Contacts of the strand formed by residues 400 - 406 (chain A) in PDB entry 4XH9
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 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A GLU* 4.5 27.0 + - + +
393A LEU* 3.7 18.1 - - - +
394A ARG* 3.6 50.1 - - - +
398A GLY 3.5 1.0 + - - -
399A HIS* 1.3 72.4 - - - +
401A LEU* 1.3 63.9 + - - +
414A ARG* 4.9 2.3 - - - +
415A PRO* 3.7 18.4 - - - +
482A GLN 5.2 1.0 + - - -
484A ASN* 3.9 19.2 + - - -
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Residues in contact with LEU 401 (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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392A GLU* 3.1 7.4 - - - +
393A LEU 2.8 34.0 + - - +
395A SER* 3.8 27.8 - - - -
399A HIS* 3.4 1.5 + - + +
400A LYS* 1.3 75.9 - - - +
402A TYR* 1.3 60.7 + - - +
403A ILE* 3.6 13.8 - - + +
412A LEU* 3.9 26.2 - - + -
413A THR 3.4 7.6 - - - +
414A ARG* 3.4 46.9 - - + +
415A PRO* 4.7 0.4 - - - -
427A TYR* 4.3 20.0 - - + -
479A HIS* 5.1 2.2 - - + +
481A LEU* 4.1 8.3 - - + -
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Residues in contact with TYR 402 (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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365A TYR* 4.2 5.6 + + - -
390A HIS* 2.6 28.0 + - + -
391A GLY* 3.5 23.9 - - - -
392A GLU* 3.3 37.0 - - + -
400A LYS 4.1 0.8 + - - -
401A LEU* 1.3 72.3 - - - +
403A ILE* 1.3 64.1 + - - +
404A PHE* 3.4 39.9 - + - -
413A THR* 2.6 53.2 + - - +
415A PRO* 3.8 17.0 - - + +
424A TYR* 3.8 20.0 - + + -
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Residues in contact with ILE 403 (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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390A HIS* 3.2 7.6 - - - +
391A GLY 2.9 30.4 + - - +
393A LEU* 4.0 23.8 - - + -
401A LEU* 3.6 35.0 - - + +
402A TYR* 1.3 74.4 - - - +
404A PHE* 1.3 68.2 + - - +
410A LEU* 3.9 24.9 - - + -
411A VAL 3.5 2.0 - - - -
412A LEU* 4.0 24.7 - - + -
481A LEU* 4.4 14.1 - - + -
492A TRP* 3.5 30.9 - - + -
496A ILE* 6.1 0.2 - - + -
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Residues in contact with PHE 404 (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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365A TYR* 3.4 45.3 - + + -
369A LEU* 4.3 10.8 - - + -
387A LEU* 4.0 13.7 - - + -
389A CYS 3.8 1.8 - - - -
390A HIS* 3.6 16.2 - - + -
402A TYR* 3.4 34.8 - + - -
403A ILE* 1.3 75.2 - - - +
405A LEU* 1.3 60.8 + - - +
406A PHE* 3.5 26.3 + + + -
409A ILE 3.7 0.7 - - - +
410A LEU* 3.5 2.4 - - - -
411A VAL* 2.8 40.2 + - + +
413A THR* 3.9 19.5 - - + -
424A TYR* 3.8 28.0 - + + -
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Residues in contact with LEU 405 (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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387A LEU* 3.5 3.4 - - - +
388A LEU* 2.8 40.5 + - + -
389A CYS* 2.7 24.5 + - + +
403A ILE* 4.1 1.2 - - - +
404A PHE* 1.3 70.8 - - - +
406A PHE* 1.3 72.4 + - - +
409A ILE 4.1 0.2 - - - -
410A LEU* 4.0 31.0 - - + +
433A VAL* 4.3 12.8 - - + -
436A LEU* 4.9 2.5 - - + -
492A TRP* 4.4 8.3 - - + -
495A CYS* 3.7 41.5 - - + +
496A ILE* 3.8 14.6 - - + +
499A ALA* 4.2 5.4 - - + -
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Residues in contact with PHE 406 (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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362A CYS* 3.5 28.7 - - - -
365A TYR* 5.4 0.7 - - + -
366A ILE* 3.9 25.6 - - + -
369A LEU* 4.8 6.7 - - + -
381A ILE* 4.3 9.2 - - + -
384A SER* 3.4 30.1 - - - +
386A VAL 3.5 6.7 - - - +
387A LEU* 3.8 17.3 - - + -
388A LEU* 4.3 1.3 - - - -
404A PHE* 3.6 32.8 - + + -
405A LEU* 1.3 89.3 - - - +
407A GLN* 1.3 67.2 + - - +
408A ASP 3.2 1.8 + - - +
409A ILE* 2.9 41.5 + - + +
411A VAL* 3.8 14.8 - - + -
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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