Contacts of the helix formed by residues 411 - 418 (chain B) in PDB entry 3B60
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 THR 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B GLU* 3.9 10.6 + - - -
331B GLY 4.5 4.5 - - - +
332B LYS* 4.2 16.4 - - - +
333B ARG 2.9 6.5 + - - -
334B VAL* 3.6 23.8 - - + -
410B TYR* 1.3 70.9 - - - +
412B LEU* 1.3 71.1 + - - +
413B ALA* 3.5 15.5 + - + +
414B SER* 2.8 36.1 - - - +
415B LEU* 3.0 15.1 + - - +
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Residues in contact with LEU 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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223A GLN* 6.2 2.0 - - - +
112B PRO* 4.6 2.5 - - + -
328B LYS* 4.4 18.8 - - + -
329B ASP 4.1 9.9 - - - +
330B GLU* 3.1 27.1 + - - +
331B GLY 4.9 0.4 - - - +
391B ARG* 3.7 21.9 - - - +
394B ASP* 4.9 9.0 - - - +
410B TYR 3.6 4.0 + - - -
411B THR* 1.3 73.5 + - - +
413B ALA* 1.3 71.7 + - - +
415B LEU* 3.0 5.8 + - + +
416B ARG* 2.9 75.0 + - + +
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Residues in contact with ALA 413 (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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223A GLN* 5.8 6.1 - - - +
330B GLU* 4.9 3.2 + - - +
411B THR* 3.1 15.5 + - + +
412B LEU* 1.3 87.6 - - - +
414B SER* 1.3 63.5 + - - +
416B ARG* 3.4 4.9 + - - +
417B ASN* 3.3 14.6 + - - +
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Residues in contact with SER 414 (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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333B ARG 4.6 0.2 + - - -
334B VAL* 3.4 16.5 - - - +
335B ILE* 3.5 29.5 + - - +
410B TYR* 5.0 0.9 - - - -
411B THR* 2.8 27.8 + - - +
413B ALA* 1.3 77.4 - - - +
415B LEU* 1.3 58.1 + - - +
417B ASN* 2.6 31.0 + - - +
418B GLN* 2.6 22.2 + - - +
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Residues in contact with LEU 415 (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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335B ILE* 6.2 0.2 - - - -
389B ILE 4.9 4.3 - - - +
390B THR* 5.3 3.4 - - - -
391B ARG* 3.6 38.1 - - + +
402B MET* 3.6 36.3 - - + -
407B LEU* 3.7 34.3 - - + +
410B TYR* 4.4 12.5 - - + +
411B THR 3.0 13.0 + - - +
412B LEU* 3.0 11.2 + - - +
414B SER* 1.3 78.4 + - - +
416B ARG* 1.3 57.9 + - + +
418B GLN* 2.8 34.7 + - - +
419B VAL* 4.1 3.0 + - - +
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Residues in contact with ARG 416 (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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218A LEU* 2.8 64.6 - - - +
219A ILE* 3.9 19.6 - - + +
112B PRO* 4.3 16.4 - - - +
113B VAL 5.6 0.2 - - - +
390B THR* 3.3 37.0 + - - +
391B ARG* 4.1 5.9 + - - +
392B PHE* 3.9 19.8 - - - +
394B ASP* 4.7 1.6 + - - -
412B LEU* 2.9 55.5 + - + +
413B ALA 3.9 4.7 - - - +
415B LEU* 1.3 82.1 - - + +
417B ASN* 1.3 58.8 + - - +
418B GLN 3.1 1.8 - - - -
419B VAL* 3.6 25.7 - - - +
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Residues in contact with ASN 417 (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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219A ILE 5.4 2.5 - - - -
335B ILE 5.8 0.2 + - - -
336B ASP* 5.7 3.2 + - - +
413B ALA 3.3 5.1 + - - +
414B SER* 2.6 29.4 + - - +
416B ARG* 1.3 71.8 - - - +
418B GLN* 1.3 71.2 + - - +
419B VAL 3.2 8.8 + - - +
441B ARG* 3.9 32.5 + - - +
499B SER* 4.2 6.4 + - - -
500B PRO* 5.3 0.7 - - - +
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Residues in contact with GLN 418 (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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335B ILE* 3.3 27.2 - - + +
336B ASP* 3.7 19.4 + - - +
337B ARG 4.5 0.2 - - - -
338B ALA* 3.4 28.9 - - + +
402B MET* 4.0 27.4 - - + -
414B SER* 2.6 24.5 + - - +
415B LEU 2.8 14.5 + - - +
417B ASN* 1.3 92.8 + - - +
419B VAL* 1.3 62.5 + - - +
499B SER* 2.8 14.1 + - - -
500B PRO* 4.2 5.9 - - - +
501B ILE* 3.4 19.4 + - - +
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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