Contacts of the helix formed by residues 376 - 386 (chain A) in PDB entry 1R4N
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A GLU* 4.7 6.7 + - - -
374A SER 4.2 1.0 + - - -
375A ILE* 1.3 79.8 - - - +
377A GLU* 1.3 65.1 + - - +
378A LYS* 3.9 14.4 - - - +
379A GLU* 2.9 40.0 + - - +
380A LEU* 3.2 18.5 + - - +
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Residues in contact with GLU 377 (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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373A GLU* 5.1 3.0 + - - -
375A ILE 3.9 0.6 + - - -
376A SER* 1.3 73.9 - - - +
378A LYS* 1.3 59.6 + - + +
380A LEU* 3.2 12.1 + - + +
381A LYS* 2.9 62.0 + - + +
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Residues in contact with LYS 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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376A SER* 4.1 11.0 - - - +
377A GLU* 1.3 80.1 - - + +
379A GLU* 1.3 63.5 + - + +
381A LYS* 3.5 4.1 + - - +
382A LEU* 3.1 25.3 + - - +
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Residues in contact with GLU 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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172A ILE* 4.8 7.0 - - + +
303A SER* 3.5 22.3 + - - -
307A LEU* 4.6 12.1 - - + +
374A SER 4.8 2.9 - - - +
375A ILE* 4.2 13.8 - - + +
376A SER* 2.9 36.8 + - - +
378A LYS* 1.3 77.9 - - + +
380A LEU* 1.3 58.2 + - - +
382A LEU* 3.6 7.3 - - - +
383A LEU* 2.9 30.4 + - - +
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Residues in contact with LEU 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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307A LEU* 4.6 3.6 - - + -
354A ALA* 3.8 14.6 - - + +
355A ALA* 5.0 2.7 - - - -
357A VAL* 4.2 9.9 - - + -
358A GLY* 3.4 37.2 - - - +
361A VAL* 4.2 12.6 - - + -
375A ILE* 4.8 4.7 - - + +
376A SER 3.2 9.3 + - - +
377A GLU* 3.4 15.3 - - + +
378A LYS 3.1 0.4 - - - -
379A GLU* 1.3 74.3 - - - +
381A LYS* 1.3 66.2 + - + +
382A LEU 2.8 11.1 + - - -
383A LEU* 3.0 14.3 + - + +
384A CYS* 3.0 36.8 + - - -
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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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351A LYS* 4.3 32.0 - - - +
354A ALA* 4.9 16.4 - - + -
377A GLU* 2.9 50.2 + - + +
378A LYS* 4.2 4.3 - - - +
380A LEU* 1.3 77.0 - - + +
382A LEU* 1.3 56.5 + - - +
384A CYS* 4.2 7.3 - - - +
385A SER* 3.3 23.2 + - - -
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Residues in contact with LEU 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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23A HIS* 5.7 4.0 - - + +
172A ILE* 4.3 14.4 - - + -
173A GLU* 4.3 27.4 - - + +
378A LYS 3.1 16.7 + - - +
379A GLU* 3.6 7.0 - - - +
380A LEU 2.9 0.8 - - - -
381A LYS* 1.3 76.4 - - - +
383A LEU* 1.3 66.9 + - - +
384A CYS 3.0 2.7 + - - -
385A SER* 3.0 16.4 + - - -
386A ASN* 3.0 41.1 + - - +
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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
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172A ILE* 3.6 24.8 - - + +
304A PHE* 5.7 1.3 - - + -
307A LEU* 3.0 55.9 - - + +
311A LEU* 3.8 27.4 - - + -
357A VAL* 4.9 1.3 - - + -
379A GLU 2.9 17.5 + - - +
380A LEU* 3.5 15.0 - - + +
382A LEU* 1.3 76.0 - - - +
384A CYS* 1.3 58.9 + - - +
386A ASN 3.5 1.6 - - - -
387A SER* 3.0 23.0 + - - -
390A LEU* 4.1 22.4 - - + -
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Residues in contact with CYS 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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311A LEU* 4.8 2.2 - - - -
324A PRO* 4.6 15.1 - - + +
325A VAL 5.8 2.9 - - - +
326A ARG* 5.5 2.1 - - - -
350A ALA 5.7 0.9 - - - +
354A ALA* 4.2 19.5 - - + -
357A VAL* 3.9 36.3 - - - -
380A LEU* 3.0 28.9 + - - +
381A LYS* 4.3 6.3 - - - +
383A LEU* 1.3 75.2 - - - +
385A SER* 1.3 59.1 + - - +
387A SER* 2.6 38.2 + - - -
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Residues in contact with SER 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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325A VAL 5.8 0.2 - - - -
326A ARG* 3.8 46.9 + - - +
328A THR* 5.9 3.1 - - - +
381A LYS 3.3 14.2 + - - -
382A LEU* 3.0 12.0 + - - -
384A CYS* 1.3 78.4 - - - +
386A ASN* 1.3 63.9 + - - +
387A SER* 3.5 2.6 + - - -
388A ALA 4.9 0.3 + - - -
389A PHE* 4.4 3.8 - - - -
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Residues in contact with ASN 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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172A ILE* 3.3 25.3 - - + +
173A GLU* 3.9 19.8 - - - +
174A SER 4.3 3.1 + - - -
175A HIS 5.0 2.1 + - - -
176A PRO* 5.4 0.9 - - - +
382A LEU* 3.0 47.8 + - - +
383A LEU 3.5 3.4 - - - -
385A SER* 1.3 79.5 - - - +
387A SER* 1.3 66.6 + - - +
388A ALA 3.2 2.9 - - - -
389A PHE* 2.8 34.5 + - + -
390A LEU* 3.3 10.1 + - - +
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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