Contacts of the helix formed by residues 222 - 234 (chain A) in PDB entry 1NBF
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LYS 4.2 3.1 + - - -
218A ASN* 3.1 10.0 + - - +
219A GLN* 3.0 37.7 + - + +
221A ALA* 1.3 77.1 - - - +
223A CYS* 1.3 65.3 + - - +
224A TYR* 3.1 18.2 - - + +
225A MET* 2.9 37.1 + - + +
226A ASN* 3.0 15.2 + - - -
276A THR* 4.6 0.2 + - - -
280A THR* 4.8 2.9 - - + -
290A SER* 3.7 28.7 - - - +
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Residues in contact with CYS 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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218A ASN* 4.0 2.0 - - - +
221A ALA 3.4 0.2 - - - -
222A THR* 1.3 71.5 - - - +
224A TYR* 1.3 62.5 + - - +
226A ASN* 3.2 2.4 + - - +
227A SER* 3.0 28.8 + - - -
464A HIS* 3.6 8.7 - - + -
465A TYR* 3.3 35.7 - - - +
482A ASP* 3.3 24.0 - - - +
375D GLY 3.6 0.7 - - - -
376D GLZ 1.9 68.6 + - - +
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Residues in contact with TYR 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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221A ALA 3.0 28.9 - - - -
222A THR* 3.7 11.8 - - + +
223A CYS* 1.3 82.1 - - - +
225A MET* 1.3 82.2 + - + +
227A SER* 3.8 0.3 + - - -
228A LEU* 3.4 8.1 + - - +
285A TRP* 3.2 35.8 - + - -
289A ASP 4.8 1.0 + - - -
292A MET 3.7 12.7 + - - -
294A HIS* 3.2 48.9 + - + +
295A ASP 4.6 0.9 - - - -
296A VAL* 3.2 28.0 - - - +
299A LEU* 3.9 28.4 - - + +
465A TYR* 3.6 23.8 - - + -
375D GLY 3.3 10.3 - - - +
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Residues in contact with MET 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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219A GLN* 4.2 0.2 - - - +
222A THR* 2.9 22.7 + - - +
224A TYR* 1.3 95.3 - - + +
226A ASN* 1.3 62.6 + - - +
228A LEU* 3.4 2.8 + - - +
229A LEU* 3.0 43.9 + - + +
276A THR* 3.0 41.7 - - + +
279A LEU* 4.1 9.2 - - + -
280A THR* 3.8 28.3 - - + -
283A PHE* 4.1 20.0 - - + -
285A TRP* 5.2 0.4 - - - -
299A LEU* 3.7 19.5 - - + +
303A LEU* 6.2 1.1 - - + -
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Residues in contact with ASN 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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216A LEU* 3.4 52.4 + - + +
217A LYS 3.4 16.9 + - - +
218A ASN* 4.0 4.0 - - - +
222A THR* 3.0 14.9 + - - +
223A CYS* 3.7 5.8 - - - +
225A MET* 1.3 79.1 - - - +
227A SER* 1.3 65.3 + - - +
229A LEU* 3.3 1.0 + - - +
230A GLN* 3.1 24.6 + - + +
276A THR* 4.0 12.6 - - - +
482A ASP* 2.9 31.1 + - - +
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Residues in contact with SER 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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223A CYS 3.0 16.5 + - - -
224A TYR 4.0 4.7 - - - -
226A ASN* 1.3 77.1 - - - +
228A LEU* 1.3 62.4 + - - +
230A GLN* 3.4 0.4 + - - -
231A THR* 2.8 29.0 + - - -
296A VAL* 4.7 1.3 - - - -
454A LEU* 4.3 11.4 - - - -
465A TYR* 3.6 28.9 + - - +
466A VAL* 3.6 9.3 + - - -
467A VAL* 3.8 27.3 + - - +
480A PHE 5.0 1.1 + - - -
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Residues in contact with LEU 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 TYR 3.4 11.8 + - - +
225A MET 3.4 8.0 + - - +
226A ASN 3.3 0.4 - - - -
227A SER* 1.3 79.7 - - - +
229A LEU* 1.3 58.0 + - + +
231A THR* 3.1 14.9 + - + -
232A LEU* 2.8 59.7 + - + +
296A VAL* 3.9 21.2 - - + +
299A LEU* 3.8 21.8 - - + -
