Contacts of the helix formed by residues 332 - 342 (chain A) in PDB entry 2BWB
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 TYR 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A PRO* 2.7 44.0 + - + +
331A ARG* 1.3 115.8 + - - +
333A GLU* 1.3 55.3 + - - +
334A HIS 3.4 1.8 - - - -
335A GLN* 3.2 25.5 + - + -
336A LEU* 2.8 38.4 + - + +
351A VAL* 4.6 6.3 - - + -
354A LEU* 3.7 29.5 + - + -
355A ARG* 3.6 36.6 + - + +
358A GLY* 5.0 1.4 - - - -
359A GLY* 3.9 21.5 + - - -
330B GLU* 5.0 0.5 + - - -
333B GLU* 4.3 8.7 + - - -
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Residues in contact with GLU 333 (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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329A GLU 3.3 19.8 + - - +
330A GLU* 3.3 21.6 + - - +
331A ARG 3.5 1.0 + - - -
332A TYR* 1.3 76.5 - - - +
334A HIS* 1.3 88.0 + - + +
336A LEU* 3.7 5.7 - - - +
337A ARG* 3.1 23.4 + - - +
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Residues in contact with HIS 334 (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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332A TYR 3.4 0.4 - - - -
333A GLU* 1.3 99.7 + - + +
335A GLN* 1.3 65.7 + - - +
337A ARG* 3.5 9.5 + - - +
338A GLN* 3.2 26.8 + - - +
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Residues in contact with GLN 335 (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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331A ARG 4.1 4.6 + - - +
332A TYR* 3.5 30.9 - - + +
334A HIS* 1.3 84.6 + - - +
336A LEU* 1.3 60.2 + - - +
338A GLN* 3.4 2.4 + - - +
339A LEU* 3.0 36.7 + - - +
354A LEU* 3.6 24.5 - - + -
359A GLY* 2.7 34.2 + - - -
361A VAL* 3.1 30.7 - - + +
337B ARG* 4.3 11.7 - - - +
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Residues in contact with LEU 336 (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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328A PRO 4.1 15.7 - - - +
329A GLU* 4.1 12.6 - - + +
332A TYR* 2.8 32.5 + - + +
333A GLU* 3.7 4.9 - - - +
335A GLN* 1.3 71.0 - - - +
337A ARG* 1.3 61.9 + - - +
339A LEU* 3.4 3.4 + - - +
340A ASN* 2.4 39.1 + - - +
347A PHE* 4.0 33.0 - - + -
350A ASN* 3.8 32.1 - - + +
351A VAL* 4.5 7.2 - - + -
354A LEU* 4.3 9.4 - - + -
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Residues in contact with ARG 337 (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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333A GLU* 3.1 15.5 + - - +
334A HIS* 3.7 13.8 - - + +
335A GLN 3.3 0.2 - - - -
336A LEU* 1.3 75.9 - - - +
338A GLN* 1.3 56.8 + - - +
340A ASN* 3.2 6.3 + - + +
341A ASP* 2.8 57.9 + - - +
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Residues in contact with GLN 338 (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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334A HIS 3.2 14.1 + - - +
335A GLN* 3.8 4.9 - - - +
336A LEU 3.4 0.2 - - - -
337A ARG* 1.3 78.8 - - - +
339A LEU* 1.3 61.0 + - - +
341A ASP* 3.4 9.0 + - + +
342A MET* 3.2 39.6 + - + +
361A VAL* 3.9 35.9 - - + +
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Residues in contact with LEU 339 (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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335A GLN 3.0 22.1 + - - +
336A LEU* 3.7 5.2 - - - +
337A ARG 3.3 0.2 - - - -
338A GLN* 1.3 75.4 - - - +
340A ASN* 1.3 60.5 + - - +
342A MET* 3.2 12.0 + - - +
343A GLY 3.3 0.2 + - - -
344A PHE* 2.9 28.6 + - + +
350A ASN* 3.8 40.6 - - + +
354A LEU* 3.9 26.9 - - + -
361A VAL* 4.5 10.1 - - + -
364A ALA* 4.4 8.5 - - + -
365A LEU* 3.8 32.3 - - + -
368A LEU* 3.9 17.0 - - + -
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Residues in contact with ASN 340 (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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336A LEU* 2.4 39.8 + - - +
337A ARG* 3.6 6.5 - - + +
339A LEU* 1.3 71.8 - - - +
341A ASP* 1.3 59.5 + - - +
342A MET 3.0 4.7 - - - -
343A GLY* 3.0 15.4 + - - -
344A PHE 3.5 8.1 - - - -
345A PHE* 3.3 46.6 + - + +
350A ASN* 3.7 14.8 - - - +
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Residues in contact with ASP 341 (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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337A ARG* 2.8 45.6 + - - +
338A GLN* 3.6 9.1 - - + +
340A ASN* 1.3 77.5 - - - +
342A MET* 1.3 62.2 + - + +
343A GLY 3.4 0.2 - - - -
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Residues in contact with MET 342 (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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338A GLN* 3.2 27.1 + - + +
339A LEU* 3.2 9.5 + - - +
340A ASN 3.0 1.4 - - - -
341A ASP* 1.3 81.6 - - + +
343A GLY* 1.3 57.1 + - - +
344A PHE* 3.5 19.0 - - + -
365A LEU* 3.7 36.1 - - + -
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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