Contacts of the helix formed by residues 455 - 466 (chain C) in PDB entry 5SUY
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 GLY 455 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C LEU* 1.3 71.8 - - - +
456C SER* 1.3 55.7 + - - +
458C VAL* 3.3 7.2 + - - +
459C VAL* 3.1 32.2 + - - +
497C PHE* 3.8 11.9 - - - -
499C GLU* 3.3 13.7 + - - -
501C CYS 3.0 13.7 + - - -
503C TYR* 3.7 22.1 - - - -
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Residues in contact with SER 456 (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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500A GLN* 3.2 35.3 + - - -
454C LEU* 3.9 9.7 - - - +
455C GLY* 1.3 76.1 - - - +
457C ASP* 1.3 64.3 + - - +
459C VAL 3.6 0.3 + - - -
460C ASP* 3.0 34.4 + - - +
472C ARG* 3.6 4.4 + - - +
499C GLU* 2.9 34.6 + - - +
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Residues in contact with ASP 457 (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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442A ARG* 3.4 22.2 + - - -
446B LYS* 3.7 15.1 + - - -
454C LEU* 3.0 25.9 + - + +
456C SER* 1.3 87.1 + - - +
458C VAL* 1.3 65.2 + - - +
460C ASP* 3.9 13.9 - - - +
461C TRP* 3.1 23.2 + - - +
437D LEU* 3.8 7.6 - - + +
438D GLU* 3.6 34.4 + - + +
440D ARG* 4.7 1.0 + - - -
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Residues in contact with VAL 458 (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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453C PHE* 3.4 37.9 - - + -
454C LEU 3.2 8.0 + - - +
455C GLY* 3.5 11.2 - - - +
457C ASP* 1.3 75.2 - - - +
459C VAL* 1.3 65.2 + - - +
461C TRP* 3.3 3.4 + - - +
462C LEU* 3.0 40.8 + - + +
479C ALA* 4.1 13.5 - - + -
482C LEU* 4.8 5.6 - - + -
488C ILE* 5.0 11.4 - - + -
497C PHE* 5.3 0.9 - - + -
503C TYR* 5.5 0.4 - - + -
430D MET* 4.1 22.2 - - + +
437D LEU* 4.2 8.1 - - + -
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Residues in contact with VAL 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C GLY 3.1 16.6 + - - +
456C SER 3.9 0.7 - - - +
458C VAL* 1.3 80.4 - - - +
460C ASP* 1.3 62.0 + - - +
462C LEU* 3.5 6.6 + - - +
463C TYR* 3.1 22.2 + - - +
472C ARG* 3.5 42.6 - - + +
475C ALA* 4.0 2.6 - - + +
476C ARG* 3.8 38.6 - - + +
479C ALA* 3.9 15.3 - - + -
497C PHE* 4.1 9.4 - - + -
499C GLU* 4.2 8.1 - - - +
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Residues in contact with ASP 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C SER* 3.0 20.7 + - - +
457C ASP* 3.9 16.7 - - - +
458C VAL 3.2 0.2 - - - -
459C VAL* 1.3 77.2 - - - +
461C TRP* 1.3 62.1 + - - +
463C TYR* 3.2 5.5 + - - +
464C HIS* 3.0 48.1 + - + +
472C ARG* 2.8 33.8 + - - -
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Residues in contact with TRP 461 (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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457C ASP 3.1 15.9 + - - +
458C VAL 3.7 3.6 - - - +
460C ASP* 1.3 78.6 - - - +
462C LEU* 1.3 68.3 + - + +
464C HIS* 3.4 0.8 + - - -
465C HIS* 2.8 75.1 + + + +
466C VAL* 4.2 19.3 - - + -
417D LEU* 3.9 23.8 - - + -
426D VAL* 4.3 5.6 - - + -
429D ALA* 4.4 3.1 - - + -
430D MET* 3.7 53.2 - - + -
435D SER* 2.9 28.7 + - - -
436D GLY 3.7 4.7 - - - -
437D LEU* 3.5 33.6 - - + +
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Residues in contact with LEU 462 (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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458C VAL* 3.0 37.9 + - + +
459C VAL 3.8 3.4 - - - +
461C TRP* 1.3 87.0 - - + +
463C TYR* 1.3 58.6 - - - +
466C VAL* 2.9 42.4 + - + +
469C PHE* 3.6 13.6 - - + -
475C ALA* 3.8 18.2 - - + +
478C TYR* 3.7 31.2 - - + -
479C ALA* 4.0 8.5 - - + -
482C LEU* 4.4 5.4 - - + -
426D VAL* 3.8 28.3 - - + -
430D MET* 4.7 5.2 - - - -
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Residues in contact with TYR 463 (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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459C VAL 3.1 18.3 + - - +
460C ASP* 3.7 5.8 - - - +
462C LEU* 1.3 76.7 - - - +
464C HIS* 1.3 77.1 + + + +
466C VAL 4.4 6.2 - - - +
469C PHE* 3.6 35.6 - - + +
470C PRO 3.9 5.9 + - - -
471C GLU* 3.5 11.6 - - - -
472C ARG* 3.5 55.1 + - + -
475C ALA* 4.0 6.7 - - + +
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Residues in contact with HIS 464 (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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460C ASP* 3.0 40.1 + - + +
461C TRP* 5.1 0.2 - - - -
463C TYR* 1.3 97.3 - + - +
465C HIS* 1.3 75.6 + - + +
466C VAL 3.9 0.2 - - - -
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Residues in contact with HIS 465 (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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461C TRP* 2.8 85.1 + + + +
464C HIS* 1.3 88.4 - - + +
466C VAL* 1.3 60.7 + - - +
467C GLU* 4.1 2.2 + - - +
417D LEU* 3.8 21.5 + - + +
435D SER 3.9 9.1 + - - -
436D GLY* 5.0 4.9 - - - -
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Residues in contact with VAL 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C TRP* 4.2 10.3 - - + -
462C LEU* 2.9 29.8 + - + +
463C TYR 4.4 5.7 - - - +
464C HIS 3.9 0.6 - - - -
465C HIS* 1.3 80.7 - - - +
467C GLU* 1.3 63.0 + - - +
468C GLY 3.7 0.5 + - - -
469C PHE* 3.7 29.9 + - + +
478C TYR* 5.4 2.9 - - + -
417D LEU* 3.8 10.1 - - + -
418D SER* 3.4 35.9 - - - +
419D VAL* 3.8 3.6 - - - +
426D VAL* 4.0 27.6 - - + -
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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