Contacts of the helix formed by residues 456 - 465 (chain C) in PDB entry 2UZ1
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 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ARG* 3.5 16.0 - - - +
454C SER 3.1 1.6 + - - -
455C ILE* 1.3 82.1 - - - +
457C GLU* 1.3 57.8 + - - +
458C PHE 3.1 0.7 - - - -
459C ASP* 3.0 30.3 + - - +
511C PHE* 4.0 18.6 - - - -
452D GLY* 4.5 11.7 + - - -
455D ILE* 4.3 8.9 - - - +
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Residues in contact with GLU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.4 8.8 - - - +
48C ARG* 2.8 34.8 + - - +
49C HIS* 3.3 6.2 + - - +
52C ALA* 3.3 32.8 - - + +
425C PHE* 3.7 23.8 - - + -
426C GLY 5.3 0.9 - - - +
429C LEU* 4.0 8.8 - - + +
454C SER* 2.9 26.2 + - - +
456C GLY* 1.3 72.2 - - - +
458C PHE* 1.3 65.0 + - - +
459C ASP 3.1 1.6 - - - -
460C THR* 2.6 31.8 + - - -
461C LEU* 2.9 25.1 + - - +
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Residues in contact with PHE 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C PHE* 3.7 17.7 - + - -
451C VAL* 4.7 4.5 - - + -
455C ILE* 3.3 38.3 + - + +
456C GLY 3.1 0.8 - - - -
457C GLU* 1.3 75.9 - - - +
459C ASP* 1.3 62.9 + - - +
461C LEU* 3.3 17.9 + - + +
462C VAL* 3.0 27.5 + - - +
470C VAL* 3.7 33.9 - - + -
472C ILE* 5.3 0.2 - - + -
504C TYR 5.0 0.7 - - - -
508C ALA* 4.0 19.7 - - + +
511C PHE* 3.8 20.9 - + + -
513C ALA* 3.9 15.9 - - + -
538C ALA 3.8 7.9 - - - -
539C CYS* 3.5 35.4 - - + -
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Residues in contact with ASP 459 (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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48C ARG* 2.9 31.2 + - + +
456C GLY 3.0 15.9 + - - +
458C PHE* 1.3 78.5 - - - +
460C THR* 1.3 56.4 + - - +
462C VAL* 3.2 3.5 + - - +
463C ARG* 2.7 58.0 + - - +
511C PHE* 3.6 23.8 - - + +
499D LEU* 4.3 0.3 - - - +
501D ASN* 2.7 46.8 + - - +
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Residues in contact with THR 460 (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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45C ILE* 4.5 5.6 - - + -
46C ASP 3.5 21.3 - - - +
47C THR* 3.6 7.6 - - + -
48C ARG* 3.6 8.8 - - - +
429C LEU* 3.8 18.6 - - + -
457C GLU* 2.6 31.1 + - - +
459C ASP* 1.3 73.4 - - - +
461C LEU* 1.3 66.5 + - - +
463C ARG* 3.2 21.0 + - - +
464C LYS* 2.9 42.0 + - + +
466C LEU* 5.4 0.2 - - + -
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Residues in contact with LEU 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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425C PHE* 3.9 14.6 - - + -
429C LEU* 3.9 28.3 - - + -
457C GLU 2.9 15.5 + - - +
458C PHE* 3.6 33.2 - - + +
460C THR* 1.3 74.5 - - - +
462C VAL* 1.3 57.7 + - - +
465C GLN* 2.8 24.8 + - - -
466C LEU* 2.9 31.5 + - + +
468C LEU* 3.7 41.1 - - + +
470C VAL* 4.4 0.7 - - + -
537C PRO* 3.8 18.1 - - + +
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Residues in contact with VAL 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 PHE 3.0 11.1 + - - +
459C ASP 3.7 5.6 - - - +
461C LEU* 1.3 76.4 - - - +
463C ARG* 1.3 66.4 + - - +
465C GLN* 3.2 19.0 + - - +
511C PHE 3.3 21.1 - - - +
512C GLY* 3.6 26.7 - - - +
513C ALA* 3.6 12.3 - - + +
537C PRO* 4.1 10.5 - - + -
501D ASN* 3.7 23.1 - - - +
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Residues in contact with ARG 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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46C ASP* 2.9 48.0 + - - -
47C THR 4.0 1.0 + - - -
48C ARG* 3.8 14.3 - - - +
459C ASP* 2.7 40.8 + - - +
460C THR* 3.2 24.3 + - - +
462C VAL* 1.3 73.9 - - - +
464C LYS* 1.3 77.3 + - + +
465C GLN* 3.8 3.8 + - - +
498D ARG 4.5 5.4 + - - -
499D LEU* 3.9 27.0 - - - +
500D GLU 4.9 2.5 - - - +
501D ASN* 3.8 22.4 - - + -
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Residues in contact with LYS 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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44C ILE 4.5 4.4 + - - -
45C ILE* 4.3 16.2 - - + +
46C ASP* 2.8 41.0 + - - +
460C THR* 2.9 30.2 + - + +
463C ARG* 1.3 99.1 + - + +
465C GLN* 1.3 71.0 + - - +
466C LEU* 3.2 23.7 + - + +
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Residues in contact with GLN 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 LEU 2.8 10.3 + - - -
462C VAL* 3.2 13.8 + - - +
463C ARG 4.7 3.8 - - - +
464C LYS* 1.3 79.7 - - - +
466C LEU* 1.3 60.2 + - - +
467C PRO* 3.6 8.5 - - - +
535C ASN 5.3 3.6 - - - +
537C PRO* 5.2 7.9 - - - -
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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