Contacts of the helix formed by residues 357 - 367 (chain B) in PDB entry 2DB3
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 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B TYR 2.8 23.5 + - - +
203B ILE* 4.0 11.7 - - - +
356B THR* 1.3 70.1 - - - +
358B PHE* 1.3 62.3 + - - +
359B ARG* 3.4 9.5 + - - +
360B HIS* 2.9 32.2 + - - +
361B GLN* 3.1 23.6 + - - +
378B ARG* 3.5 0.4 - - - -
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Residues in contact with PHE 358 (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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356B THR 3.1 5.5 + - - -
357B SER* 1.3 71.5 - - - +
359B ARG* 1.3 55.7 + - - +
361B GLN* 3.1 4.1 + - - +
362B ASN* 2.8 44.0 + - + +
378B ARG* 3.5 27.1 - - - +
381B ASP* 3.4 33.7 - - + -
382B PHE* 3.5 32.5 - + - -
385B ARG* 3.2 42.0 - - - +
387B PHE* 3.7 26.9 - + - -
7F U 6.0 3.1 - - - -
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Residues in contact with ARG 359 (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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521A GLY 6.0 0.2 + - - -
522A ASP* 4.7 21.2 + - - +
523A ARG 5.7 0.6 + - - -
524A LEU* 4.1 23.2 - - - +
357B SER* 3.2 6.9 - - - +
358B PHE* 1.3 85.7 - - - +
360B HIS* 1.3 62.0 + - - +
362B ASN* 3.3 5.5 + - - +
363B GLU* 3.0 46.4 + - + +
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Residues in contact with HIS 360 (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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203B ILE* 3.8 40.5 - - + +
204B PRO* 4.5 22.3 + - + +
206B GLU* 4.4 19.7 + - + +
357B SER* 2.9 25.5 + - - +
359B ARG* 1.3 76.7 - - - +
361B GLN* 1.3 71.5 + - + +
363B GLU* 3.4 20.9 + - - +
364B CYS* 3.1 49.2 + - - -
367B ARG* 5.9 0.9 - - - -
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Residues in contact with GLN 361 (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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204B PRO* 5.5 2.2 - - + +
351B ILE* 4.0 9.7 + - - +
352B VAL* 3.4 15.5 - - + +
353B TYR* 3.0 58.6 + - - +
356B THR* 3.2 22.8 + - - +
357B SER 3.1 15.1 + - - +
358B PHE 3.1 6.7 + - - +
360B HIS* 1.3 85.3 - - + +
362B ASN* 1.3 63.1 + - - +
364B CYS* 3.3 9.1 + - - +
365B ILE* 3.0 24.9 + - - +
378B ARG* 3.3 13.4 + - - +
382B PHE* 3.9 9.6 - - + -
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Residues in contact with ASN 362 (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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500A ARG* 4.2 13.6 + - - +
522A ASP* 5.7 2.0 + - - -
358B PHE* 2.8 22.6 + - + +
359B ARG* 3.7 5.6 - - - +
361B GLN* 1.3 74.7 - - - +
363B GLU* 1.3 60.3 + - - +
365B ILE* 3.1 4.7 + - - +
366B THR* 2.7 45.4 + - - -
382B PHE* 3.2 28.3 - - + -
387B PHE* 3.7 35.3 - - - +
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Residues in contact with GLU 363 (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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503A ASP* 5.3 1.8 - - - +
522A ASP* 4.5 11.2 - - + +
524A LEU* 5.6 4.2 - - - +
359B ARG* 3.0 49.0 + - + +
360B HIS* 3.6 26.0 + - - +
361B GLN 3.3 0.2 - - - -
362B ASN* 1.3 77.6 - - + +
364B CYS* 1.3 63.6 + - - +
365B ILE 3.3 0.2 + - - -
366B THR* 3.4 13.9 + - - -
367B ARG* 3.5 31.2 + - - +
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Residues in contact with CYS 364 (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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206B GLU* 4.6 7.2 - - - -
350B GLY* 6.1 4.0 - - - -
351B ILE 5.9 3.4 - - - +
360B HIS* 3.1 42.2 - - - -
361B GLN* 3.3 9.4 + - - +
362B ASN 3.2 0.4 - - - -
363B GLU* 1.3 81.5 - - - +
365B ILE* 1.3 61.9 + - + +
367B ARG* 3.7 42.6 + - - +
369B CYS* 3.8 12.9 - - - -
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Residues in contact with ILE 365 (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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500A ARG* 6.0 0.9 - - - +
317B GLY* 4.9 11.1 + - - -
350B GLY* 4.8 4.9 - - - -
351B ILE 5.0 3.1 - - - +
352B VAL* 4.2 18.2 - - + -
361B GLN 3.0 16.3 + - - +
362B ASN* 3.1 15.9 + - - +
364B CYS* 1.3 73.4 - - + +
366B THR* 1.3 58.1 + - - +
367B ARG 3.1 2.0 - - - -
368B GLY* 2.5 33.8 + - - -
369B CYS* 4.0 15.9 + - + +
372B VAL* 3.9 37.2 - - + -
382B PHE* 4.2 6.1 - - + -
387B PHE 4.5 8.1 - - - +
388B ILE* 4.4 23.1 - - + -
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Residues in contact with THR 366 (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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500A ARG* 3.5 49.0 + - + +
503A ASP* 3.8 21.3 - - + -
504A PHE* 3.4 21.5 - - - +
316B LEU* 3.8 10.0 - - + +
362B ASN* 2.7 37.9 + - - -
363B GLU* 3.4 10.0 + - - +
365B ILE* 1.3 76.2 - - - +
367B ARG* 1.3 59.9 + - - +
368B GLY 2.9 1.7 + - - -
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Residues in contact with ARG 367 (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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503A ASP* 4.6 14.8 + - - +
504A PHE* 4.1 10.3 - - - +
507A SER* 3.9 28.5 + - - +
206B GLU* 4.6 13.7 + - - -
348B LYS* 2.9 25.4 + - + +
360B HIS* 5.9 1.0 - - - -
363B GLU* 3.5 20.1 + - - +
364B CYS* 3.7 46.0 + - - +
365B ILE 2.9 1.0 + - - -
366B THR* 1.3 76.0 - - - +
368B GLY* 1.3 59.1 + - - +
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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