Contacts of the helix formed by residues 442 - 452 (chain B) in PDB entry 3UOA
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU* 4.7 3.1 - - + -
423B SER* 2.9 26.5 + - - +
425B MET* 4.1 29.4 - - + -
441B CYS* 1.3 71.6 - - - +
443B GLN* 1.3 67.5 + - - +
445B ILE* 3.0 11.1 + - + +
446B LEU* 3.0 19.4 + - - +
459B PHE* 3.7 29.2 - - + -
461B LEU* 3.8 26.0 - - + -
463B MET* 4.9 0.4 - - + -
488B PHE* 3.8 20.2 - - + -
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B GLY 4.1 10.1 + - - +
422B ASN* 3.5 19.9 - - - +
423B SER* 3.1 34.3 + - - +
441B CYS* 3.3 7.3 - - - -
442B VAL* 1.3 78.6 - - - +
444B ASN* 1.3 56.4 + - - +
446B LEU* 3.4 10.7 + - + +
447B LYS* 3.0 27.5 + - - +
477B LEU* 3.8 21.6 - - + +
480B LEU* 4.3 19.0 - - + +
488B PHE* 4.2 24.8 - - - -
490B TYR* 4.6 5.1 + - - -
551B ARG* 5.8 1.6 - - - +
494C GLN* 6.1 1.1 - - - +
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Residues in contact with ASN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B ARG* 6.1 0.4 - - - +
441B CYS* 3.1 29.4 + - - +
443B GLN* 1.3 77.0 - - - +
445B ILE* 1.3 62.6 + - + +
447B LYS* 3.5 12.8 + - - +
448B LEU* 3.3 30.0 + - + +
477B LEU* 2.8 30.3 - - - +
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B VAL* 4.0 40.8 - - + -
398B PHE* 5.0 7.0 - - + -
399B LEU* 5.2 1.3 - - + -
410B LEU* 4.3 13.2 - - + -
425B MET* 3.6 31.2 - - + -
440B LEU* 4.5 7.9 - - + -
441B CYS 3.8 12.3 - - - +
442B VAL* 3.0 9.1 + - - +
444B ASN* 1.3 74.6 - - + +
446B LEU* 1.3 66.3 + - - +
448B LEU* 3.1 11.4 + - + +
449B MET* 3.0 40.4 + - + +
459B PHE* 4.5 6.7 - - + -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442B VAL 3.0 10.5 + - - +
443B GLN* 3.6 12.6 - - + +
445B ILE* 1.3 75.2 - - - +
447B LYS* 1.3 64.1 + - - +
449B MET* 3.0 3.1 + - - +
450B GLN* 2.9 32.1 + - + +
457B ASN* 4.0 13.0 - - + -
459B PHE* 3.5 34.9 - - + -
480B LEU* 3.6 29.2 - - + -
486B ILE* 4.0 31.4 - - + -
488B PHE* 4.3 20.9 - - + -
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Residues in contact with LYS 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B GLN 3.0 13.2 + - - +
444B ASN* 3.6 17.3 - - - +
445B ILE 3.2 0.2 - - - -
446B LEU* 1.3 76.4 - - - +
448B LEU* 1.3 65.8 + - + +
450B GLN* 3.4 14.5 + - - +
451B GLU* 3.2 43.2 + - + +
477B LEU* 6.2 4.0 - - + -
478B ASP* 4.2 33.1 + - + +
479B ALA 5.5 2.4 + - - -
480B LEU* 4.1 11.2 - - + +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B VAL* 5.3 3.8 - - + -
396B ASP* 5.5 3.4 - - - +
399B LEU* 3.6 33.3 - - + +
444B ASN* 3.3 19.0 + - + +
445B ILE* 3.1 11.9 + - + +
447B LYS* 1.3 79.0 - - + +
449B MET* 1.3 61.3 + - - +
451B GLU* 3.3 36.8 + - - +
452B LYS* 3.5 14.6 + - - +
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Residues in contact with MET 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B PHE* 4.0 14.4 - - + -
399B LEU* 3.7 20.6 - - + -
402B LEU* 3.7 11.4 - - + -
408B GLY* 3.6 36.1 - - - +
409B LEU* 5.2 0.7 - - - -
410B LEU* 5.6 0.9 - - - +
445B ILE* 3.0 25.6 + - + +
446B LEU* 3.0 6.0 + - - +
448B LEU* 1.3 73.2 - - - +
450B GLN* 1.3 66.5 + - - +
452B LYS* 2.9 22.1 + - - +
453B GLU 3.5 0.3 + - - -
454B THR* 3.5 13.3 + - + +
457B ASN* 3.4 29.2 - - + +
458B VAL 4.8 1.6 - - - +
459B PHE* 3.5 31.6 - - + -
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LEU* 2.9 31.6 + - + +
447B LYS* 3.6 9.2 - - - +
449B MET* 1.3 76.0 - - - +
451B GLU* 1.3 59.2 + - + +
453B GLU* 2.9 24.5 + - - +
454B THR* 4.4 4.7 - - - -
457B ASN* 4.3 6.3 - - - +
480B LEU* 3.3 29.3 - - - +
481B LYS* 2.9 34.6 + - + +
483B THR* 3.0 35.8 + - + +
486B ILE* 3.7 10.9 - - - +
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Residues in contact with GLU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LYS* 3.2 43.8 + - + +
448B LEU* 3.4 28.2 - - - +
449B MET 3.1 0.8 - - - -
450B GLN* 1.3 77.4 - - + +
452B LYS* 1.3 62.5 + - + +
453B GLU* 3.2 9.8 + - - +
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Residues in contact with LYS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B LEU* 3.3 39.2 + - + +
400B LEU* 4.3 15.2 + - - +
402B LEU* 3.6 35.3 + - + +
403B ASP* 3.2 2.6 - - - +
404B LYS* 3.2 18.7 + - - +
448B LEU 3.6 14.4 - - - +
449B MET* 2.9 12.8 + - - +
451B GLU* 1.3 78.0 - - + +
453B GLU* 1.3 71.8 + - - +
454B THR* 4.5 1.1 - - + -
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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