Contacts of the helix formed by residues 238 - 252 (chain A) in PDB entry 3BRA
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 LYS 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 5.8 3.2 - - + -
236A LEU 3.6 1.5 + - - -
237A PRO* 1.3 70.0 - - - +
239A LYS* 1.3 64.4 + - + +
241A PHE* 3.2 3.5 + - - +
242A GLU* 2.8 52.5 + - - +
326A GLN* 4.0 33.5 + - + +
327A SER 3.4 16.4 + - - +
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Residues in contact with LYS 239 (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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215A MET* 3.6 10.2 - - + +
219A GLU* 3.3 30.6 + - + +
222A TYR* 3.7 40.8 - - - -
237A PRO* 3.3 1.9 - - + +
238A LYS* 1.3 84.7 - - + +
240A VAL* 1.3 61.7 + - + +
242A GLU* 3.3 13.9 - - - +
243A ALA* 3.2 16.3 + - - +
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Residues in contact with VAL 240 (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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206A VAL* 5.5 2.7 - - + -
213A LEU* 4.7 5.2 - - + -
215A MET* 4.0 9.6 - - - +
219A GLU* 3.2 46.9 - - + +
220A TYR* 3.7 33.0 - - + -
236A LEU* 4.5 18.4 - - + -
237A PRO* 3.0 19.5 + - + +
239A LYS* 1.3 74.4 - - + +
241A PHE* 1.3 55.2 + - - +
243A ALA* 3.1 2.3 + - - +
244A ALA* 2.7 38.1 + - + +
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Residues in contact with PHE 241 (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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236A LEU* 3.5 20.3 - - + +
237A PRO 2.6 19.2 + - - +
238A LYS* 3.5 4.3 - - - +
240A VAL* 1.3 71.8 - - - +
242A GLU* 1.3 63.3 + - - +
244A ALA* 4.0 2.9 - - - -
245A VAL* 2.8 57.9 + - + +
262A TRP 3.3 24.5 - - - -
263A LEU* 4.1 15.3 - - + -
322A PHE* 4.6 0.4 - + - -
324A ILE* 3.7 36.1 - - + -
325A SER* 3.9 14.4 - - - -
326A GLN* 3.4 41.7 - - + -
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Residues in contact with GLU 242 (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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238A LYS* 2.8 35.4 + - - +
239A LYS* 3.3 17.2 - - - +
241A PHE* 1.3 84.2 - - + +
243A ALA* 1.3 61.4 + - - +
245A VAL* 4.1 4.3 - - - +
246A ALA* 3.3 22.3 + - - +
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Residues in contact with ALA 243 (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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213A LEU* 4.7 8.4 - - + +
215A MET* 3.6 39.9 - - + -
239A LYS 3.2 2.1 + - - +
240A VAL 3.1 2.0 + - - +
242A GLU* 1.3 76.7 - - - +
244A ALA* 1.3 65.8 + - - +
246A ALA* 3.7 6.7 - - - +
247A SER* 3.1 23.9 + - - -
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Residues in contact with ALA 244 (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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206A VAL* 6.2 1.1 - - + -
208A ILE* 5.3 6.5 - - + -
213A LEU* 4.4 15.9 - - + +
236A LEU* 3.6 27.1 - - + -
240A VAL* 2.7 22.3 + - + +
241A PHE* 3.6 4.0 - - + +
243A ALA* 1.3 69.3 - - - +
245A VAL* 1.3 67.3 + - + +
247A SER* 3.1 6.0 + - - -
248A ILE* 2.9 36.7 + - + +
324A ILE* 5.5 0.4 - - + -
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Residues in contact with VAL 245 (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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241A PHE* 2.8 60.3 + - + +
242A GLU* 4.1 4.7 - - - +
244A ALA* 1.3 72.2 - - + +
246A ALA* 1.3 53.9 + - - +
