Contacts of the helix formed by residues 276 - 284 (chain E) 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 276 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216E LEU* 3.5 18.8 - - + -
219E GLN* 2.9 16.2 + - - +
222E THR* 4.6 5.2 - - - +
225E MET* 2.9 26.2 - - + +
226E ASN* 4.6 3.4 + - - +
229E LEU* 3.3 31.9 - - + -
263E VAL* 4.8 4.7 - - + -
274E VAL 5.0 0.2 - - - +
275E GLY* 1.3 78.3 - - - +
277E LYS* 1.3 64.8 + - - +
278E LYS 3.1 3.1 - - - +
279E LEU* 3.0 22.9 + - + +
280E THR* 3.2 15.0 + - - +
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Residues in contact with LYS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E GLN* 3.0 41.0 + - - +
275E GLY 3.6 1.6 - - - -
276E THR* 1.3 77.1 - - - +
278E LYS* 1.3 67.4 + - + +
280E THR* 2.6 32.2 + - + +
281E LYS* 3.6 15.5 + - + +
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Residues in contact with LYS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E SER* 5.7 3.6 + - - -
253E SER* 4.4 10.2 - - - +
259E ALA* 3.9 11.7 - - + +
262E ARG* 2.8 48.0 - - - +
275E GLY 5.4 0.8 + - - +
276E THR* 3.1 0.8 - - - -
277E LYS* 1.3 84.6 - - + +
279E LEU* 1.3 63.4 + - - +
280E THR 3.4 0.2 - - - -
281E LYS* 3.8 20.0 + - + +
282E SER* 3.2 20.4 + - - -
547E GLU* 4.6 5.9 + - - -
551E GLU* 3.3 24.4 + - - -
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Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E MET* 4.6 8.1 - - + -
229E LEU* 3.5 44.0 - - + -
256E VAL* 5.1 2.2 - - + -
259E ALA* 4.4 15.8 + - + +
260E LEU* 4.7 11.2 - - + +
263E VAL* 3.7 24.6 - - + +
276E THR* 3.0 18.4 + - + +
278E LYS* 1.3 77.2 - - - +
280E THR* 1.3 64.8 + - - +
282E SER* 2.9 22.5 - - - +
283E PHE* 3.0 41.4 - - + -
303E LEU* 4.2 13.2 - - + -
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Residues in contact with THR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E GLN* 5.6 2.5 - - + +
222E THR* 4.6 10.8 - - + -
225E MET* 4.7 3.8 - - + -
276E THR* 3.5 13.2 - - - +
277E LYS* 2.6 34.9 + - + +
279E LEU* 1.3 78.4 - - - +
281E LYS* 1.3 65.6 + - - +
283E PHE* 3.7 7.5 + - - -
284E GLY 3.0 18.4 + - - -
285E TRP 3.2 32.4 + - - +
286E GLU* 3.6 11.3 - - - +
291E PHE* 4.3 17.9 - - + -
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Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E SER* 4.3 22.9 + - - +
254E LYS* 5.4 1.0 - - - +
277E LYS* 3.6 15.6 + - + +
278E LYS* 3.9 24.7 - - + +
279E LEU 3.3 0.4 - - - -
280E THR* 1.3 81.3 + - - +
282E SER* 1.3 69.0 + - - +
284E GLY* 3.0 12.5 + - - -
286E GLU* 2.7 36.7 + - + +
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Residues in contact with SER 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253E SER 3.5 15.2 + - - -
254E LYS* 4.1 15.2 - - - +
256E VAL* 2.9 44.1 + - - +
259E ALA* 3.7 11.9 - - - -
278E LYS 3.2 12.6 + - - -
279E LEU* 2.9 16.5 + - - -
281E LYS* 1.3 80.6 - - - +
283E PHE* 1.3 62.2 + - - -
284E GLY 3.4 0.2 + - - -
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Residues in contact with PHE 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225E MET* 4.1 23.6 - - - -
256E VAL* 4.7 10.3 - - + -
279E LEU* 3.0 55.1 + - + -
280E THR* 4.4 3.1 - - - -
282E SER* 1.3 80.3 - - - +
284E GLY* 1.3 57.7 + - - +
285E TRP* 3.4 68.9 + + + -
291E PHE* 4.4 0.7 - + - -
299E LEU* 4.4 14.1 - - + -
302E VAL* 4.0 27.4 - - + -
303E LEU* 4.0 12.8 - - + -
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Residues in contact with GLY 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E THR 3.0 4.3 + - - -
281E LYS 3.0 15.0 + - - -
282E SER 3.3 0.4 + - - -
283E PHE* 1.3 77.4 - - - +
285E TRP* 1.3 52.0 + - - +
286E GLU* 2.5 34.5 + - - +
287E THR* 4.3 6.6 + - - +
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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