Contacts of the strand formed by residues 405 - 410 (chain C) in PDB entry 3BWE
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 ARG 405 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403C SER* 3.6 11.0 - - - +
404C LYS* 1.3 78.6 - - - +
406C ALA* 1.3 60.7 + - - +
431C ILE* 3.9 2.7 - - - -
432C LYS* 3.3 18.2 - - + +
434C THR* 5.5 0.8 + - - -
464C GLU* 2.5 48.3 + - - +
465C GLY* 4.8 3.2 - - - -
466C PRO* 4.3 15.1 + - - +
467C TYR* 3.1 29.2 + - + +
468C ASP* 2.7 44.6 + - - +
469C VAL 3.5 2.4 + - - -
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Residues in contact with ALA 406 (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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405C ARG* 1.3 73.7 - - - +
407C LEU* 1.3 60.3 + - - +
408C VAL 4.0 0.2 - - - -
426C MSE 3.7 23.1 - - + -
431C ILE* 3.3 23.1 - - + +
432C LYS 2.8 9.0 + - - +
433C VAL* 4.4 4.0 - - + +
434C THR 3.1 25.5 + - - -
467C TYR* 3.5 10.3 - - - -
469C VAL* 3.4 19.5 - - + -
471C VAL* 5.0 0.9 - - + -
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Residues in contact with LEU 407 (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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406C ALA* 1.3 74.1 - - - +
408C VAL* 1.3 62.9 + - - +
409C ILE* 4.0 17.5 - - + -
434C THR 3.9 4.7 - - - +
436C ALA* 3.7 28.3 - - + -
458C LEU* 4.2 3.8 - - + -
461C ALA* 4.8 6.1 - - + -
462C LYS* 5.9 2.2 - - - -
467C TYR* 3.7 35.2 - - + -
469C VAL 2.7 16.9 + - - +
470C VAL* 3.1 10.2 - - + +
471C VAL* 2.6 33.8 + - - +
491C ILE* 4.0 34.5 - - + -
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Residues in contact with VAL 408 (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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406C ALA 4.0 0.2 + - - -
407C LEU* 1.3 75.1 - - - +
409C ILE* 1.3 63.6 + - - +
410C LEU* 3.5 1.9 + - - +
419C THR* 4.6 11.2 - - - +
422C PRO* 5.8 0.2 - - + -
423C VAL* 4.0 14.4 - - + -
426C MSE 3.8 23.1 - - + -
433C VAL* 3.8 15.7 - - + -
434C THR 3.1 12.4 + - - +
435C VAL* 3.7 10.7 - - + +
436C ALA* 2.8 32.4 + - - -
471C VAL* 3.2 28.9 - - + -
473C PRO* 4.3 15.0 - - + -
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Residues in contact with ILE 409 (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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407C LEU* 4.0 29.4 - - + -
408C VAL* 1.3 74.3 - - - +
410C LEU* 1.3 61.8 + - - +
411C ALA 3.7 2.6 + - - -
436C ALA 3.5 8.3 - - - +
438C LEU* 4.1 12.6 - - + -
458C LEU* 4.1 17.7 - - + -
470C VAL* 4.2 14.1 - - + -
471C VAL 3.3 12.1 + - - +
472C LEU* 4.3 8.1 - - + -
473C PRO* 3.3 22.7 - - - +
482C LEU* 3.4 30.5 - - + +
488C VAL* 4.0 25.1 - - + -
491C ILE* 4.2 8.5 - - + -
492C LEU* 5.7 0.2 - - + -
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Residues in contact with LEU 410 (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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408C VAL* 3.5 2.8 + - + +
409C ILE* 1.3 70.6 - - - +
411C ALA* 1.3 65.6 + - - +
414C ALA* 3.8 15.7 - - + -
419C THR* 4.4 13.2 - - - +
435C VAL* 3.7 29.6 - - + -
436C ALA 2.7 15.5 + - - +
437C GLY* 3.4 3.7 - - - -
438C LEU* 2.9 24.4 + - - -
439C ALA 4.9 0.2 + - - -
444C VAL* 3.3 47.8 - - + +
446C CYS* 4.3 9.6 - - - -
452C ILE* 3.7 26.7 - - + +
454C PRO* 4.5 4.9 - - + -
473C PRO* 5.5 0.7 - - - -
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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