Contacts of the strand formed by residues 411 - 416 (chain A) in PDB entry 1P22
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 THR 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A HIS* 3.4 14.7 - - - -
406A ALA* 3.3 4.2 - - - +
407A SER 3.2 24.6 + - - -
409A ASP* 3.0 33.4 + - - +
410A ARG* 1.3 80.2 - - + +
412A ILE* 1.3 63.2 + - - +
413A LYS* 3.5 14.7 - - - +
425A THR* 3.4 22.2 - - + +
426A LEU 3.6 6.3 - - - -
427A ASN* 5.3 7.4 - - + -
433A ILE* 3.7 2.3 - - - +
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Residues in contact with ILE 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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404A VAL* 4.3 6.5 - - + -
405A SER 3.1 15.5 - - - +
406A ALA* 3.9 13.2 - - + -
411A THR* 1.3 73.7 - - - +
413A LYS* 1.3 65.0 + - - +
414A VAL* 5.0 1.3 - - + -
425A THR* 3.6 0.5 - - - -
426A LEU* 2.6 51.4 + - + +
433A ILE* 3.9 9.4 - - + -
436A LEU* 3.4 32.1 - - + -
443A VAL* 4.5 4.9 - - + -
445A SER* 3.7 12.1 - - - +
455A TRP* 3.2 46.9 - - + +
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Residues in contact with LYS 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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388A GLY 3.3 28.3 + - - -
389A HIS* 3.4 25.7 - - + +
404A VAL* 3.5 4.0 - - - +
405A SER* 3.0 41.3 + - - +
409A ASP* 4.1 3.1 - - - -
411A THR* 3.5 17.4 + - - +
412A ILE* 1.3 72.9 - - - +
414A VAL* 1.3 61.6 + - - +
415A TRP* 3.6 24.5 - - + +
422A PHE* 3.3 28.0 - - + -
424A ARG 3.9 8.3 - - - +
425A THR* 3.5 24.0 + - + +
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Residues in contact with VAL 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A TYR* 3.4 31.6 - - + -
403A ILE 3.7 2.5 - - - -
404A VAL* 4.5 6.7 - - + +
412A ILE* 4.5 2.2 - - + +
413A LYS* 1.3 77.4 - - - +
415A TRP* 1.3 56.3 + - - +
422A PHE* 3.7 1.9 - - - -
423A VAL* 2.7 56.5 + - + +
424A ARG* 3.6 14.0 + - + +
426A LEU* 4.2 28.3 - - + -
457A ILE* 3.8 32.8 - - + +
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Residues in contact with TRP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 3.7 16.9 - - + +
386A LEU* 3.5 45.3 - - + -
387A VAL 4.2 21.1 - - - -
388A GLY* 4.3 4.9 - - - -
389A HIS* 4.7 3.1 - + - -
402A TYR* 3.2 10.1 - - - -
403A ILE* 2.7 71.2 + - + +
405A SER* 3.0 20.8 + - - -
413A LYS* 3.6 32.3 + - + +
414A VAL* 1.3 75.3 - - - +
416A ASN* 1.3 63.8 + - - +
420A CYS* 4.6 4.9 - - - -
421A GLU 3.2 8.5 - - - +
422A PHE* 3.4 47.8 - + - -
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Residues in contact with ASN 416 (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 LYS* 4.2 10.7 + - - +
402A TYR* 4.3 5.2 - - - -
403A ILE* 5.0 0.9 - - - +
415A TRP* 1.3 69.2 - - - +
417A THR* 1.3 60.3 + - - +
418A SER* 2.9 37.2 + - - +
419A THR* 3.1 24.8 + - - +
420A CYS* 2.8 32.7 + - - -
421A GLU* 2.9 31.5 + - + +
423A VAL* 4.3 11.6 - - + +
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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