Contacts of the strand formed by residues 414 - 421 (chain A) in PDB entry 5U9D
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 GLY 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A THR* 3.4 3.0 - - - +
411A GLY 2.9 34.7 + - - +
412A GLN 3.4 0.2 - - - -
413A PHE* 1.3 80.2 - - - +
415A VAL* 1.3 67.7 + - - +
431A MET 3.2 8.7 - - - -
433A LYS* 3.7 14.3 - - - +
701A 83P 3.4 7.0 + - - +
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Residues in contact with VAL 415 (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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407A GLU* 3.7 28.3 - - + +
409A GLY 3.4 10.1 - - - +
410A THR* 4.0 16.6 - - + +
414A GLY* 1.3 81.3 - - - +
416A VAL* 1.3 65.0 + - - +
417A LYS* 3.8 20.4 - - + -
429A ILE 3.6 1.4 - - - +
430A LYS 3.6 0.3 - - - -
431A MET* 2.7 51.4 + - + +
701A 83P 4.0 0.6 - - - +
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Residues in contact with VAL 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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407A GLU* 3.8 2.8 - - - +
408A LEU* 2.8 41.2 + - + -
409A GLY 2.8 15.1 + - - +
415A VAL* 1.3 74.2 - - - +
417A LYS* 1.3 62.7 + - - +
428A ALA* 4.0 8.7 - - + -
429A ILE 3.3 8.1 - - - +
430A LYS* 3.9 18.8 - - + -
701A 83P 3.5 76.9 - - + +
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Residues in contact with LYS 417 (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 PHE* 3.8 25.8 - - + -
406A LYS 3.3 8.3 - - - +
407A GLU* 2.9 27.2 + - - -
408A LEU* 3.6 5.0 - - - +
415A VAL* 3.8 11.6 - - + +
416A VAL* 1.3 78.1 - - - +
418A TYR* 1.3 62.7 + - - +
428A ALA* 3.3 5.0 - - - -
429A ILE* 2.8 36.9 + - + +
431A MET* 4.1 22.0 - - - -
704A EDO 2.7 47.4 + - - +
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Residues in contact with TYR 418 (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 PHE* 3.9 1.9 - - - -
405A LEU* 2.9 55.7 + - + +
406A LYS* 2.7 30.1 + - + +
408A LEU* 3.5 26.2 - - + +
417A LYS* 1.3 75.4 - - - +
419A GLY* 1.3 70.0 + - - +
420A LYS* 3.6 12.3 + - - -
426A ASP* 2.7 38.5 + - + -
427A VAL 3.7 5.6 - - - -
429A ILE* 4.5 0.7 - - - -
476A TYR* 3.6 35.4 - + - -
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Residues in contact with GLY 419 (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 THR 2.9 14.6 - - - -
405A LEU* 4.1 6.5 - - - -
417A LYS 4.0 0.6 + - - -
418A TYR* 1.3 84.5 - - - +
420A LYS* 1.3 64.5 + - - +
426A ASP* 3.5 5.9 - - - -
427A VAL* 2.9 34.8 + - - +
429A ILE* 4.0 9.5 - - - +
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Residues in contact with LYS 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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401A ASP 3.6 0.5 - - - +
402A LEU* 3.3 7.4 - - - +
403A THR* 2.8 43.2 + - + +
405A LEU* 3.7 21.1 - - + -
418A TYR* 3.6 10.4 + - - -
419A GLY* 1.3 73.8 - - - +
421A TRP* 1.3 59.3 + - - +
423A GLY* 4.1 11.9 - - - +
424A GLN 3.5 30.9 + - - +
425A TYR 3.2 5.6 - - - +
426A ASP* 2.7 28.4 + - - +
427A VAL* 4.0 3.8 - - - -
706A PEG 3.5 20.8 + - - -
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Residues in contact with TRP 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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397A ILE* 3.9 27.6 - - + +
398A ASP 5.4 0.2 - - - +
401A ASP* 3.4 27.7 + - + +
402A LEU* 4.1 7.4 - - + -
420A LYS* 1.3 71.2 - - - +
422A ARG* 1.3 114.8 + - + +
423A GLY 3.2 0.7 - - - -
424A GLN 3.3 0.2 + - - -
425A TYR* 2.8 54.7 + + + +
427A VAL* 3.9 23.3 - - + +
473A ILE* 5.4 0.9 - - + -
705A PEG 3.5 44.7 - - - +
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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