Contacts of the strand formed by residues 441 - 445 (chain A) in PDB entry 3BRF
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 ASN 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A GLU* 5.6 1.7 - - - +
438A GLU 4.8 3.3 - - - +
439A THR 3.2 9.3 + - - +
440A ASP* 1.3 78.0 - - + +
442A PHE* 1.3 60.1 + - - +
939D MET* 3.1 29.1 - - - +
940D ILE 3.4 8.5 + - - -
941D ASN* 3.2 37.4 - - - +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A HIS* 4.4 2.5 - + - -
430A PHE* 3.6 35.4 - + + -
433A GLU* 5.7 0.9 - - - -
438A GLU 6.3 0.9 - - - -
439A THR* 3.4 20.0 - - - +
440A ASP 3.9 7.0 - - - -
441A ASN* 1.3 74.7 - - - +
443A ALA* 1.3 60.1 + - - +
444A VAL* 3.6 26.1 + - + +
456A LYS* 3.6 42.4 - - + -
458A VAL* 4.1 11.2 - - + -
938D ARG 3.9 0.2 - - - +
939D MET* 3.5 9.2 - - - -
940D ILE* 3.0 61.1 + - + +
942D ALA* 4.2 10.3 - - + -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A PHE* 3.7 6.6 - - - -
431A ASP* 2.8 42.1 + - + +
432A ASP 4.4 4.7 - - - +
433A GLU* 3.5 23.7 + - - +
442A PHE* 1.3 77.1 - - - +
444A VAL* 1.3 62.1 + - - +
938D ARG 3.3 11.7 - - - +
939D MET* 4.1 9.8 - - + -
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER* 5.3 0.4 - - - +
428A HIS* 3.8 28.9 - - + +
429A LEU 3.2 11.2 - - - +
430A PHE* 4.9 0.2 - - - -
431A ASP* 4.2 2.6 - - - +
442A PHE* 3.6 28.0 - - + +
443A ALA* 1.3 81.0 - - - +
445A ARG* 1.3 67.2 + - - +
446A ASP* 5.8 0.4 - - - +
938D ARG* 3.1 44.9 + - + +
940D ILE* 3.7 26.9 - - + -
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Residues in contact with ARG 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A SER* 2.9 24.1 + - - -
429A LEU* 2.9 48.8 + - - +
430A PHE 2.9 29.3 + - - -
431A ASP* 2.7 28.9 + - - +
444A VAL* 1.3 77.7 - - - +
446A ASP* 1.3 71.6 + - - +
453A SER* 4.7 9.5 + - - +
454A VAL* 4.0 14.5 + - - +
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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