Contacts of the helix formed by residues 349 - 358 (chain A) in PDB entry 4BPW
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 THR 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 4.6 10.6 - - + +
327A THR 3.5 24.2 - - - +
328A GLY* 3.3 12.1 - - - -
329A ARG* 3.8 25.6 - - - +
330A ILE* 4.5 2.2 - - - -
347A VAL 3.4 0.8 + - - -
348A PRO* 1.3 75.8 - - - +
350A ILE* 1.3 65.1 + - - +
351A SER* 3.7 13.8 + - - -
352A PHE* 3.1 27.0 + - - +
353A ILE* 3.2 15.1 + - - +
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Residues in contact with ILE 350 (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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4A PHE* 3.7 24.9 - - + -
9A LEU* 4.1 5.2 - - + -
12A LEU* 3.5 40.2 - - + +
13A LEU* 3.8 20.6 - - + +
16A TYR* 3.6 27.8 - - + -
323A VAL* 3.9 24.0 - - + -
328A GLY 2.9 14.1 + - - +
330A ILE* 4.2 6.6 - - + +
349A THR* 1.3 72.3 - - - +
351A SER* 1.3 65.7 + - - +
353A ILE* 3.6 7.9 + - - +
354A CYS* 3.1 26.2 + - - -
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Residues in contact with SER 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.9 24.2 - - - +
8A GLU* 4.6 7.4 - - - -
12A LEU* 3.9 24.1 - - - +
349A THR* 3.2 10.9 + - - -
350A ILE* 1.3 82.6 - - - +
352A PHE* 1.3 61.2 + - - +
354A CYS* 4.0 0.5 - - - +
355A ARG* 2.9 29.3 + - - +
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Residues in contact with PHE 352 (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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348A PRO* 5.0 6.1 - - + -
349A THR* 3.1 26.9 + - - +
351A SER* 1.3 81.7 + - - +
353A ILE* 1.3 62.0 + - + +
355A ARG* 3.4 33.1 + - - +
356A GLU* 3.1 62.1 + - + +
387A SER* 3.7 16.2 - - - -
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Residues in contact with ILE 353 (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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16A TYR* 3.6 35.9 - - + -
20A LEU* 3.4 17.6 - - + +
330A ILE* 4.3 13.0 - - + -
348A PRO* 3.7 29.2 - - + -
349A THR 3.2 5.3 + - - +
350A ILE* 3.6 10.8 - - - +
352A PHE* 1.3 76.0 - - + +
354A CYS* 1.3 62.5 - - - +
356A GLU* 3.9 7.0 - - - +
357A LEU* 3.3 8.3 + - - +
386A THR* 3.3 29.2 - - - +
387A SER* 4.3 4.7 - - - +
388A LEU* 4.0 35.4 - - + +
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Residues in contact with CYS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 44.4 - - + -
15A LEU* 3.8 25.4 - - + -
16A TYR 4.1 2.0 - - - -
20A LEU* 4.0 17.0 - - - -
350A ILE* 3.1 29.7 + - - +
351A SER 4.2 0.2 - - - +
353A ILE* 1.3 77.8 - - - +
355A ARG* 1.3 64.2 + - - +
356A GLU 3.2 0.2 - - - -
357A LEU* 3.3 1.7 + - - +
358A ASP* 3.0 30.5 + - - +
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Residues in contact with ARG 355 (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 SER 2.9 21.5 + - - +
352A PHE* 3.5 34.4 - - - +
354A CYS* 1.3 77.2 - - - +
356A GLU* 1.3 63.5 + - + +
358A ASP* 3.3 15.8 + - - +
359A ALA* 3.5 13.1 + - + +
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Residues in contact with GLU 356 (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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352A PHE* 3.1 40.7 + - + +
353A ILE* 4.3 1.4 - - - -
354A CYS 3.2 0.4 - - - -
355A ARG* 1.3 77.4 - - + +
357A LEU* 1.3 64.3 + - - +
359A ALA* 3.2 19.5 + - - +
360A ILE* 3.8 13.3 - - - +
385A LYS* 4.9 5.1 - - - +
386A THR* 3.0 18.8 - - + -
387A SER* 2.5 50.7 + - - -
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Residues in contact with LEU 357 (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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15A LEU* 4.0 20.4 - - + -
19A ARG* 3.7 48.9 + - + +
20A LEU* 4.2 17.0 - - + -
353A ILE 3.3 15.6 + - - +
354A CYS* 3.3 5.3 + - - +
356A GLU* 1.3 77.4 - - - +
358A ASP* 1.3 59.1 + - - +
359A ALA 3.1 2.7 - - - -
360A ILE* 3.3 24.9 + - + +
382A ASP* 3.5 51.4 - - + +
386A THR* 4.1 4.2 - - + +
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 22.9 - - - +
19A ARG* 5.1 3.6 + - - -
354A CYS 3.0 18.7 + - - +
355A ARG* 3.7 8.5 - - - +
356A GLU 3.2 0.6 - - - -
357A LEU* 1.3 79.0 - - - +
359A ALA* 1.3 59.2 + - - +
360A ILE 3.6 2.0 + - - -
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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