Contacts of the strand formed by residues 486 - 490 (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 ILE 486 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LEU* 4.0 25.1 - - + -
450B GLN* 3.7 24.9 - - - +
457B ASN* 3.5 15.9 - - - +
459B PHE* 4.4 1.1 - - + -
480B LEU* 5.2 4.9 - - + -
481B LYS 4.9 3.4 - - - +
483B THR* 3.9 5.2 - - - +
485B ASN* 1.3 88.4 - - - +
487B VAL* 1.3 69.4 + - - +
488B PHE* 3.6 31.4 - - + -
551B ARG 5.4 0.7 - - - +
552B SER* 3.3 1.9 - - - -
553B SER* 3.0 41.1 + - - +
554B LEU 3.7 1.4 + - - +
493C CYS* 6.5 0.2 - - - -
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU* 4.7 4.3 - - + -
457B ASN 2.9 10.7 + - - +
458B VAL* 3.3 10.8 - - + +
459B PHE* 2.9 24.9 + - - +
486B ILE* 1.3 80.4 - - - +
488B PHE* 1.3 65.1 + - - +
525B ILE* 3.9 17.0 - - + -
526B THR* 4.0 13.5 - - + -
529B LEU* 3.7 28.7 - - + -
550B ILE* 4.8 2.0 - - + -
551B ARG 3.4 7.2 - - - +
552B SER* 3.6 15.3 - - - +
554B LEU* 3.6 28.3 - - + -
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Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B VAL* 3.8 20.6 - - + -
443B GLN* 4.2 16.6 - - - -
446B LEU* 4.3 12.6 - - + -
459B PHE* 3.3 46.7 - + + -
461B LEU* 4.0 8.7 - - + -
486B ILE* 3.6 23.1 - - + -
487B VAL* 1.3 77.4 - - - +
489B GLY* 1.3 58.4 + - - +
490B TYR* 3.4 46.2 - + + -
549B GLU 3.7 0.2 - - - +
550B ILE* 3.4 10.7 - - - +
551B ARG* 2.8 40.6 + - + +
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Residues in contact with GLY 489 (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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459B PHE 2.8 11.6 + - - -
460B LEU* 3.3 20.2 - - - +
461B LEU* 3.0 24.7 + - - -
487B VAL 4.1 0.4 - - - -
488B PHE* 1.3 72.0 - - - +
490B TYR* 1.3 62.7 + - - -
491B ALA 3.9 0.3 + - - -
511B PHE* 4.1 6.7 - - - -
529B LEU* 4.0 15.2 - - - +
548B LEU* 4.5 6.1 - - - -
549B GLU 3.7 4.5 - - - -
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Residues in contact with TYR 490 (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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418B GLU* 5.1 0.3 + - - -
423B SER* 3.7 21.7 + - - -
443B GLN* 4.6 5.2 + - - -
461B LEU* 3.7 28.0 - - + +
465B ARG* 3.3 39.9 + - + +
488B PHE* 3.4 34.6 - + + -
489B GLY* 1.3 74.1 - - - -
491B ALA* 1.3 62.1 + - - +
492B THR 3.3 17.3 - - - +
511B PHE* 5.1 0.7 - - - -
548B LEU* 3.3 9.4 - - - +
549B GLU* 2.9 47.7 + - + +
551B ARG* 3.4 44.9 + - + -
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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