Contacts of the strand formed by residues 448 - 451 (chain D) in PDB entry 4BUR
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 GLY 448 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443D TYR* 3.8 13.2 - - - -
444D ASP* 2.8 35.7 + - - +
445D ILE 4.7 1.0 + - - -
446D LYS 3.6 1.4 - - - -
447D LEU* 1.3 80.5 - - - +
449D ARG* 1.3 67.7 + - - -
450D ARG* 3.4 4.3 + - - +
569D ARG* 5.3 0.2 - - - -
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Residues in contact with ARG 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B GLU* 2.5 47.0 + - - +
422B ARG* 4.2 13.1 - - - +
415D ASP* 3.3 20.6 - - - -
418D PHE* 3.3 27.7 - - + -
422D ARG* 3.4 24.3 - - - +
423D VAL 3.2 21.4 + - - -
424D ASN* 4.5 1.0 - - - +
441D CYS* 3.0 40.7 + - - -
442D PHE 3.4 10.8 - - - -
443D TYR* 3.6 17.5 - - + +
447D LEU 5.2 0.5 - - - +
448D GLY* 1.3 71.7 - - - -
450D ARG* 1.3 63.7 + - - +
497D LEU* 6.1 0.2 - - - +
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Residues in contact with ARG 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D PHE* 4.4 11.4 - - + -
441D CYS* 3.4 6.5 - - - -
442D PHE* 2.9 52.9 + - + +
444D ASP* 3.4 13.3 + - - -
447D LEU* 3.6 12.6 - - - +
448D GLY 3.6 13.7 - - - +
449D ARG* 1.3 76.6 - - - +
451D ARG* 1.3 62.7 + - - +
452D VAL* 3.8 23.9 - - + +
476D TYR* 3.8 10.7 + - - -
479D GLN* 2.6 30.9 + - - +
480D SER* 4.9 3.8 + - - -
496D GLY* 3.3 31.7 + - - +
497D LEU* 3.8 25.4 - - + +
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Residues in contact with ARG 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ARG* 5.2 5.5 - - - +
400D LEU* 4.7 2.8 + - - +
402D PRO* 3.6 26.5 - - - +
418D PHE* 2.8 49.2 + - + -
419D GLY* 3.1 17.8 + - - -
420D GLY* 4.3 0.9 - - - -
438D ASP 3.3 28.7 + - - +
439D ALA 4.3 3.6 - - - -
440D ALA 3.4 23.8 - - - +
441D CYS* 4.1 2.9 - - - -
442D PHE* 4.4 0.4 - - - -
450D ARG* 1.3 79.1 - - - +
452D VAL* 1.3 65.4 + - - +
453D GLU* 2.6 38.4 + - - +
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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