Contacts of the helix formed by residues 360 - 369 (chain K) in PDB entry 2BWE
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 360 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354K LEU* 4.2 0.9 - - - -
357K SER* 2.7 34.3 + - - -
358K GLY 3.4 1.8 + - - -
359K GLY* 1.3 74.3 - - - +
361K VAL* 1.3 63.8 + - - +
362K GLN* 3.4 10.0 + - - +
363K GLY* 3.0 15.7 + - - -
364K ALA* 3.0 11.3 + - - +
337L ARG* 3.7 13.8 - - - +
340L ASN* 3.8 17.7 + - - +
341L ASP* 3.8 18.9 + - - -
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Residues in contact with VAL 361 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335K GLN* 3.5 30.7 - - + +
338K GLN* 3.5 45.5 - - + +
339K LEU* 4.3 19.1 - - + -
342K MET* 5.2 5.2 - - - -
354K LEU* 4.4 7.2 - - + -
359K GLY 3.3 1.8 + - - -
360K SER* 1.3 68.7 - - - +
362K GLN* 1.3 68.7 + - - +
363K GLY 3.2 0.2 + - - -
364K ALA* 3.2 1.1 + - - -
365K LEU* 2.8 33.0 + - + +
337L ARG* 5.2 0.2 - - - +
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Residues in contact with GLN 362 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C LEU* 4.4 28.0 + - + +
360K SER* 3.3 7.8 - - - +
361K VAL* 1.3 82.6 - - - +
363K GLY* 1.3 60.9 + - - +
365K LEU* 3.4 19.9 - - - +
366K ASP* 3.4 9.2 + - - +
340L ASN 4.4 8.8 + - - +
341L ASP* 4.7 11.4 + - - +
343L GLY* 5.3 2.8 - - - +
345L PHE* 3.7 28.0 - - + -
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Residues in contact with GLY 363 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357K SER* 3.9 5.8 - - - -
360K SER* 3.0 14.4 + - - -
362K GLN* 1.3 76.0 - - - +
364K ALA* 1.3 65.1 + - - +
365K LEU 3.2 0.2 - - - -
366K ASP* 3.2 5.4 + - - +
367K SER* 3.0 21.7 + - - -
340L ASN* 3.5 22.2 - - - -
345L PHE* 3.5 17.1 - - - +
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Residues in contact with ALA 364 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K LEU* 4.8 8.1 - - + -
353K ALA* 3.8 38.4 - - + +
354K LEU* 3.8 18.6 - - + -
357K SER* 3.7 1.6 + - - -
360K SER 3.0 15.7 + - - +
361K VAL* 3.9 2.5 - - - +
363K GLY* 1.3 75.0 - - - +
365K LEU* 1.3 63.9 + - - +
367K SER* 3.2 5.1 + - - -
368K LEU* 2.8 28.7 + - - +
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Residues in contact with LEU 365 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344C PHE* 4.7 1.6 - - + -
365C LEU* 5.0 4.3 - - + -
369C LEU* 3.1 35.2 - - + -
339K LEU* 4.4 10.6 - - + +
342K MET* 3.9 31.9 - - + -
344K PHE* 3.6 37.5 - - + -
361K VAL* 2.8 21.5 + - + +
362K GLN* 3.4 7.6 - - - +
364K ALA* 1.3 76.0 - - - +
366K ASP* 1.3 64.3 + - - +
368K LEU* 3.0 8.4 + - + +
369K LEU* 3.0 35.5 + - + +
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Residues in contact with ASP 366 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C ASP* 3.0 26.7 - - - +
369C LEU* 4.2 10.5 - - + +
370C ASN* 4.0 6.9 + - - +
362K GLN 3.4 6.5 + - - +
363K GLY 3.2 9.3 + - - +
365K LEU* 1.3 78.0 - - - +
367K SER* 1.3 58.1 + - - +
369K LEU* 3.2 12.7 + - - +
370K ASN* 2.7 34.4 + - - -
345L PHE* 3.2 46.0 - - + +
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Residues in contact with SER 367 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353K ALA* 4.2 16.3 + - - -
356K ARG* 4.3 17.9 + - - +
357K SER* 5.9 0.7 - - - -
363K GLY 3.0 10.4 + - - -
364K ALA* 3.3 13.8 - - - -
366K ASP* 1.3 80.8 + - - +
368K LEU* 1.3 51.8 + - - +
370K ASN* 3.2 5.3 + - - +
371K GLY* 2.6 36.2 + - - -
372K ASP* 3.6 17.3 - - - -
345L PHE* 4.5 11.1 + - - +
347L PHE* 5.9 0.3 - - - +
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Residues in contact with LEU 368 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339K LEU* 3.9 24.0 - - + -
344K PHE* 3.9 30.2 - - + -
349K ARG* 3.2 50.8 + - + +
350K ASN* 3.6 26.0 - - - +
353K ALA* 3.9 20.0 - - + -
364K ALA 2.8 23.7 + - - +
365K LEU* 3.0 5.1 + - - +
367K SER* 1.3 74.5 - - - +
369K LEU* 1.3 63.0 + - - +
370K ASN 3.3 0.7 + - - -
371K GLY* 3.6 5.2 + - - +
372K ASP* 4.8 3.8 - - - +
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Residues in contact with LEU 369 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C GLN* 4.5 31.4 + - + +
365C LEU* 3.2 41.1 - - + -
366C ASP* 4.2 13.0 - - - +
369C LEU* 4.3 13.7 - - + -
345D PHE* 3.8 20.3 - - + -
344K PHE* 3.6 28.3 - - + -
365K LEU* 3.0 21.2 + - + +
366K ASP* 3.8 6.5 - - - +
367K SER 3.2 0.6 - - - -
368K LEU* 1.3 77.4 - - - +
370K ASN* 1.3 63.8 + - - +
47T SER* 4.9 1.9 + - - -
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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