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Residues in contact with TYR 544 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E PHE* 3.7 13.1 - + - -
478E GLN* 4.7 11.9 + - - +
479E LEU* 3.3 29.4 - - + +
500E PRO* 5.7 9.0 - - + -
503E LEU* 3.6 28.9 - - + -
504E LEU* 3.9 32.7 - - + +
507E TYR* 4.3 14.9 - - + +
540E LEU* 3.2 34.7 + - + +
541E SER 3.6 0.2 - - - -
543E LEU* 1.3 102.4 - - + +
545E CYS* 1.3 60.4 + - - +
546E SER 5.5 0.4 - - - -
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Residues in contact with CYS 545 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507E TYR* 3.9 28.9 - - - -
516E GLN* 3.5 37.2 - - - +
541E SER* 2.7 28.8 + - - +
544E TYR* 1.3 80.7 - - - +
546E SER* 1.3 66.1 + - - +
547E TYR* 3.0 25.7 - - - -
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Residues in contact with SER 546 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541E SER 4.3 0.4 + - - -
542E GLN* 3.0 24.4 + - - +
543E LEU 5.4 1.0 - - - +
544E TYR 5.5 0.2 - - - -
545E CYS* 1.3 76.0 - - - +
547E TYR* 1.3 63.9 + - - +
548E GLY 3.3 9.5 + - - +
549E PRO 4.7 2.2 + - - -
550E LEU* 3.2 22.7 - - - +
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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