Contacts of the strand formed by residues 419 - 423 (chain A) in PDB entry 1DQU
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 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ARG* 4.7 0.2 - - - +
29A TYR* 4.3 9.9 + - - -
60A TRP* 3.5 17.6 - - + -
63A LEU* 3.7 24.5 - - + +
64A GLU* 2.8 50.7 + - - +
67A PHE* 4.2 29.3 - - + +
390A ASP 3.8 11.4 + - - +
391A LEU* 3.1 43.5 - - + -
392A ILE 3.2 4.2 + - - -
417A GLU 4.7 2.4 + - - +
418A GLN* 1.3 82.2 + - - +
420A LEU* 1.3 62.2 + - - +
450A GLY 4.3 0.4 - - - -
452A ALA* 4.8 7.9 - - + -
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Residues in contact with LEU 420 (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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391A LEU* 4.6 4.2 - - - +
392A ILE* 3.4 41.7 - - + +
407A PHE* 4.0 17.5 - - + -
408A ALA* 4.3 14.8 - - - +
411A VAL* 4.5 12.3 - - + -
412A HIS* 3.7 31.6 - - + +
418A GLN* 4.3 3.4 - - + +
419A LYS* 1.3 77.4 - - - +
421A ALA* 1.3 61.3 + - - +
449A LEU 4.5 1.1 - - - +
450A GLY 3.1 17.1 + - - +
451A TYR* 3.2 26.1 - - + -
452A ALA* 3.0 26.5 + - - +
453A TRP 3.6 3.5 + - - -
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Residues in contact with ALA 421 (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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241A ILE* 5.0 4.9 - - + -
391A LEU* 4.2 15.4 - - + +
392A ILE 3.0 16.7 + - - +
393A TRP* 3.7 24.9 - - + +
394A MET 4.5 1.2 + - - -
420A LEU* 1.3 75.8 - - - +
422A TYR* 1.3 61.1 + - - +
451A TYR* 4.0 8.8 - - - -
453A TRP* 3.1 33.2 - - + +
455A PHE* 4.6 4.5 - - + -
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Residues in contact with TYR 422 (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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393A TRP* 4.5 3.6 - - - -
394A MET 5.9 1.3 - - - -
396A SER* 3.6 18.7 + - - -
398A LEU 3.6 7.1 + - - -
399A PRO* 3.1 21.5 - - + +
400A ASP 3.6 1.8 + - - -
403A GLN* 6.3 0.4 - - - -
404A ALA* 4.2 13.0 - - + -
421A ALA* 1.3 74.9 - - - +
423A ASN* 1.3 82.6 + - - +
424A LEU* 3.6 24.6 + - + -
425A SER 5.0 1.6 - - - -
442A TYR* 2.7 23.2 + + - -
446A LEU* 3.4 23.1 - - + -
451A TYR* 3.8 26.0 - + + -
453A TRP 3.1 6.7 + - - -
454A GLN* 3.3 33.0 - - + +
455A PHE* 3.4 11.2 + - - -
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Residues in contact with ASN 423 (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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393A TRP* 2.9 31.9 + - + +
395A GLU* 3.2 22.6 + - - +
396A SER* 3.1 31.2 + - - +
422A TYR* 1.3 88.8 - - - +
424A LEU* 1.3 63.4 + - - +
425A SER* 3.5 2.5 + - - +
426A PRO* 5.5 3.8 - - - +
455A PHE* 3.4 29.4 - - + +
457A THR* 4.7 12.5 + - + +
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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