Contacts of the helix formed by residues 377 - 385 (chain A) in PDB entry 7JDW
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 VAL 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A ILE* 5.0 2.9 - - + -
374A ALA 4.4 6.3 - - - +
375A ASN* 3.0 11.0 + - - +
376A GLU* 1.3 70.3 - - - +
378A PRO* 1.3 71.6 - - + +
380A GLN* 3.1 24.1 + - - +
381A LYS* 3.0 46.5 + - + +
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Residues in contact with PRO 378 (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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341A PRO* 3.4 27.3 - - + +
342A THR 4.6 6.1 - - - +
344A ILE* 3.8 31.6 - - + -
376A GLU* 3.3 7.6 - - - +
377A VAL* 1.3 96.2 - - + +
379A ILE* 1.3 60.2 + - - +
381A LYS* 3.6 9.3 + - + +
382A MET* 3.4 14.4 + - - +
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Residues in contact with ILE 379 (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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317A LEU* 5.1 1.1 - - + -
340A PRO* 3.8 22.0 - - + -
341A PRO* 3.6 17.9 - - + +
359A SER* 3.7 27.6 - - - +
360A MET* 3.9 14.1 - - + -
372A VAL* 3.8 16.2 - - + -
376A GLU* 3.2 30.4 + - + +
378A PRO* 1.3 76.9 - - - +
380A GLN* 1.3 66.4 + - - +
382A MET* 3.3 12.4 + - + +
383A PHE* 3.1 42.6 + - + -
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Residues in contact with GLN 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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372A VAL* 4.1 16.8 - - + -
373A ASP 3.1 16.4 - - - +
374A ALA* 2.9 29.3 + - - +
376A GLU 3.3 9.0 + - - +
377A VAL* 3.1 28.1 + - - +
379A ILE* 1.3 79.5 - - - +
381A LYS* 1.3 66.7 + - + +
383A PHE* 3.2 6.1 + - - +
384A GLU* 3.0 34.2 + - - +
390A THR* 3.7 13.4 - - + +
392A LYS* 3.3 31.5 - - - +
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Residues in contact with LYS 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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377A VAL* 3.0 38.3 + - + +
378A PRO* 3.7 9.6 - - + +
380A GLN* 1.3 79.9 - - - +
382A MET* 1.3 65.0 + - - +
384A GLU* 3.2 24.4 + - + +
385A LYS* 2.9 49.9 + - - +
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Residues in contact with MET 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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317A LEU* 4.3 7.9 - - + -
338A ILE* 3.5 32.1 - - + -
339A THR 4.7 1.1 - - - +
340A PRO* 3.9 21.8 - - - -
341A PRO* 4.0 9.6 - - + -
378A PRO 3.4 10.4 + - - +
379A ILE* 3.3 14.5 + - + +
380A GLN 3.2 0.4 - - - -
381A LYS* 1.3 80.0 - - - +
383A PHE* 1.3 110.6 + - + +
385A LYS* 3.4 8.2 + - - +
386A LEU* 3.3 28.5 + - + +
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Residues in contact with PHE 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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311A ILE* 3.8 24.0 - - + -
317A LEU* 3.8 17.3 - - + -
362A VAL* 3.9 28.3 - - + -
364A MET* 5.1 0.9 - - - -
370A VAL* 4.0 19.3 - - + -
372A VAL* 4.5 6.3 - - + -
379A ILE* 3.1 36.9 + - + -
380A GLN* 3.2 7.4 + - - +
382A MET* 1.3 99.7 - - + +
384A GLU* 1.3 61.0 + - - +
386A LEU* 3.0 15.0 + - + +
387A GLY 3.2 0.2 + - - -
388A ILE* 2.9 50.5 + - + +
390A THR* 3.8 16.8 - - + -
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Residues in contact with GLU 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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380A GLN* 3.0 17.9 + - - +
381A LYS* 3.2 39.0 + - + +
383A PHE* 1.3 76.1 - - - +
385A LYS* 1.3 57.5 + - + +
387A GLY* 2.9 19.6 + - - -
388A ILE 3.8 9.0 - - - +
389A THR* 5.7 0.4 - - - -
390A THR* 2.7 32.3 + - + +
392A LYS* 3.8 14.2 + - - -
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Residues in contact with LYS 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 LYS* 2.9 40.1 + - - +
382A MET* 3.4 7.4 + - - +
383A PHE 3.3 0.2 - - - -
384A GLU* 1.3 76.4 - - + +
386A LEU* 1.3 61.3 + - + +
387A GLY 3.2 1.5 + - - -
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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