Contacts of the strand formed by residues 402 - 406 (chain B) in PDB entry 5NNZ
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 VAL 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 3.5 24.9 - - + -
361B LEU* 3.7 24.5 - - + -
369B ALA* 6.0 0.2 - - + -
371B ILE* 5.6 1.8 - - + -
383B LEU* 4.6 10.3 - - + -
394B ALA 3.4 4.3 - - - +
395B PHE* 3.5 28.3 - - + -
401B ILE* 1.3 76.5 - - - +
403B ILE* 1.3 64.2 + - - +
404B THR* 3.8 21.3 - - + -
413B ILE* 3.6 2.4 - - - -
414B TRP* 2.8 50.1 + - + +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B VAL* 4.3 22.7 - - + -
100B LEU* 3.5 45.3 - - + -
107B PHE* 4.2 16.4 - - + -
392B SER* 4.0 2.3 + - - +
393B CYS* 3.0 23.0 + - - -
394B ALA* 3.0 12.2 + - + +
401B ILE* 6.1 1.1 - - + -
402B VAL* 1.3 73.2 - - - +
404B THR* 1.3 66.6 + - - +
411B CYS* 3.9 20.4 - - + -
412B ARG 3.5 14.4 - - - +
413B ILE* 3.6 22.9 - - + -
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Residues in contact with THR 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ALA* 4.4 15.3 - - + -
383B LEU* 5.1 0.4 - - + -
386B HIS* 2.8 30.9 + - - -
390B ILE* 4.4 7.4 - - - -
392B SER 3.2 8.1 - - - -
393B CYS* 4.2 10.8 - - + -
402B VAL* 3.8 15.7 - - + -
403B ILE* 1.3 81.4 - - - +
405B GLY* 1.3 59.8 + - - +
411B CYS* 3.1 4.8 - - - -
412B ARG 2.9 29.2 + - - -
414B TRP* 3.5 24.2 + - - +
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B VAL* 4.2 9.6 - - - +
390B ILE* 3.5 4.6 - - - +
391B PHE* 3.0 39.7 + - - -
392B SER* 3.0 27.6 + - - -
403B ILE* 5.1 0.2 - - - +
404B THR* 1.3 72.2 - - - +
406B SER* 1.3 58.7 + - - -
410B THR 3.8 4.3 - - - -
411B CYS* 4.4 4.7 - - - -
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Residues in contact with SER 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.1 4.7 - - - +
386B HIS* 3.0 29.4 + - - +
388B ASP 2.9 19.1 + - - -
389B GLU 2.4 26.7 + - - -
390B ILE* 3.8 1.2 + - - -
391B PHE* 3.1 17.7 - - - -
405B GLY* 1.3 73.1 - - - -
407B LYS* 1.3 61.0 + - - +
408B ASP* 3.1 21.4 + - - -
409B ASN* 3.4 12.3 + - - -
410B THR 3.2 7.3 + - - -
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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