Contacts of the strand formed by residues 437 - 443 (chain A) in PDB entry 3RFU
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 LYS 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A HIS 4.8 1.3 - - - +
436A PRO* 1.3 77.5 - - - +
438A LEU* 1.3 78.9 + - - +
439A THR* 3.3 24.8 + - + +
469A ALA* 4.5 4.3 - - - +
473A ALA* 6.4 0.4 - - + -
476A GLU* 5.8 3.8 - - - -
551A VAL* 3.3 7.5 - - - +
552A GLU 2.8 31.5 + - - +
554A PRO* 4.4 19.0 - - + +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS* 1.3 85.3 - - - +
439A THR* 1.3 62.8 + - - +
440A ARG 3.5 17.0 - - - +
441A ILE* 4.0 27.6 - - + -
452A LEU* 4.7 5.2 - - + -
469A ALA* 4.0 16.7 + - - +
470A ILE* 3.7 33.2 - - + -
473A ALA* 3.5 24.9 - - + +
549A LEU* 4.4 4.5 - - + -
550A VAL 3.1 34.8 - - - +
551A VAL* 4.0 5.7 - - + +
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Residues in contact with THR 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LYS* 3.4 38.1 - - + +
438A LEU* 1.3 80.4 - - - +
440A ARG* 1.3 66.1 + - - +
550A VAL* 3.2 12.0 + - - +
552A GLU* 3.1 33.2 + - + +
554A PRO* 5.6 5.4 - - + -
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Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A LEU* 3.5 5.6 - - - +
439A THR* 1.3 84.5 + - - +
441A ILE* 1.3 72.2 + - - +
442A VAL* 4.1 23.6 - - + +
525A LYS* 5.4 10.3 - - - +
529A LEU* 5.4 5.8 - - + +
548A LEU 3.9 0.3 - - - +
550A VAL* 3.0 45.2 + - + +
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Residues in contact with ILE 441 (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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438A LEU* 4.0 14.4 - - + -
440A ARG* 1.3 81.3 - - - +
442A VAL* 1.3 67.4 + - - +
448A GLU* 3.1 49.0 + - + +
451A ALA* 4.7 1.3 - - + -
452A LEU* 3.6 46.7 - - + -
547A ALA* 4.4 9.0 - - + -
548A LEU 3.1 12.3 - - - +
549A LEU* 3.5 25.6 - - + -
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ARG* 4.4 27.4 - - + +
441A ILE* 1.3 76.9 - - - +
443A THR* 1.3 67.9 + - - +
448A GLU* 4.8 0.9 - - - -
522A LEU* 4.3 13.5 - - + -
525A LYS* 4.9 23.1 - - + -
529A LEU* 4.5 15.3 - - + -
547A ALA* 3.5 6.9 - - - +
548A LEU* 3.0 56.3 + - + +
550A VAL* 4.8 2.7 - - + -
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Residues in contact with THR 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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441A ILE 3.8 0.4 + - - -
442A VAL* 1.3 86.0 + - - +
444A ASP* 1.3 72.4 + - - +
445A ASP 4.7 0.4 - - - +
446A PHE* 2.7 46.9 + - - +
448A GLU* 3.7 29.4 + - + +
522A LEU* 4.4 4.1 - - - +
546A VAL 3.6 7.5 + - - -
547A ALA* 4.2 2.6 - - - +
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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