Contacts of the helix formed by residues 217 - 228 (chain A) in PDB entry 3BRW
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A TYR* 3.3 33.5 - - - -
215A GLU 4.0 0.8 + - - -
216A GLU* 1.3 77.0 - - - +
218A PRO* 1.4 78.7 - - - +
219A ALA 3.4 8.0 + - - -
220A PHE* 4.0 13.9 + - - +
221A VAL* 3.2 21.7 + - - +
299A ASP* 2.9 20.7 + - - -
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Residues in contact with PRO 218 (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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216A GLU 4.4 2.0 - - - +
217A SER* 1.4 89.2 - - - +
219A ALA* 1.3 61.2 + - + +
221A VAL* 3.6 7.0 + - + +
222A GLU* 3.4 19.8 + - - +
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Residues in contact with ALA 219 (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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217A SER* 3.2 2.2 + - - +
218A PRO* 1.3 77.9 - - + +
220A PHE* 1.3 60.6 - - - +
222A GLU* 3.4 15.5 + - - +
223A PHE* 2.9 28.8 + - - +
297A PHE* 3.7 14.2 - - + -
299A ASP* 3.6 23.6 - - - +
322A ALA* 4.1 12.6 - - + -
330A PRO* 6.3 1.8 - - + -
332A TYR* 4.7 1.6 + - + -
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Residues in contact with PHE 220 (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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197A VAL* 4.0 16.2 - - + -
198A ILE 4.3 2.2 - - - -
199A TYR* 3.7 31.6 - + + -
216A GLU* 3.2 27.4 - - + -
217A SER* 3.3 23.7 + - - +
219A ALA* 1.3 75.8 - - - +
221A VAL* 1.3 58.7 + - - +
223A PHE* 3.2 2.3 + + - +
224A LEU* 3.0 71.4 + - + +
268A VAL* 4.1 12.8 - - + -
269A SER* 5.9 0.2 - - - -
270A THR* 4.3 7.6 - - + -
297A PHE* 3.1 51.8 - + + -
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Residues in contact with VAL 221 (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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216A GLU* 3.5 24.9 - - + +
217A SER 3.2 15.3 + - - +
218A PRO* 3.8 8.7 - - + +
220A PHE* 1.3 77.0 - - - +
222A GLU* 1.3 62.2 + - - +
223A PHE 3.3 0.3 + - - -
224A LEU* 3.3 14.3 + - - +
225A GLU* 3.5 26.7 + - - +
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Residues in contact with GLU 222 (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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218A PRO 3.4 10.1 + - - +
219A ALA* 3.4 14.5 + - - +
220A PHE 3.4 0.4 - - - -
221A VAL* 1.3 79.2 - - - +
223A PHE* 1.3 59.9 + - - +
225A GLU* 3.4 27.7 - - - +
226A PHE* 3.5 12.3 + - - +
330A PRO* 3.4 36.9 - - - +
332A TYR* 3.5 11.1 + - - -
357A LYS* 3.5 29.1 + - - +
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Residues in contact with PHE 223 (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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197A VAL* 4.9 6.1 - - + -
219A ALA 2.9 18.2 + - - +
220A PHE 3.4 4.7 - - - +
221A VAL 3.2 0.2 - - - -
222A GLU* 1.3 76.8 - - - +
224A LEU* 1.3 75.6 + - + +
226A PHE* 3.4 23.1 - + - -
227A LEU* 3.0 59.6 + - + +
295A VAL* 4.4 16.8 - - + -
297A PHE* 3.6 38.4 - + + -
320A VAL* 3.9 21.1 - - + -
332A TYR* 4.1 20.4 + + - +
361A PHE* 4.5 6.3 - + - -
365A LEU* 4.3 8.3 - - + -
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Residues in contact with LEU 224 (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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197A VAL* 4.6 7.4 - - + -
216A GLU* 4.6 2.2 - - + +
220A PHE* 3.0 58.1 + - + +
221A VAL* 3.3 6.7 + - - +
223A PHE* 1.3 95.0 - - + +
225A GLU* 1.3 58.0 + - - +
227A LEU* 4.0 5.9 - - + +
228A GLY 3.1 23.6 + - - +
230A LYS* 5.7 2.4 - - + +
255A VAL* 4.0 23.7 - - + +
268A VAL* 3.9 22.7 - - + -
271A LYS* 4.0 26.2 - - - +
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Residues in contact with GLU 225 (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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221A VAL* 3.5 23.0 + - - +
222A GLU* 3.4 27.5 - - - +
224A LEU* 1.3 76.7 - - - +
226A PHE* 1.3 62.2 + - + +
228A GLY 3.0 18.3 - - - +
229A GLN* 5.0 0.7 - - - -
230A LYS* 3.5 31.4 + - - +
357A LYS* 5.4 2.9 + - - +
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Residues in contact with PHE 226 (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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222A GLU 3.5 13.2 + - - +
223A PHE* 3.4 28.5 + + - -
224A LEU 3.3 0.2 - - - -
225A GLU* 1.3 81.7 - - - +
227A LEU* 1.3 79.7 - - + +
228A GLY* 3.5 0.5 + - - -
332A TYR* 4.7 7.6 - + - -
357A LYS* 3.1 42.8 - - - +
358A GLY* 3.3 20.4 - - - -
359A PRO* 5.1 0.4 - - + -
361A PHE* 3.3 39.3 - + - -
362A GLN* 3.5 37.4 - - + +
365A LEU* 5.5 2.9 - - + -
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Residues in contact with LEU 227 (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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197A VAL* 5.6 4.7 - - + -
223A PHE* 3.0 47.7 + - + +
224A LEU* 4.0 6.7 - - + +
225A GLU 3.5 0.2 - - - -
226A PHE* 1.3 87.7 - - + +
228A GLY* 1.3 59.8 + - - +
255A VAL* 3.6 16.6 - - + -
257A CYS* 3.9 11.4 - - - -
266A PHE* 3.4 46.7 - - + -
295A VAL* 4.9 5.8 - - + -
362A GLN* 3.6 21.5 - - + +
365A LEU* 3.8 19.7 - - + -
366A LEU* 4.6 4.6 - - + +
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Residues in contact with GLY 228 (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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224A LEU 3.1 13.4 + - - +
225A GLU* 3.0 22.5 - - - +
226A PHE 3.3 1.0 - - - -
227A LEU* 1.3 82.8 - - - +
229A GLN* 1.3 64.2 + - - -
230A LYS 3.8 0.5 + - - -
255A VAL* 3.8 13.9 - - - +
256A TYR 4.2 4.9 - - - -
257A CYS* 4.3 8.7 - - - -
362A GLN* 5.2 1.6 - - - -
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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