Contacts of the helix formed by residues 269 - 283 (chain C) in PDB entry 3P9K
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 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268C TRP* 1.3 79.1 - - - +
270C ASP* 1.3 65.0 + - - +
271C GLN* 3.7 7.6 + - - +
272C HIS* 2.8 34.1 + - - +
273C CYS* 2.9 20.4 + - - -
322C PRO 3.2 14.9 + - - -
323C GLY* 3.6 17.7 - - - -
325C ARG* 5.8 0.7 - - - +
327C ARG* 3.5 0.9 - - - +
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C SER* 1.3 73.4 - - - +
271C GLN* 1.3 57.8 + - - +
273C CYS* 3.3 5.9 + - - +
274C ALA* 2.9 28.8 + - - +
325C ARG* 4.1 9.2 - - - -
327C ARG* 2.7 40.3 + - - +
331C GLU* 5.7 1.6 - - - +
335C LEU* 4.2 17.0 - - + +
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Residues in contact with GLN 271 (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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269C SER* 3.2 8.5 + - - +
270C ASP* 1.3 76.0 - - - +
272C HIS* 1.3 68.2 + - + +
274C ALA* 3.3 11.8 + - - +
275C THR* 3.2 30.8 + - - +
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Residues in contact with HIS 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C PHE* 3.4 32.4 - + + -
268C TRP* 3.6 43.9 - + + -
269C SER* 2.8 29.9 + - - +
271C GLN* 1.3 81.7 - - + +
273C CYS* 1.3 58.0 + - - +
275C THR* 3.1 9.0 + - - -
276C LEU 2.9 23.9 + - - -
322C PRO* 4.4 8.9 + - + -
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Residues in contact with CYS 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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265C LEU* 3.5 48.7 - - + -
268C TRP* 3.7 11.0 - - - -
269C SER 2.9 19.5 + - - +
270C ASP 3.7 5.6 - - - +
272C HIS* 1.3 74.8 - - - +
274C ALA* 1.3 57.1 + - - +
276C LEU* 4.2 7.4 - - - -
277C LEU* 2.7 41.4 + - + +
327C ARG* 3.8 10.3 - - - -
335C LEU* 4.1 18.6 - - + -
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Residues in contact with ALA 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 ASP 2.9 14.7 + - - +
271C GLN* 3.4 18.6 - - - +
272C HIS 3.2 0.2 - - - -
273C CYS* 1.3 76.2 - - - +
275C THR* 1.3 62.8 + - - +
277C LEU* 4.1 3.8 - - - +
278C LYS* 3.1 25.5 + - - +
335C LEU* 4.8 8.5 - - + +
338C GLY 6.6 0.2 - - - -
339C ALA* 5.1 3.3 - - - +
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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
----------------------------------------------------------
250C PHE* 3.5 35.9 - - + +
271C GLN* 3.2 23.4 + - - +
272C HIS* 3.1 10.6 + - - -
274C ALA* 1.3 78.7 - - - +
276C LEU* 1.3 62.6 + - - +
278C LYS* 3.3 6.9 + - - +
279C ASN* 3.1 26.3 + - - +
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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
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204C VAL* 4.3 2.7 - - + -
249C MET* 3.7 44.2 - - + +
250C PHE* 4.0 12.1 - - + -
253C VAL* 4.3 2.5 - - + -
261C MET* 3.5 31.0 - - + -
264C ILE* 3.7 17.5 - - + -
265C LEU* 3.6 17.7 - - + -
268C TRP* 5.4 2.0 - - + -
272C HIS 2.9 16.8 + - - +
273C CYS* 3.6 5.6 - - - +
275C THR* 1.3 77.1 - - - +
277C LEU* 1.3 62.0 + - - +
279C ASN* 3.1 6.7 + - - +
280C CYS* 3.0 36.3 + - - -
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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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261C MET* 3.7 28.9 - - + -
265C LEU* 4.2 17.5 - - + -
273C CYS 2.7 25.3 + - - +
274C ALA* 4.2 3.1 - - - +
276C LEU* 1.3 68.8 - - - +
278C LYS* 1.3 60.6 + - - +
280C CYS* 3.2 4.3 + - - +
281C TYR* 2.9 28.8 + - - +
290C VAL* 4.6 4.9 - - + -
335C LEU* 3.8 37.7 - - + +
336C ALA* 4.7 0.4 - - - -
339C ALA* 3.6 16.4 - - + -
341C PHE* 3.8 8.1 - - + -
358C PHE* 3.9 30.3 - - + -
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Residues in contact with LYS 278 (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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274C ALA 3.1 19.7 + - - +
275C THR* 3.5 7.0 - - - +
277C LEU* 1.3 74.7 - - - +
279C ASN* 1.3 65.1 + - - +
281C TYR* 3.2 10.8 + - + +
282C ASP* 3.0 44.2 + - - +
338C GLY 4.8 6.1 + - - +
339C ALA* 4.2 27.8 + - + +
340C GLY* 5.6 1.0 - - - -
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Residues in contact with ASN 279 (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 MET 2.8 28.1 + - - +
250C PHE* 3.0 24.5 + - - +
251C LYS 3.6 14.7 - - - +
252C GLU* 4.3 6.3 - - - -
253C VAL* 3.7 12.6 + - + +
275C THR* 3.1 18.8 + - - +
276C LEU 3.1 8.3 + - - +
278C LYS* 1.3 81.2 - - - +
280C CYS* 1.3 61.5 + - - +
282C ASP* 3.5 11.3 + - - +
283C ALA* 3.2 23.4 + - - +
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Residues in contact with CYS 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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204C VAL* 4.8 0.4 - - - -
253C VAL* 4.1 6.7 - - - -
259C ILE* 3.6 29.4 - - + -
261C MET* 3.5 31.4 - - - -
276C LEU* 3.0 29.5 + - - -
277C LEU* 3.6 8.3 - - - +
279C ASN* 1.3 74.4 - - - +
281C TYR* 1.3 68.2 + - - +
283C ALA* 3.1 11.4 + - - +
284C LEU* 3.1 19.4 + - - +
290C VAL* 3.7 16.2 - - + -
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Residues in contact with TYR 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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277C LEU 2.9 14.0 + - - +
278C LYS* 3.3 14.8 - - + +
280C CYS* 1.3 78.5 - - - +
282C ASP* 1.3 74.8 + - - +
284C LEU* 3.2 4.0 + - - +
339C ALA 3.4 20.6 - - - +
340C GLY* 3.5 30.7 + - - -
341C PHE* 3.8 22.8 - + + -
360C LYS* 3.0 66.5 + - + +
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Residues in contact with ASP 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 LYS* 3.0 36.4 + - - +
279C ASN* 3.8 11.0 - - - +
280C CYS 3.2 0.2 - - - -
281C TYR* 1.3 90.1 - - - +
283C ALA* 1.3 58.3 + - - +
284C LEU 3.2 5.7 + - - +
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C VAL* 3.5 34.3 - - + +
254C PRO 3.6 7.9 - - - +
255C SER* 3.5 12.6 + - - +
256C GLY 3.2 24.9 + - - +
259C ILE* 4.4 1.6 - - + -
279C ASN 3.2 15.8 + - - +
280C CYS 3.1 5.8 + - - +
282C ASP* 1.3 75.4 - - - +
284C LEU* 1.3 59.1 + - - +
285C PRO* 4.4 0.3 - - - +
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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