248A ILE* 3.1 8.9 + - + +
249A LYS* 2.6 57.0 + - + +
262A TRP* 4.2 23.1 - - + +
322A PHE* 4.4 15.3 - - + -
324A ILE* 5.6 0.7 - - + -
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Residues in contact with ALA 246 (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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242A GLU 3.3 16.7 + - - +
243A ALA* 3.7 9.0 - - - +
244A ALA 3.3 0.6 - - - -
245A VAL* 1.3 80.7 - - - +
247A SER* 1.3 57.4 + - - +
249A LYS* 3.5 10.8 - - - +
250A ALA* 3.2 27.5 + - - +
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Residues in contact with SER 247 (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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208A ILE* 3.7 27.1 + - - +
211A GLN* 5.4 3.1 + - - +
213A LEU* 4.8 8.7 - - - +
243A ALA 3.1 15.8 + - - -
244A ALA 3.1 5.7 + - - -
246A ALA* 1.3 74.6 - - - +
248A ILE* 1.3 59.8 + - - +
250A ALA* 3.4 4.2 + - - +
251A ALA* 2.8 30.4 + - - +
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Residues in contact with ILE 248 (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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208A ILE* 4.0 24.0 - - + -
236A LEU* 6.1 0.2 - - + -
244A ALA* 2.9 32.7 + - + +
245A VAL* 3.7 5.4 - - + +
247A SER* 1.3 72.5 - - - +
249A LYS* 1.3 54.5 + - - +
251A ALA* 3.6 7.3 - - - +
252A SER* 2.6 39.5 + - - +
262A TRP* 4.1 21.1 - - + -
280A PHE* 4.7 7.2 - - + -
281A PRO* 4.3 17.0 - - + -
283A ILE* 4.2 11.4 - - + -
305A TYR* 4.8 4.7 - - + +
322A PHE* 4.2 12.3 - - + -
324A ILE* 4.2 25.8 - - + -
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Residues in contact with LYS 249 (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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245A VAL* 2.6 37.2 + - + +
246A ALA* 3.5 9.9 - - - +
248A ILE* 1.3 75.4 - - - +
250A ALA* 1.3 60.5 + - - +
252A SER* 3.4 12.7 + - - -
253A SER* 3.5 14.0 + - - -
257A PHE 5.3 2.2 + - - -
259A ASP* 4.3 16.2 + - - +
262A TRP* 3.2 45.9 - - + +
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Residues in contact with ALA 250 (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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246A ALA 3.2 14.5 + - - +
247A SER* 4.1 4.5 - - - +
249A LYS* 1.3 75.8 - - - +
251A ALA* 1.3 62.2 + - - +
252A SER 3.2 1.5 + - - -
253A SER* 3.6 19.5 + - - -
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Residues in contact with ALA 251 (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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208A ILE* 4.4 5.2 - - + -
209A ASN* 5.5 4.0 - - + -
247A SER* 2.8 19.6 + - - +
248A ILE* 3.2 5.4 + - - +
250A ALA* 1.3 77.8 - - - +
252A SER* 1.3 58.0 + - - +
253A SER 3.5 0.7 + - - -
254A THR* 4.5 4.3 + - - -
279A ILE 3.8 7.6 - - - +
281A PRO* 3.8 29.1 - - + +
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Residues in contact with SER 252 (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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248A ILE 2.6 21.8 + - - -
249A LYS* 3.4 9.4 + - - -
250A ALA 3.2 0.2 - - - -
251A ALA* 1.3 78.0 - - - +
253A SER* 1.3 54.8 + - - +
254A THR* 2.8 14.3 + - - +
255A GLU 3.7 15.1 + - - +
257A PHE* 5.3 2.6 - - - -
262A TRP* 3.9 15.8 - - - -
279A ILE* 3.2 29.4 - - - +
280A PHE* 4.2 20.2 - - - -
281A PRO* 4.8 0.9 - - - -
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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