Contacts of the strand formed by residues 403 - 407 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323D PHE* 5.6 4.0 - - + -
324D VAL* 5.0 2.7 - - + -
327D LEU* 3.9 14.8 - - + -
361D THR* 4.2 15.3 - - + +
365D ALA* 4.1 13.7 - - + -
367D VAL* 3.7 24.0 - - + -
368D PRO 3.2 6.0 + - - +
369D PHE* 3.3 33.6 - - + -
370D ILE* 2.9 25.3 + - - +
402D CYS* 1.3 82.2 - - - +
404D LEU* 1.3 63.9 + - - +
448D VAL* 3.3 25.4 - - + +
450D LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D ILE* 3.4 16.6 - - + +
372D VAL* 5.1 1.1 - - + -
392D LEU* 3.8 35.2 - - + -
393D PHE* 5.0 8.3 - - + -
396D ALA* 3.7 30.1 - - + -
402D CYS* 4.9 3.8 - - - -
403D ILE* 1.3 74.4 - - - +
405D PHE* 1.3 58.8 + - - +
406D ILE* 3.7 30.3 - - + -
447D VAL* 5.4 0.9 - - + -
448D VAL 2.6 14.1 + - - +
449D ILE* 3.5 23.1 - - + -
450D LEU* 2.6 37.4 + - - +
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Residues in contact with PHE 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D LEU* 4.7 4.0 - - + -
354D LYS 4.4 9.9 - - - -
355D THR* 4.3 6.3 - - + -
358D ALA* 3.6 26.2 - - + -
369D PHE* 3.6 20.6 - - + -
370D ILE 2.9 11.2 + - - +
371D THR* 3.5 5.7 - - + +
372D VAL* 2.9 29.6 + - - +
404D LEU* 1.3 74.6 - - - +
406D ILE* 1.3 62.2 + - - +
407D ASP* 3.6 40.2 - - + -
450D LEU* 3.2 20.2 - - + -
451D ALA* 4.0 4.3 - - - -
452D GLY* 3.9 22.7 - - - -
441E PHE* 3.5 31.6 - + - -
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Residues in contact with ILE 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372D VAL* 3.3 14.6 - - + -
373D SER 4.3 4.3 - - - +
374D GLY* 4.2 22.0 - - - +
377D PHE* 4.8 8.7 - - + -
392D LEU* 4.7 6.7 - - + -
393D PHE* 5.5 0.7 - - + -
404D LEU* 3.7 27.1 - - + -
405D PHE* 1.3 72.0 - - - +
407D ASP* 1.3 61.9 + - - +
408D GLN 3.7 0.3 + - - -
409D ILE* 4.0 31.2 + - + -
412D VAL* 6.5 0.4 - - + -
434D LEU* 4.6 20.6 - - + -
438D MET* 5.8 0.4 - - - -
449D ILE* 4.4 12.6 - - + -
450D LEU 3.0 8.0 + - - +
451D ALA* 3.3 26.3 - - + +
452D GLY 3.3 5.2 + - - +
469D PHE* 5.6 1.3 - - + -
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Residues in contact with ASP 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D THR* 3.6 12.5 + - - +
371D THR* 5.7 2.0 - - + -
372D VAL 3.0 13.7 + - - +
373D SER* 3.3 3.0 + - - -
374D GLY 2.7 32.4 + - - -
405D PHE* 3.6 27.1 - - + -
406D ILE* 1.3 71.4 - - - +
408D GLN* 1.3 79.3 + - - +
452D GLY* 4.1 6.7 - - - +
801D ANP 4.9 0.2 + - - -
802D MG 3.2 23.9 - - - -
436E VAL* 3.9 32.0 - - + +
440E GLY* 4.6 2.6 - - - -
441E PHE* 5.1 1.7 + - + -
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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