Contacts of the helix formed by residues 531 - 539 (chain E) in PDB entry 4CYM
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 THR 531 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501E HIS* 3.5 1.8 - - - -
522E ALA 3.5 13.0 - - - +
523E GLU* 4.2 13.7 - - - +
524E VAL 3.4 9.4 - - - +
525E GLN* 4.5 3.6 - - + -
529E GLY 4.9 0.2 - - - +
530E ASN* 1.3 76.2 - - - +
532E PRO* 1.3 78.9 - - - +
533E LEU* 3.1 10.0 + - - +
534E HIS* 2.7 49.6 + - + +
535E LEU* 3.1 11.6 + - - +
560E ILE* 4.2 23.3 - - + -
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Residues in contact with PRO 532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E THR* 5.5 0.2 - - - -
500E LEU* 3.7 44.0 - - + +
501E HIS* 3.5 35.6 - - + +
504E CYS* 3.4 22.8 - - + +
521E SER 4.6 2.0 - - - +
522E ALA* 3.2 21.8 - - - +
524E VAL 3.8 2.9 - - - +
531E THR* 1.3 82.1 - - - +
533E LEU* 1.3 60.2 + - - +
535E LEU* 3.2 3.6 + - + +
536E ALA* 3.0 20.1 + - - +
548E LEU* 3.9 6.1 - - + -
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Residues in contact with LEU 533 (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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522E ALA* 4.8 3.5 + - + +
531E THR* 3.0 10.5 + - - +
532E PRO* 1.3 78.7 - - - +
534E HIS* 1.3 63.7 + - - +
535E LEU 3.2 0.2 + - - -
536E ALA* 3.3 1.7 + - - +
537E CYS* 2.9 33.3 + - - -
545E VAL* 4.1 23.8 - - + +
548E LEU* 3.5 31.6 - - + +
549E VAL* 4.7 2.5 - - + -
556E CYS* 4.8 7.9 - - - -
557E ARG 4.7 8.1 - - - +
558E LEU* 4.2 24.5 - - + -
568E PRO* 3.6 27.6 - - + -
584E LEU* 4.6 3.4 - - + -
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Residues in contact with HIS 534 (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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529E GLY 4.6 0.4 + - - -
530E ASN* 3.3 29.0 + - - +
531E THR* 2.7 52.7 + - - +
533E LEU* 1.3 76.3 - - - +
535E LEU* 1.3 63.5 + - - +
537E CYS* 3.5 4.9 + - - +
538E THR* 3.1 29.3 + - - +
560E ILE* 2.9 26.8 + - - +
562E ASN* 3.6 12.5 - - + +
566E ASP 2.9 29.2 + - - -
568E PRO* 3.8 21.6 - - + +
571E ILE* 3.6 17.9 - - + +
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Residues in contact with LEU 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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501E HIS* 3.6 43.3 - - + +
504E CYS 4.4 2.2 - - - -
505E GLN* 4.3 34.8 - - + +
526E ASP* 4.3 7.2 - - - +
530E ASN* 3.9 28.3 - - + +
531E THR 3.1 10.0 + - - +
532E PRO* 3.6 6.5 - - + +
533E LEU 3.1 0.8 - - - -
534E HIS* 1.3 76.0 - - - +
536E ALA* 1.3 66.4 + - - +
538E THR* 2.9 28.8 + - + +
539E TYR* 3.1 13.7 + - + +
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Residues in contact with ALA 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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504E CYS* 3.6 26.2 + - + +
532E PRO 3.0 12.6 + - - +
533E LEU 3.6 7.0 - - - +
535E LEU* 1.3 76.1 - - - +
537E CYS* 1.3 61.3 + - - +
539E TYR 3.6 0.5 + - - -
540E GLY* 3.2 4.0 + - - -
541E HIS* 3.0 29.2 + - - +
544E CYS* 4.2 6.1 - - + -
545E VAL* 3.8 30.6 - - + +
548E LEU* 4.3 6.1 - - + -
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Residues in contact with CYS 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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533E LEU* 2.9 31.5 + - - +
534E HIS* 3.8 6.1 - - - +
536E ALA* 1.3 74.2 - - - +
538E THR* 1.3 65.3 + - - +
539E TYR 3.3 0.5 + - - -
540E GLY* 3.3 8.6 + - - +
545E VAL* 4.0 6.3 - - - -
568E PRO* 3.7 37.5 - - + +
571E ILE* 3.7 11.0 - - + +
572E ALA* 4.6 3.9 - - - +
577E TYR* 3.3 17.2 - - - -
580E VAL* 3.9 25.5 - - + +
584E LEU* 4.1 3.8 - - - -
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Residues in contact with THR 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530E ASN* 5.7 3.8 - - - +
534E HIS* 3.1 16.9 + - + +
535E LEU* 2.9 24.6 + - + +
537E CYS* 1.3 77.0 - - - +
539E TYR* 1.3 84.5 + - - +
540E GLY 3.4 0.9 - - - -
571E ILE* 3.2 32.3 - - + -
575E TRP* 3.5 23.3 - - - +
577E TYR* 3.3 14.3 + - - -
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Residues in contact with TYR 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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505E GLN* 3.2 54.8 + - + -
535E LEU* 3.1 12.7 + - + +
536E ALA 3.6 0.2 + - - -
537E CYS 3.1 0.2 - - - -
538E THR* 1.3 103.0 + - - +
540E GLY* 1.3 63.9 + - - +
541E HIS* 3.1 28.8 + + + +
575E TRP* 5.0 14.6 - + - -
577E TYR* 3.6 9.7 + - - -
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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