Contacts of the strand formed by residues 403 - 407 (chain E) in PDB entry 6NYY
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 ILE 403 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E PHE* 5.7 1.1 - - + -
324E VAL* 5.2 1.1 - - + -
327E LEU* 4.7 10.8 - - + -
361E THR* 3.3 42.2 - - + +
362E ALA* 4.9 0.2 - - + -
365E ALA* 5.1 0.4 - - + -
367E VAL* 3.7 19.3 - - + -
368E PRO 3.2 5.3 + - - +
369E PHE* 3.4 31.6 - - + -
370E ILE 3.7 9.0 + - - -
401E PRO 4.6 2.2 - - - +
402E CYS* 1.3 82.3 - - - +
404E LEU* 1.3 62.4 + - - +
448E VAL* 3.6 31.2 - - + +
450E LEU* 3.7 28.0 - - + -
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Residues in contact with LEU 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E ILE* 3.6 42.2 - - + +
372E VAL* 4.8 1.1 - - + -
392E LEU* 3.9 34.8 - - + -
393E PHE* 4.1 15.3 - - + -
396E ALA* 4.3 15.9 - - + -
402E CYS* 4.2 4.8 + - - -
403E ILE* 1.3 71.2 - - - +
405E PHE* 1.3 59.9 + - - +
406E ILE* 4.3 13.5 - - + -
447E VAL* 5.8 0.2 - - + -
448E VAL 2.7 13.2 + - - +
449E ILE* 3.4 26.8 - - + -
450E LEU* 2.5 37.3 + - - +
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Residues in contact with PHE 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E LEU* 4.5 5.8 - - + -
354E LYS* 4.4 6.3 - - + -
355E THR* 3.4 40.6 - - + -
358E ALA* 3.7 20.2 - - + -
369E PHE* 3.6 32.1 - + + -
370E ILE 3.1 12.8 + - - +
371E THR* 5.4 6.1 - - + -
372E VAL* 3.3 25.3 + - - +
403E ILE 3.8 0.6 + - - -
404E LEU* 1.3 74.4 - - - +
406E ILE* 1.3 60.7 + - - +
407E ASP* 3.8 28.5 - - + -
450E LEU* 3.3 17.7 - - + -
451E ALA 4.0 1.8 - - - -
452E GLY* 3.5 30.7 - - - -
801E ADP 5.0 0.2 - - - -
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Residues in contact with ILE 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E VAL* 3.5 24.9 - - + +
374E GLY* 4.8 4.9 - - - +
377E PHE* 4.6 15.0 - - + -
392E LEU* 4.2 16.4 - - + -
393E PHE* 4.9 0.7 - - + -
404E LEU* 4.3 10.5 - - + -
405E PHE* 1.3 72.2 - - - +
407E ASP* 1.3 66.8 + - - +
408E GLN 3.7 0.5 + - - -
409E ILE* 4.0 34.4 + - + -
412E VAL* 5.8 0.2 - - + -
434E LEU* 4.3 22.4 - - + -
438E MET* 5.9 0.2 - - - -
449E ILE* 4.3 20.4 - - + -
450E LEU 2.9 12.6 + - - +
451E ALA* 3.3 20.9 - - + +
452E GLY 3.4 4.3 + - - +
469E PHE* 5.6 0.2 - - + -
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Residues in contact with ASP 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E THR* 4.0 8.5 + - - -
372E VAL 2.6 18.1 + - - +
373E SER* 3.3 10.7 + - - +
374E GLY* 2.4 35.3 + - - -
405E PHE* 3.7 28.3 + - + -
406E ILE* 1.3 71.3 - - - +
408E GLN* 1.3 83.9 + - - +
452E GLY* 4.5 2.8 - - - +
801E ADP 3.8 17.2 + - - -
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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