Contacts of the helix formed by residues 272 - 288 (chain C) in PDB entry 4NQJ
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 ASP 272 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C LYS* 2.6 35.0 + - - -
263C GLN* 5.5 2.8 + - - -
268C ASP 4.7 2.5 - - - -
271C LYS* 1.3 92.5 + - - +
273C ILE* 1.3 64.8 + - - +
274C THR* 3.0 3.8 + - - +
275C THR* 2.8 32.7 + - + +
276C LEU* 3.1 9.1 + - - +
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Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 4.2 18.4 - - + -
164A LEU* 3.9 22.9 - - + -
260C LYS* 4.0 14.4 - - + -
269C PHE* 3.6 36.2 + - + +
270C LEU* 3.3 31.3 + - + +
272C ASP* 1.3 80.4 + - - +
274C THR* 1.3 64.5 + - - +
276C LEU* 3.3 8.2 + - + -
277C LEU* 2.9 48.0 + - + +
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Residues in contact with THR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C LEU 4.9 0.4 + - - -
271C LYS 6.0 0.7 - - - -
272C ASP* 3.1 1.7 - - - -
273C ILE* 1.3 85.8 - - - +
275C THR* 1.3 71.2 + - + +
277C LEU* 3.4 6.5 + - - +
278C HIS* 3.1 44.6 + - + +
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Residues in contact with THR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASP* 2.8 33.0 + - + +
274C THR* 1.3 85.1 - - + +
276C LEU* 1.3 58.0 + - - +
278C HIS* 3.5 5.7 + - - +
279C SER* 3.0 30.3 + - - -
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.5 10.5 - - + -
256C SER* 4.1 29.2 - - - +
257C ILE* 4.9 1.3 - - - -
260C LYS* 3.5 44.6 - - + -
272C ASP* 3.1 10.8 + - - +
273C ILE* 3.7 13.9 - - + +
275C THR* 1.3 80.0 + - - +
277C LEU* 1.3 65.5 + - - +
279C SER* 3.0 10.9 + - - -
280C LEU* 3.0 41.5 + - + +
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.6 37.2 - - + +
163A GLU* 4.5 17.7 - - + +
164A LEU* 3.7 30.7 - - + -
167A GLN* 5.1 3.6 - - + +
273C ILE* 2.9 32.5 + - + +
274C THR* 3.8 6.1 - - - +
276C LEU* 1.3 77.3 - - - +
278C HIS* 1.3 67.3 + - + +
280C LEU* 3.5 8.3 + - + +
281C GLU* 3.2 30.4 + - - +
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Residues in contact with HIS 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C THR* 3.1 41.4 + - + +
275C THR* 4.0 6.1 - - - +
277C LEU* 1.3 76.1 - - + +
279C SER* 1.3 65.0 + - - +
281C GLU* 3.2 23.4 + - - +
282C GLN* 3.1 32.0 + - + +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C MET* 4.7 2.4 - - - +
275C THR 3.0 16.4 + - - -
276C LEU* 3.3 17.7 - - - -
278C HIS* 1.3 74.5 - - - +
280C LEU* 1.3 63.0 + - - +
282C GLN* 3.4 5.7 + - - +
283C GLY* 2.9 26.2 + - - -
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.8 21.3 - - + -
167A GLN* 3.6 23.3 - - + +
171A LEU* 4.4 1.3 - - + -
253C MET* 3.3 37.6 - - + +
256C SER* 5.1 1.3 - - - -
257C ILE* 3.8 37.7 - - + -
276C LEU* 3.0 29.9 + - + +
277C LEU* 3.8 8.5 - - + +
278C HIS 3.3 0.2 - - - -
279C SER* 1.3 74.4 - - - +
281C GLU* 1.3 54.9 + - - +
283C GLY 3.1 1.2 + - - -
284C MET* 2.7 40.6 + - + +
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Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 4.4 7.2 + - - +
277C LEU* 3.2 17.3 + - - +
278C HIS* 3.2 35.2 + - - +
280C LEU* 1.3 76.2 - - - +
282C GLN* 1.3 71.1 + - - +
284C MET* 3.2 12.7 + - - +
285C LYS* 3.2 33.6 + - - +
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Residues in contact with GLN 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278C HIS* 3.1 20.4 + - + +
279C SER* 3.8 5.6 - - - +
281C GLU* 1.3 77.9 - - - +
283C GLY* 1.3 66.9 + - - +
285C LYS* 3.1 42.0 + - - +
286C VAL* 3.2 18.2 + - + +
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Residues in contact with GLY 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C LEU* 4.0 14.1 - - - +
253C MET* 3.7 21.3 - - - -
279C SER 2.9 16.4 + - - -
280C LEU 3.5 3.4 - - - -
282C GLN* 1.3 73.2 - - - +
284C MET* 1.3 64.9 + - - +
286C VAL* 3.0 7.6 + - - +
287C LEU* 3.0 22.0 + - - +
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Residues in contact with MET 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLN* 4.1 26.2 - - - +
170A GLN* 4.6 13.9 - - + +
171A LEU* 3.4 44.0 - - + +
174A THR* 4.9 7.4 - - - +
285B LYS* 6.3 1.3 - - - +
253C MET* 3.7 6.4 - - + +
280C LEU 2.7 34.8 + - - +
281C GLU* 3.2 10.3 + - - +
283C GLY* 1.3 71.9 - - - +
285C LYS* 1.3 63.9 + - + +
287C LEU* 3.2 10.8 + - + +
288C ALA* 3.1 22.0 + - - +
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C GLU* 3.2 17.6 + - - +
282C GLN* 3.1 39.5 + - - +
283C GLY 3.1 0.4 - - - -
284C MET* 1.3 78.2 - - + +
286C VAL* 1.3 62.6 + - + +
288C ALA* 3.3 20.3 + - - +
289C THR* 4.0 8.1 - - - +
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C GLN* 3.0 22.5 + - + +
249C LEU* 3.9 21.1 - - + -
282C GLN 3.5 14.6 - - - +
283C GLY* 3.0 9.3 + - - +
285C LYS* 1.3 76.6 - - + +
287C LEU* 1.3 59.0 + - + +
289C THR* 3.1 18.3 + - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.6 31.4 - - + -
174A THR* 4.0 21.1 - - + -
178A LEU* 4.2 5.8 - - + +
246C GLN* 3.2 43.7 + - + +
249C LEU* 3.6 26.0 - - + -
250C ALA* 4.0 9.6 - - + -
253C MET* 3.9 14.4 - - - -
283C GLY 3.0 6.7 + - - +
284C MET* 3.2 14.5 + - + +
286C VAL* 1.3 72.2 - - - +
288C ALA* 1.3 61.9 + - - +
289C THR 3.1 3.8 + - - -
290C ARG* 2.8 28.1 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C MET 3.1 11.1 + - - +
285C LYS* 3.4 15.3 - - - +
286C VAL 3.2 0.4 - - - -
287C LEU* 1.3 77.6 - - - +
289C THR* 1.3 58.8 + - + +
290C ARG* 3.3 20.6 + - - +
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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