Contacts of the strand formed by residues 408 - 413 (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 LEU 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TYR 5.1 1.3 - - - +
80A PHE* 4.2 25.1 - - + -
246A THR 4.4 3.1 - - - +
247A THR 4.3 3.6 - - - +
248A CYS* 3.7 39.4 - - - +
249A CYS* 3.7 17.4 - - + +
385A SER* 3.3 0.4 + - - -
404A VAL* 3.6 20.6 - - - +
405A ILE 5.0 1.4 + - - -
406A LEU 3.4 3.9 + - - +
407A GLY* 1.3 79.0 - - - +
409A VAL* 1.3 64.4 + - - +
410A CYS* 4.2 7.0 + - - -
447A ARG* 4.1 24.9 - - + -
448A PHE 3.4 22.2 - - - +
449A ALA* 4.0 12.3 - - + -
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Residues in contact with VAL 409 (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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385A SER* 3.3 39.5 - - - +
388A PHE* 3.9 33.2 - - + -
389A GLU* 4.4 3.4 - - - +
392A VAL* 5.5 0.2 - - + -
400A ILE* 4.2 19.5 - - + -
404A VAL* 3.9 20.0 - - + -
408A LEU* 1.3 74.1 - - - +
410A CYS* 1.3 67.2 + - - +
411A PHE* 3.7 4.3 + - + -
446A LEU 3.5 1.9 - - - +
447A ARG* 3.5 2.8 - - - -
448A PHE* 2.7 45.3 + - + +
450A ILE* 5.4 0.4 - - + -
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Residues in contact with CYS 410 (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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247A THR 3.7 8.5 - - - -
248A CYS* 3.5 38.8 - - - -
400A ILE* 3.6 6.4 - - - +
401A CYS* 2.7 32.9 + - + -
402A VAL* 3.9 20.7 + - + +
404A VAL* 4.9 3.6 - - - +
408A LEU* 4.2 7.7 + - - -
409A VAL* 1.3 76.4 - - - +
411A PHE* 1.3 53.2 + - - +
438A CYS* 4.9 2.0 - - - -
440A LEU* 4.9 0.7 - - + -
445A VAL* 3.8 16.8 - - + -
446A LEU 3.6 3.6 - - - -
447A ARG* 4.0 15.5 - - - -
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Residues in contact with PHE 411 (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 PHE* 3.8 35.2 - + - -
392A VAL* 4.2 19.3 - - + -
398A PHE* 4.2 21.5 - + - -
399A GLU 3.3 13.0 - - - +
400A ILE* 4.6 0.4 - - + -
401A CYS* 4.0 2.0 - - - -
409A VAL* 3.9 12.3 - - + -
410A CYS* 1.3 74.4 - - - +
412A ARG* 1.3 76.1 + - - +
423A LEU* 5.0 2.0 - - + -
435A LEU* 4.3 11.4 - - + -
445A VAL* 3.3 4.4 - - - +
446A LEU* 2.9 76.5 + - + +
447A ARG 4.5 0.7 - - - -
448A PHE* 3.9 13.0 - - + -
464A TRP* 4.8 2.0 - + - -
467A ILE* 4.3 20.0 - - + -
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Residues in contact with ARG 412 (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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398A PHE* 3.1 11.9 - - - +
399A GLU* 2.8 53.8 + - + -
401A CYS* 3.7 20.9 - - - -
411A PHE* 1.3 84.8 - - - +
413A LEU* 1.3 68.0 + - - +
415A GLY 2.9 30.5 + - - +
417A ASN* 2.6 39.0 + - - +
420A ASN* 3.1 26.7 - - - +
443A LYS* 4.1 25.9 - - - +
444A PHE 3.0 23.9 + - - +
445A VAL* 4.7 0.4 - - - -
446A LEU* 4.7 2.5 - - - -
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Residues in contact with LEU 413 (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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397A ARG 3.5 15.3 - - - +
398A PHE* 3.4 32.4 - - + -
412A ARG* 1.3 80.4 + - - +
414A LYS* 1.3 69.9 + - - +
419A VAL* 3.8 25.4 - - + -
420A ASN* 2.7 36.3 + - - +
423A LEU* 3.6 28.8 - - + +
471A ALA* 4.1 13.2 - - + -
474A VAL* 4.6 2.7 - - + -
475A LEU* 3.8 28.0 - - + -
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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