Contacts of the helix formed by residues 379 - 387 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A SER* 5.1 3.2 + - - -
358A GLU* 4.1 9.1 + - - -
376A PRO* 5.3 0.4 - - - -
378A SER* 1.3 79.1 + - - +
380A PRO* 1.3 67.9 - - - +
381A MET 3.3 2.5 - - - -
382A CYS* 3.0 4.2 + - - +
383A ASP* 2.8 44.2 + - - -
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Residues in contact with PRO 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A PHE* 3.5 30.4 - - + -
358A GLU* 4.0 18.8 - - - +
361A VAL* 5.1 9.6 - - + -
365A ASP* 6.3 2.9 - - + -
369A ILE* 4.1 18.8 - - + -
379A GLY* 1.3 83.3 - - - +
381A MET* 1.3 67.0 + - - +
383A ASP* 3.2 0.8 + - - +
384A LEU* 2.9 28.6 + - - +
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Residues in contact with MET 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG* 3.3 30.5 - - - +
340A LEU* 3.9 18.5 - - + +
369A ILE* 4.0 24.0 - - + +
371A ARG* 3.5 24.5 - - - +
373A ARG* 3.8 30.5 - - + +
375A PRO* 3.8 21.5 - - + -
376A PRO* 4.0 15.2 - - + +
379A GLY 3.3 0.6 - - - -
380A PRO* 1.3 82.7 - - - +
382A CYS* 1.3 62.7 + - - +
384A LEU* 3.6 3.1 + - - +
385A LEU* 3.5 28.4 + - + +
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Residues in contact with CYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A PRO* 4.7 4.9 - - - -
376A PRO* 3.3 24.7 - - - +
377A ASP 3.6 16.2 - - - -
378A SER* 3.8 12.8 - - - +
379A GLY 3.0 9.9 + - - +
381A MET* 1.3 78.2 - - - +
383A ASP* 1.3 63.3 + - - +
385A LEU 3.3 2.1 + - - -
386A TRP* 3.0 35.2 + - - +
402A VAL* 3.3 34.3 - - - -
403A SER* 4.2 9.4 - - - -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A GLY 3.6 1.2 + - - +
355A LEU 3.4 16.4 - - - +
356A PHE* 3.6 10.3 - - + -
357A SER* 2.9 44.4 + - - -
358A GLU* 3.3 11.6 - - - +
378A SER* 5.7 0.3 - - - -
379A GLY 2.8 22.3 + - - +
380A PRO 3.2 6.3 + - - +
382A CYS* 1.3 75.1 - - - +
384A LEU* 1.3 63.0 + - - +
387A SER* 3.0 28.4 + - - -
403A SER* 2.8 34.1 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A LEU* 3.9 30.7 - - + +
341A ALA* 4.6 2.9 - - + -
351A MET* 3.7 33.1 - - + +
352A HIS 3.9 2.9 + - - -
353A GLY* 2.7 32.2 + - - -
354A GLY 3.2 12.3 + - - +
356A PHE* 3.7 24.5 - - + -
366A ILE* 3.9 30.5 - - + -
369A ILE* 3.9 16.4 - - + -
380A PRO 2.9 20.0 + - - +
381A MET 3.8 4.5 - - - +
383A ASP* 1.3 75.1 - - - +
385A LEU* 1.3 55.9 + - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ARG* 3.1 47.8 - - + +
302A GLY* 3.7 12.6 - - - +
303A ASN* 3.4 16.9 - - + +
306A THR* 4.9 2.7 - - + -
340A LEU* 4.4 12.8 - - + +
352A HIS* 3.2 23.7 - - + +
353A GLY* 3.8 4.4 - - - +
375A PRO* 3.9 29.4 - - + -
381A MET* 3.5 27.8 - - + +
382A CYS 3.3 2.5 + - - +
383A ASP 3.2 0.4 - - - -
384A LEU* 1.3 82.6 - - + +
386A TRP* 1.3 70.6 + - + +
427A HIS* 3.6 3.3 - - - -
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Residues in contact with TRP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ASN* 3.3 40.4 + - + +
306A THR* 5.5 1.5 + - - -
309A MET* 3.8 35.9 - - + -
375A PRO* 4.9 11.9 - - + +
382A CYS* 3.0 27.1 + - - +
385A LEU* 1.3 90.8 - - + +
387A SER* 1.3 60.6 + - - +
388A ASP* 4.0 0.9 - - - +
398A SER* 5.1 1.0 + - - -
400A ARG* 3.9 44.1 + - + -
402A VAL* 3.5 39.4 - - + +
403A SER* 3.8 16.4 - - - -
427A HIS* 2.8 21.1 + + - -
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLY* 3.2 22.7 - - - +
354A GLY* 3.3 1.9 - - - -
355A LEU 3.0 35.5 + - - -
383A ASP 3.0 13.1 + - - -
386A TRP* 1.3 81.4 - - - +
388A ASP* 1.3 59.3 + - - +
398A SER* 6.1 0.2 - - - -
403A SER* 3.1 21.1 + - - -
404A CYS* 3.3 15.7 - - - -
406A PHE* 3.4 6.4 - - - -
425A ARG* 3.2 6.6 + - - -
427A HIS* 3.4 2.3 - - - -
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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