Contacts of the strand formed by residues 443 - 449 (chain A) in PDB entry 3RCH
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A GLU* 4.4 13.5 + - - -
401A CYS* 5.0 12.6 - - + -
412A ARG* 4.1 27.2 - - - +
417A ASN* 4.0 4.0 - - - -
439A HIS* 3.4 7.0 - - - -
440A LEU* 3.0 37.6 + - + +
442A ASP* 1.3 86.8 + - - +
444A PHE* 1.3 61.5 + - - +
445A VAL* 3.6 13.4 - - + +
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Residues in contact with PHE 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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412A ARG* 3.0 27.2 + - - +
417A ASN* 2.9 30.2 + - + +
420A ASN* 3.2 35.7 - - + -
421A GLU* 3.6 38.6 - - + +
424A LEU* 4.2 10.3 - - + -
437A PRO* 3.5 32.8 - - + -
438A CYS 3.9 3.1 - - - -
439A HIS* 3.7 28.6 + + + -
442A ASP 3.7 1.8 + - - -
443A LYS* 1.3 71.0 - - - +
445A VAL* 1.3 61.6 + - - +
446A LEU* 3.7 14.1 - - + -
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Residues in contact with VAL 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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401A CYS* 3.8 15.3 - - + -
410A CYS* 3.8 18.8 - - + -
411A PHE 3.3 22.9 - - - +
412A ARG* 4.7 0.7 - - - -
437A PRO* 3.3 5.2 - - - +
438A CYS* 2.9 44.3 + - - +
440A LEU* 3.6 24.0 - - + -
443A LYS* 3.6 21.8 - - + +
444A PHE* 1.3 84.9 - - - +
446A LEU* 1.3 73.7 + - - +
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Residues in contact with LEU 446 (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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409A VAL 3.5 0.3 - - - +
410A CYS* 3.6 1.7 - - - -
411A PHE* 2.9 71.8 + - + +
412A ARG* 4.7 1.8 - - - -
420A ASN* 3.7 30.7 - - + +
423A LEU* 4.0 25.4 - - + -
424A LEU* 4.1 27.1 - - + +
427A ILE* 4.2 9.4 - - + -
435A LEU* 4.3 3.8 - - + -
436A VAL 5.3 0.2 - - - -
437A PRO* 4.6 3.8 - - - -
444A PHE* 3.7 22.0 - - + -
445A VAL* 1.3 73.0 - - - +
447A ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 447 (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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77A PHE 4.1 3.8 - - - +
79A TYR* 5.1 16.9 + - - +
246A THR* 4.1 26.6 + - - +
247A THR* 3.4 24.9 + - - +
408A LEU* 4.1 17.5 - - + -
409A VAL 3.5 4.5 - - - -
410A CYS* 4.0 13.5 - - - -
411A PHE* 4.5 0.4 - - - -
435A LEU* 3.5 24.1 - - - +
436A VAL* 3.1 47.5 + - + +
437A PRO 3.6 8.9 + - - -
438A CYS* 3.2 37.0 - - - +
445A VAL 3.9 0.2 + - - -
446A LEU* 1.3 72.7 - - - +
448A PHE* 1.3 58.8 + - - +
449A ALA* 4.1 1.9 + - + -
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Residues in contact with PHE 448 (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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77A PHE* 3.5 52.3 - + + -
388A PHE* 3.6 62.4 - + + -
408A LEU* 3.4 3.0 - - - +
409A VAL* 2.7 42.8 + - + +
411A PHE* 3.9 5.1 - - + -
433A ILE* 4.9 0.4 - - + -
435A LEU* 4.0 19.5 - - + -
446A LEU 3.9 1.0 + - - -
447A ARG* 1.3 73.4 - - - +
449A ALA* 1.3 59.4 + - - +
450A ILE* 3.9 24.3 + - + -
460A VAL* 4.6 8.3 - - + -
463A ALA* 3.9 14.8 - - + -
467A ILE* 4.4 6.1 - - + -
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Residues in contact with ALA 449 (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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77A PHE* 3.1 44.8 + - - +
78A ALA* 4.5 1.3 - - - -
79A TYR 3.4 26.0 - - - +
80A PHE* 5.0 3.6 - - + -
407A GLY 3.8 5.6 - - - +
408A LEU* 4.0 12.3 - - + -
447A ARG* 5.4 1.1 - - + +
448A PHE* 1.3 76.1 - - - +
450A ILE* 1.3 67.7 + - - +
451A CYS* 3.2 9.0 + - - -
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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