Contacts of the strand formed by residues 409 - 414 (chain A) in PDB entry 4PO2
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 VAL 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A GLU* 3.4 4.7 - - - -
405A THR* 2.9 45.4 + - - +
406A ALA 4.1 2.2 - - - +
408A GLY* 1.3 78.8 - - - +
410A MET* 1.3 74.9 + - - +
411A THR* 3.3 5.4 + - - +
448A ALA 3.8 7.4 - - - +
449A MET* 4.4 8.1 - - + -
450A THR* 3.8 1.6 - - - -
533A ARG* 4.8 20.4 - - + +
536A VAL* 3.5 43.5 - - + -
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Residues in contact with MET 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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400A SER 3.8 8.5 - - - +
401A LEU 4.0 2.5 - - - -
402A GLY* 3.6 20.2 - - - +
403A LEU 4.6 0.4 - - - -
408A GLY 3.8 0.6 + - - -
409A VAL* 1.3 76.2 - - - +
411A THR* 1.3 63.8 + - - +
412A ALA* 3.8 10.5 + - + +
443A TYR* 3.4 49.4 - - - +
445A GLY 3.6 25.1 - - - +
447A ARG 3.5 13.5 - - - +
448A ALA* 2.8 23.5 + - - +
450A THR* 3.7 12.0 - - + +
453A ASN* 3.4 17.3 - - - +
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Residues in contact with THR 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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402A GLY* 3.1 2.6 - - - -
403A LEU* 2.9 41.1 + - - -
405A THR* 2.7 32.5 + - - +
409A VAL* 3.3 4.8 + - - +
410A MET* 1.3 72.1 - - - +
412A ALA* 1.3 64.6 + - - +
413A LEU* 3.7 5.2 - - + +
426A GLN* 4.2 16.6 - - - +
428A PHE* 4.3 10.8 - - + -
3C LEU* 3.6 26.9 - - + +
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Residues in contact with ALA 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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400A SER* 4.3 21.3 - - - +
401A LEU 3.5 12.8 - - - +
402A GLY* 3.8 2.5 - - - -
410A MET* 3.8 12.0 + - + +
411A THR* 1.3 77.3 - - - +
413A LEU* 1.3 63.6 + - - +
414A ILE 4.4 4.0 - - - +
415A LYS* 4.4 24.2 + - + -
426A GLN* 4.5 4.5 - - - +
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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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401A LEU 2.8 6.0 + - - +
402A GLY* 4.6 0.4 - - - -
403A LEU* 3.6 30.7 - - + -
411A THR* 3.7 7.0 - - + +
412A ALA* 1.3 74.8 - - - +
414A ILE* 1.3 61.3 + - - +
415A LYS* 4.1 4.4 + - - +
424A GLN* 3.2 37.3 + - + +
425A THR 4.4 0.9 - - - -
426A GLN* 3.9 26.0 - - + +
428A PHE* 4.0 10.8 - - + -
476A VAL* 3.5 28.5 - - + +
478A PHE* 3.5 38.4 - - + -
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Residues in contact with ILE 414 (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 ALA* 4.3 14.6 - - + -
400A SER* 3.2 5.4 - - - -
401A LEU* 2.8 44.1 + - + +
412A ALA* 4.4 0.6 - - - +
413A LEU* 1.3 82.4 - - - +
415A LYS* 1.3 72.1 + - - +
418A SER* 3.9 16.4 - - - -
422A THR* 3.7 17.3 - - + -
424A GLN* 3.9 17.0 - - + -
478A PHE* 3.7 32.1 - - + +
480A ILE* 3.6 33.9 - - + -
486A LEU* 4.7 1.8 - - + -
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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