300A CYS* 4.0 32.8 - - + -
303A LEU* 3.8 16.8 - - + -
454A LEU* 4.7 0.9 - - + -
515A MET* 4.8 7.0 - - + -
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Residues in contact with LEU 229 (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 LEU* 3.8 13.7 - - + -
225A MET* 3.0 33.1 + - + +
226A ASN* 3.7 4.7 - - - +
227A SER 3.3 0.2 - - - -
228A LEU* 1.3 74.8 - - + +
230A GLN* 1.3 59.7 + - - +
232A LEU* 4.5 5.2 - - + +
233A PHE* 2.8 32.5 + - - +
260A LEU* 3.7 30.7 - - + -
263A VAL* 4.4 11.2 - - + -
264A PHE* 4.1 12.3 - - + -
267A LEU* 5.0 1.6 - - + -
276A THR* 4.1 19.5 - - + -
279A LEU* 3.6 26.5 - - + -
303A LEU* 5.0 12.6 - - + -
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Residues in contact with GLN 230 (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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214A VAL 3.3 22.0 + - - +
215A GLY* 3.9 4.6 - - - -
216A LEU* 3.3 28.8 - - + +
226A ASN* 3.1 20.0 + - + +
227A SER 3.8 4.5 - - - +
229A LEU* 1.3 76.5 - - - +
231A THR* 1.3 64.9 + - - +
233A PHE* 3.6 2.6 - - - +
234A PHE* 3.0 52.3 + - - +
267A LEU* 3.7 13.9 - - - +
467A VAL* 4.0 4.3 - - + -
469A LEU* 4.0 16.6 - - + -
480A PHE* 3.5 29.6 - - + +
482A ASP 5.1 0.8 + - - -
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Residues in contact with THR 231 (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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227A SER 2.8 16.5 + - - -
228A LEU* 3.1 23.5 + - + +
230A GLN* 1.3 81.0 - - - +
232A LEU* 1.3 64.0 + - + +
234A PHE* 3.8 3.5 + - - +
235A THR* 2.8 22.6 + - - +
403A HIS* 4.7 5.6 - - - +
451A HIS* 5.1 1.9 + - - -
452A ALA* 4.7 4.0 - - + -
454A LEU* 3.6 12.0 - - + +
467A VAL* 3.5 18.5 - - - +
469A LEU* 4.4 11.5 - - + +
515A MET* 5.0 1.8 - - + -
517A VAL* 3.9 30.4 - - + +
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Residues in contact with LEU 232 (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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228A LEU* 2.8 54.8 + - + +
229A LEU* 4.2 6.7 - - + +
231A THR* 1.3 77.0 - - + +
233A PHE* 1.3 65.4 + - - +
234A PHE 3.2 0.7 - - - -
235A THR* 3.1 23.8 + - - +
238A LEU* 4.0 26.2 - - + +
239A ARG 4.6 2.1 + - - -
260A LEU* 6.1 3.6 - - + -
264A PHE* 4.2 13.5 - - + -
300A CYS* 5.0 0.9 - - - -
303A LEU* 4.5 11.4 - - + -
304A LEU* 4.3 25.1 - - + -
324A PHE* 4.5 11.0 - - + -
403A HIS* 4.5 12.8 - - + +
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Residues in contact with PHE 233 (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 TYR* 5.5 1.8 - + - -
229A LEU 2.8 19.8 + - - +
230A GLN* 3.2 5.1 + - - +
232A LEU* 1.3 78.6 - - - +
234A PHE* 1.3 97.4 + + - +
235A THR 3.3 2.9 + - - -
236A ASN* 3.9 0.3 - - - +
239A ARG* 2.9 71.1 + - - +
264A PHE* 3.3 49.0 - + + -
267A LEU* 3.6 38.8 - - + -
268A GLN* 3.7 13.7 - - + -
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Residues in contact with PHE 234 (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 TYR* 3.5 47.3 - + + -
230A GLN* 3.0 40.1 + - - +
231A THR 4.1 0.7 - - - +
232A LEU 3.2 0.2 - - - -
233A PHE* 1.3 99.3 - + - +
235A THR* 1.3 55.6 + - - +
236A ASN* 3.1 20.7 + - - +
239A ARG* 4.1 8.3 - - - -
451A HIS* 3.2 19.7 + - + -
469A LEU* 3.8 28.5 - - + -
471A PRO* 3.6 22.4 - - + +
480A PHE* 3.4 23.1 - + - -
528A LEU* 3.4 7.3 - - - +
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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