Contacts of the helix formed by residues 379 - 387 (chain B) in PDB entry 3H60
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 GLY 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B SER* 5.2 2.0 + - - -
358B GLU* 4.0 9.6 + - - -
376B PRO* 5.3 0.7 - - - -
378B SER* 1.3 79.5 + - - +
380B PRO* 1.3 71.9 - - - +
381B MET 3.4 3.4 - - - -
382B CYS* 3.2 4.5 + - - +
383B ASP* 3.0 35.9 + - - -
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Residues in contact with PRO 380 (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 PHE* 3.5 28.5 - - + -
358B GLU* 3.8 17.7 - - - +
361B VAL* 5.1 10.1 - - + -
365B ASP* 6.2 2.9 - - + -
369B ILE* 3.8 24.0 - - + -
379B GLY* 1.3 84.5 - - - +
381B MET* 1.3 57.9 + - - +
383B ASP* 3.3 0.7 + - - +
384B LEU* 2.9 34.5 + - - +
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Residues in contact with MET 381 (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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301B ARG* 3.3 31.4 - - - +
340B LEU* 4.0 19.2 - - + +
369B ILE* 4.0 22.4 - - + +
371B ARG* 3.4 25.6 - - - +
373B ARG* 3.7 31.6 - - - +
375B PRO* 3.9 24.7 - - + -
376B PRO* 4.1 10.1 - - + +
379B GLY 3.4 0.6 - - - -
380B PRO* 1.3 83.0 - - - +
382B CYS* 1.3 63.3 + - - +
384B LEU* 3.6 6.6 + - - +
385B LEU* 3.5 24.9 + - + +
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Residues in contact with CYS 382 (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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375B PRO* 4.7 5.2 - - - -
376B PRO* 3.4 23.2 - - - +
377B ASP 3.6 15.9 - - - -
378B SER* 3.8 12.6 - - - +
379B GLY 3.2 10.8 + - - +
381B MET* 1.3 77.8 - - - +
383B ASP* 1.3 66.6 + - - +
385B LEU 3.2 2.9 + - - -
386B TRP* 3.0 34.1 + - - +
402B VAL* 3.4 33.2 - - - -
403B SER* 4.3 9.6 - - - -
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Residues in contact with ASP 383 (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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354B GLY 3.6 1.2 + - - -
355B LEU 3.3 17.5 - - - +
356B PHE* 3.5 10.6 - - + +
357B SER* 2.8 44.2 + - - -
358B GLU* 3.3 11.4 - - - +
378B SER* 5.9 0.3 - - - -
379B GLY 3.0 17.9 + - - +
380B PRO 3.7 6.5 - - - +
382B CYS* 1.3 77.3 - - - +
384B LEU* 1.3 62.8 - - - +
387B SER* 3.1 28.8 + - - -
403B SER* 2.7 33.5 + - - +
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Residues in contact with LEU 384 (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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340B LEU* 4.0 32.5 - - + +
341B ALA* 4.6 4.9 - - + -
351B MET* 3.9 28.5 - - + +
352B HIS* 3.9 3.6 + - - +
353B GLY* 2.7 31.0 + - - -
354B GLY 3.3 14.4 + - - +
356B PHE* 3.5 25.6 - - + -
366B ILE* 4.1 17.7 - - + -
369B ILE* 3.7 25.1 - - + -
380B PRO 2.9 22.1 + - - +
381B MET* 3.8 5.4 - - - +
382B CYS 3.3 0.2 - - - -
383B ASP* 1.3 75.3 - - - +
385B LEU* 1.3 55.7 + - + +
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Residues in contact with LEU 385 (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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301B ARG* 3.2 48.2 - - + +
302B GLY* 3.7 19.1 - - - +
303B ASN* 3.4 16.8 - - + +
306B THR* 4.6 2.2 - - + -
340B LEU* 4.6 9.9 - - + +
352B HIS* 3.1 24.5 - - + +
353B GLY* 4.0 4.5 - - - +
375B PRO* 3.9 29.6 - - + -
381B MET* 3.5 19.7 - - + +
382B CYS 3.2 3.8 + - - +
384B LEU* 1.3 81.3 - - + +
386B TRP* 1.3 72.9 + - + +
427B HIS* 3.6 2.6 + - - -
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Residues in contact with TRP 386 (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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303B ASN* 3.2 42.0 + - + +
306B THR* 5.8 0.2 - - - +
309B MET* 3.7 37.7 - - + -
375B PRO* 5.0 11.7 - - + +
382B CYS* 3.0 28.2 + - - +
385B LEU* 1.3 89.5 - - + +
387B SER* 1.3 63.2 + - - +
388B ASP* 3.8 6.8 - - - +
398B SER* 5.0 0.9 + - - -
400B ARG* 3.8 35.5 - - + -
402B VAL* 3.5 42.4 - - + +
403B SER* 3.7 16.8 - - - -
427B HIS* 2.9 19.0 + + - -
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Residues in contact with SER 387 (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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353B GLY* 3.2 21.3 - - - +
354B GLY 3.2 2.1 - - - -
355B LEU 2.9 38.3 + - - -
383B ASP 3.1 12.2 + - - -
385B LEU 4.0 0.4 - - - -
386B TRP* 1.3 80.6 - - - +
388B ASP* 1.3 58.8 + - - +
403B SER* 3.1 21.1 - - - -
404B CYS* 3.4 15.5 - - - -
406B PHE* 3.5 5.6 - - - -
425B ARG* 3.2 6.4 + - - -
427B HIS* 3.4 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