Contacts of the helix formed by residues 405 - 412 (chain B) in PDB entry 3N2Z
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 SER 405 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLU* 3.5 24.0 - - - -
404B PRO* 1.3 77.2 - - - +
406B TRP* 1.3 66.5 + - - +
407B ILE 3.6 1.6 - - - -
408B THR* 3.4 10.4 + - - +
409B THR* 3.0 26.5 + - - -
492B SO4 3.1 27.3 + - - -
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Residues in contact with TRP 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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148B GLU* 2.9 28.8 + - + -
366B GLU* 3.1 33.0 + - + -
403B ARG* 3.4 36.1 + - + +
405B SER* 1.3 78.7 + - - +
407B ILE* 1.3 55.3 + - + +
409B THR* 2.8 46.1 + - + -
410B MET* 2.9 39.1 + - + +
492B SO4 3.8 2.7 + - - +
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Residues in contact with ILE 407 (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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147B SER* 4.1 7.4 - - - +
187B TRP* 3.8 26.0 - - + +
206B ILE 5.3 2.2 - - - +
209B PHE* 3.6 44.9 - - + -
366B GLU* 3.3 48.8 + - + +
367B VAL* 4.5 3.8 - - + +
403B ARG 5.0 0.2 + - - -
404B PRO 5.5 0.8 + - - +
405B SER 3.6 0.8 - - - -
406B TRP* 1.3 74.1 - - + +
408B THR* 1.3 56.4 + - - +
410B MET* 3.9 1.8 - - - +
411B TYR* 2.9 55.8 + - + +
412B GLY 4.0 0.2 + - - -
413B GLY 4.9 0.2 + - - -
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Residues in contact with THR 408 (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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209B PHE* 4.5 11.4 - - - +
210B GLU* 3.1 29.1 + - - +
212B LEU* 4.0 24.6 - - + +
404B PRO 5.7 0.2 - - - -
405B SER* 3.4 12.1 + - - +
407B ILE* 1.3 77.5 - - - +
409B THR* 1.3 63.4 + - - +
412B GLY* 3.2 25.6 + - - -
413B GLY* 4.2 11.2 - - - +
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Residues in contact with THR 409 (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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405B SER* 3.0 21.8 + - - -
406B TRP* 2.8 31.0 + - + -
408B THR* 1.3 76.5 - - - +
410B MET* 1.3 64.9 + - - +
412B GLY* 4.5 1.9 + - - -
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Residues in contact with MET 410 (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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60B PHE* 6.3 1.3 - - + -
148B GLU* 3.5 39.7 - - + +
151B LEU* 6.2 0.7 - - + -
191B LYS* 2.8 54.4 + - + +
406B TRP* 2.9 40.7 + - + +
407B ILE* 4.5 0.4 - - - -
409B THR* 1.3 81.2 - - - +
411B TYR* 1.3 83.1 - - + +
412B GLY 3.6 0.5 + - - -
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Residues in contact with TYR 411 (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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147B SER* 3.0 28.9 + - - -
148B GLU* 3.6 21.3 + - - +
151B LEU* 3.7 15.9 - - + +
187B TRP* 3.4 68.9 - + + +
190B MET* 3.8 11.4 - - - +
191B LYS* 3.9 24.5 - - + +
407B ILE* 2.9 38.2 + - + +
410B MET* 1.3 91.7 - - + +
412B GLY* 1.3 55.4 + - - +
413B GLY 3.5 5.6 + - - +
416B ILE* 3.7 17.0 - - - +
419B HIS* 5.3 1.0 + - - -
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Residues in contact with GLY 412 (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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407B ILE 4.0 0.2 + - - -
408B THR* 3.2 19.8 + - - -
409B THR 5.0 1.8 - - - -
410B MET 3.5 3.6 + - - -
411B TYR* 1.3 74.6 - - - +
413B GLY* 1.3 61.8 - - - +
414B LYS 3.4 0.3 + - - -
415B ASN* 3.3 37.5 + - - +
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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