Contacts of the helix formed by residues 380 - 391 (chain A) in PDB entry 5HGU
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 CYS 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A VAL* 4.5 2.2 - - - -
355A VAL* 4.0 26.9 - - + -
357A LYS* 5.7 0.7 - - + -
378A PRO 3.6 1.2 + - - -
379A MET* 1.3 73.5 - - - +
381A GLU* 1.3 67.5 + - - +
383A LEU* 3.2 41.0 + - - +
384A VAL* 3.1 17.2 + - - +
501A PLM 2.6 34.3 + - - +
356B GLU* 3.4 23.3 - - - +
358B VAL* 5.3 4.5 - - + -
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Residues in contact with GLU 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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379A MET 4.4 2.9 - - - +
380A CYS* 1.3 71.5 - - - +
382A TYR* 1.3 67.6 + - - +
384A VAL* 3.7 9.8 - - - +
385A ASN* 2.9 31.8 + - - +
282B LYS* 3.5 38.1 - - + +
283B GLY* 3.5 12.0 - - - +
288B LEU* 5.7 1.2 - - - +
344B SER* 4.5 6.0 + - - -
346B LYS* 2.9 35.5 + - - -
353B GLN* 4.6 2.9 - - - +
356B GLU* 2.6 28.3 + - - +
358B VAL* 5.6 0.2 - - - +
411B VAL* 5.7 0.7 - - - +
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Residues in contact with TYR 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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347A VAL* 4.4 15.3 - - + -
349A SER* 3.6 23.3 + - - -
354A VAL* 3.9 34.0 - - + +
355A VAL* 3.7 13.0 - - + -
380A CYS* 3.2 1.0 - - - -
381A GLU* 1.3 78.0 - - - +
383A LEU* 1.3 64.0 + - + +
385A ASN* 3.7 4.4 - - - +
386A PHE* 2.8 46.8 + + + +
406A PHE* 4.5 12.4 - + - -
353B GLN* 3.5 43.8 - - + +
356B GLU* 3.6 9.8 + - - +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 4.2 11.4 - - + -
379A MET* 3.8 11.9 - - + -
380A CYS* 3.2 20.7 + - - +
381A GLU 3.2 0.4 - - - -
382A TYR* 1.3 80.6 - - + +
384A VAL* 1.3 56.6 + - - +
386A PHE* 3.5 8.1 - - + +
387A LEU* 2.7 41.8 + - + +
406A PHE* 3.2 41.1 - - + -
408A ILE* 4.6 1.1 - - + -
501A PLM 3.1 61.0 - - + +
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Residues in contact with VAL 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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327A TYR* 3.5 50.0 - - + -
379A MET* 4.0 14.8 - - - +
380A CYS 3.1 16.4 + - - +
381A GLU* 3.3 5.6 + - - +
383A LEU* 1.3 75.4 - - - +
385A ASN* 1.3 64.2 + - - +
387A LEU* 3.3 5.6 + - - +
388A HIS* 3.1 30.3 + - + -
282B LYS* 3.8 42.6 - - + +
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Residues in contact with ASN 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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381A GLU* 2.9 24.4 + - - +
382A TYR* 3.7 4.1 - - - +
384A VAL* 1.3 74.8 - - - +
386A PHE* 1.3 64.1 + - - +
388A HIS* 3.3 8.5 + - - +
389A LYS* 3.2 40.0 + - - +
280B GLU 3.4 18.1 + - - +
281B LYS* 3.6 5.6 + - - +
282B LYS* 3.2 45.9 + - - +
353B GLN* 5.2 3.8 - - - +
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Residues in contact with PHE 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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382A TYR* 2.8 35.0 + + + +
383A LEU* 3.5 9.9 - - + +
385A ASN* 1.3 77.0 - - - +
387A LEU* 1.3 60.4 + - + +
389A LYS* 3.3 14.6 + - + +
390A LEU* 2.9 45.6 + - + +
402A VAL* 3.9 29.6 - - + -
403A LEU* 3.8 28.3 - - + -
406A PHE* 3.8 39.5 - + + -
501A PLM 4.9 3.1 - - + -
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Residues in contact with LEU 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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251A PHE* 3.8 32.5 - - + -
306A LEU* 3.8 25.9 - - + +
308A TRP* 4.3 9.6 - - + -
327A TYR* 4.4 7.9 - - + -
379A MET* 3.9 18.8 - - - -
383A LEU* 2.7 25.9 + - + +
384A VAL 3.6 4.5 - - - +
386A PHE* 1.3 77.6 - - + +
388A HIS* 1.3 61.6 + - - +
390A LEU* 3.7 8.7 - - + +
391A ARG* 3.1 28.0 + - - +
501A PLM 3.8 35.9 - - + -
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Residues in contact with HIS 388 (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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308A TRP* 5.2 0.9 - + - -
327A TYR* 2.8 32.9 + + - -
384A VAL* 3.1 30.1 + - + +
385A ASN* 3.3 8.9 + - - +
387A LEU* 1.3 77.6 - - - +
389A LYS* 1.3 62.9 + - + +
391A ARG* 3.4 39.0 + - - +
392A GLN* 3.2 24.4 + - - +
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Residues in contact with LYS 389 (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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385A ASN* 3.2 26.8 + - - +
386A PHE* 3.6 16.1 - - + +
387A LEU 3.2 0.2 - - - -
388A HIS* 1.3 76.2 - - + +
390A LEU* 1.3 65.6 + - - +
392A GLN* 3.0 35.9 + - - +
393A LEU* 3.6 11.1 - - + +
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Residues in contact with LEU 390 (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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306A LEU* 3.7 27.1 - - + -
386A PHE* 2.9 43.2 + - + +
387A LEU* 3.3 7.4 + - + +
389A LYS* 1.3 78.6 - - - +
391A ARG* 1.3 62.7 - - - +
392A GLN 3.0 1.4 + - - -
393A LEU* 3.1 39.3 + - + +
399A MET* 3.4 31.8 - - + +
402A VAL* 4.2 19.7 - - + -
403A LEU* 3.9 16.4 - - + -
501A PLM 4.0 6.5 - - + -
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Residues in contact with ARG 391 (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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306A LEU* 4.0 22.8 + - + +
308A TRP* 3.1 81.7 - - + +
387A LEU 3.1 9.2 + - - +
388A HIS* 3.4 40.7 - - - +
390A LEU* 1.3 78.7 - - - +
392A GLN* 1.3 63.1 + - + +
393A LEU 3.4 1.8 + - - +
399A MET* 4.0 15.4 - - - +
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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