Contacts of the strand formed by residues 438 - 444 (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 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A THR 4.9 1.3 - - - +
430A THR* 4.3 7.9 - - + -
435A GLN* 3.6 17.9 - - - +
437A GLY* 1.3 74.1 - - - -
439A LEU* 1.3 60.0 + - - +
440A ILE* 3.7 18.1 + - + +
460A GLU* 3.4 4.6 - - - +
461A LEU* 2.9 52.7 + - + +
464A ILE* 3.9 12.6 - - + -
474A ILE* 4.1 24.0 - - + -
5C LEU* 3.9 27.8 - - + +
6C THR 3.6 2.5 - - - -
7C GLY* 4.4 2.0 - - - -
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Residues in contact with LEU 439 (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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404A GLU 5.0 6.4 - - - +
438A VAL* 1.3 70.9 - - - +
440A ILE* 1.3 64.0 + - - +
441A GLN* 3.5 41.5 + - + +
458A ARG* 4.5 21.5 - - + +
459A PHE 3.8 20.0 - - - +
460A GLU* 4.5 8.3 - - + +
5C LEU* 5.0 5.7 - - - +
6C THR* 2.9 22.6 + - - +
7C GLY* 3.8 23.4 - - - +
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Residues in contact with ILE 440 (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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403A LEU* 4.1 20.4 - - + -
438A VAL* 4.0 14.6 - - + +
439A LEU* 1.3 70.0 - - - +
441A GLN* 1.3 61.1 + - - +
442A VAL* 4.0 8.3 + - + +
458A ARG* 3.2 5.9 - - - +
459A PHE* 2.8 81.6 + - + +
461A LEU 5.1 0.9 - - - +
476A VAL* 4.2 6.5 - - + -
488A VAL* 4.2 14.6 - - + -
490A ALA* 3.9 17.5 - - + -
5C LEU* 3.8 28.3 - - + -
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Residues in contact with GLN 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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403A LEU* 3.1 8.6 - - - +
404A GLU* 3.0 61.8 + - + +
439A LEU* 3.5 37.1 + - + +
440A ILE* 1.3 77.0 - - - +
442A VAL* 1.3 61.8 + - - +
443A TYR* 3.4 18.9 + - + -
457A GLY 3.8 4.7 - - - -
458A ARG* 2.7 39.0 + - + +
6C THR* 4.7 10.1 + - - -
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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
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401A LEU* 5.7 0.2 - - + -
402A GLY 3.5 11.0 - - - +
403A LEU* 4.5 0.4 - - - +
440A ILE* 4.2 11.4 - - + +
441A GLN* 1.3 72.2 - - - +
443A TYR* 1.3 59.0 + - - +
455A LEU* 3.6 5.2 - - - +
456A LEU* 2.8 41.8 + - + -
457A GLY 2.9 18.9 + - - +
459A PHE* 4.8 0.4 - - + -
478A PHE* 4.0 16.8 - - + -
486A LEU* 4.3 2.0 - - + -
488A VAL* 4.1 26.5 - - + -
501A ILE* 4.2 17.0 - - + -
503A ILE* 3.7 24.7 - - + -
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Residues in contact with TYR 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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401A LEU* 3.6 4.2 - - - +
402A GLY 2.9 33.1 + - - +
403A LEU* 5.2 0.2 - - - -
404A GLU* 3.9 14.7 + - - -
410A MET* 3.4 24.2 - - - +
441A GLN* 3.4 25.1 + - + -
442A VAL* 1.3 75.8 - - - +
444A GLU* 1.3 60.9 + - - +
450A THR* 3.2 53.3 + - + -
451A LYS* 5.3 1.7 - - - -
453A ASN* 4.1 5.6 - - + -
454A ASN 3.3 18.8 - - - -
455A LEU* 3.5 33.8 - - + +
456A LEU* 4.4 3.4 - - - -
458A ARG* 3.9 19.1 + - - -
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Residues in contact with GLU 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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399A LEU* 3.6 28.6 - - + +
400A SER 3.4 4.3 - - - -
401A LEU* 3.2 26.4 - - + +
410A MET* 4.2 0.7 - - - -
443A TYR* 1.3 75.1 - - - +
445A GLY* 1.3 60.6 + - - +
453A ASN* 3.2 4.5 - - - +
454A ASN* 2.9 37.0 + - + +
456A LEU* 3.7 12.6 - - + +
506A ASP* 2.6 31.4 - - - +
509A ARG* 3.1 26.9 + - - -
510A LEU* 3.7 12.1 - - - +
518A MET* 3.6 6.2 - - + +
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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