Contacts of the helix formed by residues 442 - 451 (chain C) in PDB entry 3UO8
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 VAL 442 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C LEU* 5.0 1.8 - - + -
423C SER* 2.9 23.0 + - - +
425C MET* 4.0 29.4 - - + -
440C LEU 3.6 0.4 + - - -
441C CYS* 1.3 71.4 - - - +
443C GLN* 1.3 67.0 + - - +
445C ILE* 3.0 12.3 + - - +
446C LEU* 3.0 19.6 + - - +
459C PHE* 3.5 30.5 - - + -
461C LEU* 3.8 25.8 - - + -
488C PHE* 3.8 21.8 - - + -
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Residues in contact with GLN 443 (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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421C GLY 4.0 9.4 + - - +
422C ASN* 3.3 27.0 - - - +
423C SER* 3.0 32.7 + - - +
441C CYS* 3.2 3.5 - - - -
442C VAL* 1.3 79.3 - - - +
444C ASN* 1.3 61.1 + - - +
446C LEU* 3.4 10.5 + - + +
447C LYS* 3.1 22.7 + - - +
477C LEU* 3.2 24.7 - - + +
480C LEU* 4.3 17.5 - - + +
488C PHE* 4.1 26.5 - - - -
490C TYR* 4.7 4.6 + - - -
551C ARG* 6.1 0.2 - - - +
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Residues in contact with ASN 444 (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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392C ARG* 6.0 2.2 - - - +
441C CYS* 3.1 27.5 + - + +
443C GLN* 1.3 76.0 - - - +
445C ILE* 1.3 62.7 + - + +
447C LYS* 3.4 10.2 + - - +
448C LEU* 3.2 30.7 + - + +
477C LEU* 3.2 27.2 - - - +
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Residues in contact with ILE 445 (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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395C VAL* 3.9 40.8 - - + -
398C PHE* 5.1 5.2 - - + -
399C LEU* 4.9 1.8 - - + -
410C LEU* 4.3 13.0 - - + -
425C MET* 3.6 30.5 - - + -
440C LEU* 4.5 7.6 - - + -
441C CYS 3.6 13.9 - - - +
442C VAL* 3.0 9.8 + - - +
444C ASN* 1.3 75.8 - - + +
446C LEU* 1.3 66.0 + - - +
448C LEU* 3.1 10.9 + - + +
449C MET* 2.9 45.2 + - + +
459C PHE* 4.4 5.8 - - + -
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Residues in contact with LEU 446 (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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442C VAL 3.0 10.7 + - - +
443C GLN* 3.6 14.4 - - + +
445C ILE* 1.3 75.5 - - - +
447C LYS* 1.3 63.9 + - - +
449C MET* 3.3 2.9 + - - +
450C GLN* 3.0 29.7 + - + +
457C ASN* 4.1 11.4 - - + +
459C PHE* 3.5 35.4 - - + -
480C LEU* 3.7 28.3 - - + -
486C ILE* 3.8 33.2 - - + -
488C PHE* 4.1 22.4 - - + -
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Residues in contact with LYS 447 (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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443C GLN 3.1 13.5 + - - +
444C ASN* 3.5 14.4 - - - +
445C ILE 3.1 0.2 - - - -
446C LEU* 1.3 78.0 - - - +
448C LEU* 1.3 62.2 + - + +
450C GLN* 3.4 14.1 + - - +
451C GLU* 3.2 46.3 + - - +
477C LEU* 5.5 5.8 - - + -
478C ASP* 3.6 44.8 + - - +
479C ALA 5.2 3.1 - - - -
480C LEU* 4.0 16.4 - - + +
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Residues in contact with LEU 448 (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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395C VAL* 5.4 3.4 - - + -
396C ASP* 5.3 3.6 - - - +
399C LEU* 3.7 31.4 - - + -
444C ASN* 3.2 19.0 + - + +
445C ILE* 3.1 9.9 + - + +
447C LYS* 1.3 74.3 - - + +
449C MET* 1.3 66.0 + - - +
451C GLU* 3.2 32.7 + - - +
452C LYS* 3.0 19.2 - - - +
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Residues in contact with MET 449 (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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398C PHE* 4.0 15.3 - - + -
399C LEU* 3.6 18.8 - - + -
402C LEU* 3.6 18.6 - - + -
408C GLY* 3.6 31.2 - - - +
409C LEU* 5.2 0.4 - - - -
410C LEU* 5.6 0.4 - - - +
445C ILE* 2.9 20.2 + - + +
446C LEU* 3.6 6.3 - - - +
448C LEU* 1.3 77.6 - - - +
450C GLN* 1.3 62.7 + - - +
452C LYS* 3.0 25.3 + - - +
453C GLU 3.6 0.2 + - - -
454C THR* 3.5 12.8 + - - +
457C ASN* 3.4 23.1 - - + +
458C VAL 5.2 1.6 - - - +
459C PHE* 3.3 37.5 - - + -
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Residues in contact with GLN 450 (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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446C LEU* 3.0 22.5 + - + +
447C LYS* 3.7 7.6 - - - +
449C MET* 1.3 70.7 - - - +
451C GLU* 1.3 58.4 + - + +
452C LYS 2.9 5.4 - - - -
453C GLU* 2.8 25.4 + - - +
454C THR* 4.4 4.9 - - - +
457C ASN* 4.1 13.5 - - - +
480C LEU* 3.6 29.2 - - - +
481C LYS* 2.9 43.9 + - + +
483C THR* 3.1 34.5 + - + +
486C ILE* 3.7 15.1 - - - +
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Residues in contact with GLU 451 (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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447C LYS* 3.2 44.8 + - + +
448C LEU* 3.5 29.2 - - - +
449C MET 3.1 1.4 - - - -
450C GLN* 1.3 76.2 - - + +
452C LYS* 1.3 62.3 + - + +
453C GLU* 3.3 6.6 + - - +
481C LYS* 6.3 5.4 - - + +
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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