Contacts of the strand formed by residues 490 - 494 (chain B) in PDB entry 4OE4
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 THR 490 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ASN* 2.9 34.0 + - - +
323B PHE* 3.4 1.9 + - - -
352B SER* 3.0 30.9 + - - -
488B ALA* 3.9 7.1 - - - +
489B LEU* 1.3 93.0 - - + +
491B GLY* 1.3 58.7 + - - +
512B ALA* 3.7 5.4 - - - -
514B ASN* 3.3 23.6 - - + +
516B TYR* 4.3 4.5 - - + +
521B CYS* 3.0 30.5 + - - +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 3.3 31.2 - - - -
490B THR* 1.3 76.5 + - - +
492B ALA* 1.3 61.4 + - - -
512B ALA* 3.7 2.1 - - - +
514B ASN 3.1 6.9 + - - +
515B PHE* 3.3 10.8 - - - -
516B TYR* 2.8 26.5 + - - -
521B CYS* 4.0 2.9 - - - -
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Residues in contact with ALA 492 (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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323B PHE* 3.0 9.4 + - - +
324B HIS* 3.8 20.6 - - + +
325B LEU* 2.7 35.0 + - - +
491B GLY* 1.3 75.8 - - - +
493B ILE* 1.3 55.8 + - - +
494B PHE* 4.0 6.7 - - + -
515B PHE* 4.3 5.6 - - - -
516B TYR* 3.2 13.0 - - + +
519B ASP 3.3 26.2 - - - +
521B CYS* 4.2 2.0 - - + -
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Residues in contact with ILE 493 (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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325B LEU* 3.2 15.9 - - + +
327B HIS* 4.7 1.1 - - + -
474B PHE* 3.7 22.4 - - + -
492B ALA* 1.3 75.4 - - - +
494B PHE* 1.3 66.0 + - - +
495B ALA* 4.0 20.8 + - + -
500B ALA 4.0 8.3 - - - +
501B ILE* 4.2 10.8 - - + -
504B ALA* 3.5 26.2 - - + -
515B PHE* 3.6 28.2 - - + -
516B TYR 2.9 12.4 + - - +
517B ILE* 3.6 16.1 - - + +
518B ASN* 2.8 25.8 + - - +
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Residues in contact with PHE 494 (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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324B HIS* 3.4 33.2 - + + -
325B LEU 2.8 20.3 + - - +
326B VAL* 4.1 13.5 - - + -
327B HIS* 2.8 29.8 + - - +
330B ALA* 3.2 20.3 - - + +
331B ASN 5.6 0.4 - - - +
334B HIS* 4.1 7.0 - + - -
335B ALA* 3.8 21.5 - - + -
338B SER* 3.6 36.3 - - - -
339B THR* 4.6 2.2 - - - -
492B ALA* 4.0 9.4 - - + -
493B ILE* 1.3 72.8 - - - +
495B ALA* 1.3 61.5 + - - +
518B ASN* 3.3 18.4 - - - +
519B ASP 3.6 30.5 - - - -
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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