Contacts of the helix formed by residues 369 - 378 (chain A) in PDB entry 4B92
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 ASP 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A VAL* 4.2 3.6 - - - -
368A MET* 1.3 77.5 - - - +
370A GLU* 1.3 67.9 + - + +
371A ASN* 3.0 20.9 + - - +
372A ARG* 3.1 21.9 + - - +
373A PHE* 3.1 18.0 + - - +
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Residues in contact with GLU 370 (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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18A VAL* 3.6 24.1 - - + +
23A THR* 2.4 37.8 + - - +
57A LEU* 4.2 12.8 - - + +
59A ILE* 6.0 0.2 - - - +
359A TRP* 3.9 23.8 - - + -
363A VAL* 4.3 7.9 - - + +
369A ASP* 1.3 73.3 - - + +
371A ASN* 1.3 74.9 + - - +
373A PHE* 3.5 13.3 - - - +
374A VAL* 3.4 16.3 + - - +
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Residues in contact with ASN 371 (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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18A VAL* 3.3 4.6 - - - +
19A ASN 2.9 23.3 + - - +
20A ASP* 3.2 33.6 - - - +
21A ASP 4.6 2.8 - - - +
22A CYS* 3.3 19.2 - - - -
23A THR* 2.8 27.2 + - - -
369A ASP* 3.0 17.6 - - - +
370A GLU* 1.3 85.2 - - - +
372A ARG* 1.3 61.8 + - - +
373A PHE 3.2 1.3 - - - -
374A VAL* 3.4 1.6 + - - +
375A ALA 3.1 19.9 + - - -
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Residues in contact with ARG 372 (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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20A ASP 5.3 0.4 - - - -
314A LEU 2.7 27.3 + - - -
315A ALA* 3.6 17.6 + - - +
317A ASP* 3.1 45.5 + - - +
319A LEU 3.3 6.3 + - - -
368A MET* 3.9 27.1 - - + -
369A ASP* 3.1 22.2 + - - +
371A ASN* 1.3 75.3 - - - +
373A PHE* 1.3 59.3 + - - +
375A ALA* 3.0 14.3 + - - +
376A VAL* 2.8 43.5 + - - +
380A ASN* 3.7 15.9 + - - +
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Residues in contact with PHE 373 (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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59A ILE* 4.2 14.4 - - + -
355A MET* 3.4 51.1 - - + -
358A ILE* 3.8 22.2 - - + -
359A TRP* 3.6 42.8 - + + -
363A VAL* 3.5 25.1 - - + -
368A MET* 3.9 9.5 - - - -
369A ASP 3.1 5.8 + - - +
370A GLU* 3.5 11.9 - - - +
372A ARG* 1.3 73.2 - - - +
374A VAL* 1.3 65.0 + - + +
376A VAL* 3.5 1.7 - - - +
377A THR* 2.4 51.1 + - + +
405A TRP* 4.5 5.2 - + - -
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Residues in contact with VAL 374 (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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18A VAL* 3.9 25.4 - - + +
20A ASP 3.9 14.4 - - - +
59A ILE* 4.3 13.7 - - + -
60A PRO* 3.8 23.8 - - + +
370A GLU 3.4 13.8 + - - +
371A ASN 3.4 7.5 + - - +
372A ARG 3.3 0.2 - - - -
373A PHE* 1.3 78.1 - - + +
375A ALA* 1.3 68.7 + - - +
377A THR* 3.6 4.7 - - - -
378A SER* 2.8 38.8 + - - +
379A SER* 3.1 17.9 + - - +
392A GLY 4.5 0.2 - - - +
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Residues in contact with ALA 375 (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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20A ASP* 3.8 13.4 - - + +
371A ASN 3.1 13.1 + - - +
372A ARG* 3.0 37.5 + - - +
374A VAL* 1.3 78.0 - - - +
376A VAL* 1.3 60.7 + - - +
378A SER 3.9 0.5 + - - -
379A SER* 3.4 13.3 + - - -
380A ASN* 3.0 37.3 + - - +
381A ALA 4.5 0.3 + - - -
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Residues in contact with VAL 376 (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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314A LEU* 3.6 26.5 - - + +
320A ASN 3.7 13.7 - - - +
321A ILE* 3.6 7.0 - - - +
322A VAL* 3.0 36.3 + - + +
358A ILE* 4.6 5.6 - - + -
368A MET* 4.2 10.3 - - - -
372A ARG* 2.8 57.8 + - + +
373A PHE* 3.5 12.1 - - - +
375A ALA* 1.3 76.8 - - - +
377A THR* 1.3 70.3 + - + +
381A ALA* 5.9 1.1 + - - +
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Residues in contact with THR 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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59A ILE* 5.7 0.5 - - - +
62A GLY* 3.8 0.6 - - - -
63A ILE 3.0 31.2 + - - +
322A VAL* 3.9 17.5 - - + -
354A ARG* 3.1 11.5 + - + +
355A MET* 3.7 25.3 - - - +
358A ILE* 4.2 5.6 - - + -
373A PHE* 2.4 52.7 + - + +
374A VAL* 3.6 4.9 + - - -
376A VAL* 1.3 84.4 - - + +
378A SER* 1.3 59.2 + - - +
381A ALA* 5.4 1.6 - - - -
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Residues in contact with SER 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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60A PRO* 3.7 6.1 + - - +
61A GLY 3.4 26.5 - - - -
62A GLY* 4.3 1.8 - - - -
63A ILE* 3.5 15.6 - - - +
374A VAL* 2.8 29.4 + - - +
376A VAL 3.7 0.6 - - - -
377A THR* 1.3 75.9 - - - +
379A SER* 1.3 60.6 + - - -
380A ASN 3.5 2.0 - - - -
381A ALA* 3.2 8.3 - - - +
382A ALA* 2.9 24.6 + - - +
392A GLY* 3.6 17.9 - - - -
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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