Contacts of the strand formed by residues 448 - 451 (chain C) in PDB entry 4LQL
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 448 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A ARG* 6.3 0.9 - - - +
311C MET* 3.7 9.6 - - - +
329C LEU* 4.2 3.5 - - - +
330C MET* 3.0 35.1 + - + +
331C GLU 3.9 5.6 - - - +
332C ASP* 5.7 2.5 - - + +
390C ASP* 3.4 17.5 - - + +
391C ILE 3.7 16.7 + - - -
392C THR* 4.3 5.6 - - - +
426C TRP* 5.3 6.7 - - + -
439C TRP* 4.8 9.4 - - + -
445C GLY 5.3 0.4 - - - +
446C HIS* 3.3 15.0 + - - +
447C HIS* 1.3 74.5 - - - +
449C VAL* 1.3 98.3 + - - +
450C LEU* 3.9 1.4 + - - +
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Residues in contact with VAL 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C MET 4.7 2.9 - - - +
314C LEU* 3.5 35.4 - - + +
315C THR* 4.3 11.7 - - - +
318C LEU* 4.2 17.3 - - + -
327C THR* 4.0 17.0 - - - +
328C ALA 3.1 26.0 - - - +
329C LEU* 4.3 4.0 - - - -
330C MET 4.5 1.1 - - - +
389C TYR 4.0 0.3 - - - +
390C ASP* 3.1 1.9 - - - -
391C ILE* 3.0 32.6 + - + +
448C THR* 1.3 90.4 + - - +
450C LEU* 1.3 60.2 - - - +
451C THR* 3.9 4.4 + - - +
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Residues in contact with LEU 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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327C THR* 4.5 2.3 - - - -
328C ALA* 3.3 20.9 + - - +
330C MET* 4.4 22.6 - - + +
390C ASP* 4.1 14.6 - - + -
407C VAL* 5.2 8.7 - - + -
409C CYS* 4.6 20.0 - - - -
426C TRP* 4.8 19.5 - - + -
448C THR* 3.9 1.1 + - - +
449C VAL* 1.3 73.1 - - - +
451C THR* 1.3 64.7 + - - +
452C LEU* 4.1 5.8 + - + +
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Residues in contact with THR 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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318C LEU* 4.8 4.0 - - - +
327C THR* 3.1 27.7 + - - -
387C LYS 4.1 0.3 - - - -
388C GLY* 3.0 28.2 + - - -
389C TYR* 3.1 17.9 + - - -
409C CYS* 4.9 1.4 - - - -
449C VAL* 3.9 5.4 + - - +
450C LEU* 1.3 76.2 - - - +
452C LEU* 1.3 62.8 + - - +
454C LEU* 3.8 33.2 + - - +
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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