Contacts of the helix formed by residues 273 - 294 (chain C) in PDB entry 2YVC
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 ARG 273 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LYS* 5.5 4.4 - - - +
55C TYR* 3.2 41.7 + - - -
252C ASP 4.7 0.3 - - - +
253C LYS* 4.2 9.0 - - - +
271C ALA* 4.0 5.9 - - - +
272C PRO* 1.3 92.1 - - - +
274C LEU* 1.3 67.8 + - - +
275C ARG* 4.0 16.2 - - + +
276C ILE* 3.3 36.4 + - + +
277C ASN* 3.8 2.8 + - - +
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Residues in contact with LEU 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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250C PHE* 4.1 13.7 - - + -
252C ASP* 3.2 46.1 + - - +
253C LYS* 4.2 5.8 - - - +
273C ARG* 1.3 68.0 - - - +
275C ARG* 1.3 59.3 + - + +
276C ILE 2.7 16.5 + - - -
277C ASN* 2.8 19.1 + - - +
278C LYS* 3.3 29.7 + - + +
6F GLN* 3.5 40.4 - - + +
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Residues in contact with ARG 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C TYR* 5.3 1.6 + - - -
51C ASP* 2.6 30.1 + - - -
55C TYR* 3.5 25.2 - - + +
57C THR* 3.5 28.1 + - - +
60C LYS* 5.1 6.1 - - - +
273C ARG* 3.4 17.2 - - + +
274C LEU* 1.3 81.1 - - + +
276C ILE* 1.3 57.7 + - + +
278C LYS* 3.9 23.4 - - + +
279C ARG* 3.2 37.9 + - - +
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Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 5.4 3.6 - - + -
206C PHE* 4.0 20.4 - - + -
207C GLU 5.7 0.4 - - - +
208C ILE* 5.6 0.2 - - + -
271C ALA* 3.8 18.2 - - + -
272C PRO* 4.6 11.0 - - + -
273C ARG* 3.4 43.1 - - + +
274C LEU 2.7 6.5 + - - -
275C ARG* 1.3 73.9 - - + +
277C ASN* 1.3 54.2 + - - +
279C ARG* 2.8 28.6 + - - +
280C ILE* 2.8 46.6 + - + +
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Residues in contact with ASN 277 (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 31.7 - - + +
252C ASP 3.8 1.9 - - - +
253C LYS* 3.2 34.7 + - - -
255C PHE* 3.3 32.0 + - + +
269C PHE* 4.2 1.2 - - - -
271C ALA* 3.4 23.0 - - - +
273C ARG 4.9 0.2 - - - -
274C LEU 2.8 14.0 + - - +
276C ILE* 1.3 74.3 - - - +
278C LYS* 1.3 55.4 + - - +
280C ILE* 3.7 10.0 - - - +
281C LEU* 3.0 31.5 + - - +
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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
----------------------------------------------------------
250C PHE* 3.4 31.4 - - + -
274C LEU* 3.3 26.3 + - + +
275C ARG* 3.9 25.8 - - + +
276C ILE 3.2 0.2 - - - -
277C ASN* 1.3 75.6 - - - +
279C ARG* 1.3 57.9 + - - +
281C LEU* 3.8 1.1 - - - +
282C ALA* 3.1 32.1 + - - +
6F GLN* 3.7 36.4 + - - +
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Residues in contact with ARG 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TYR* 3.5 34.2 - - - +
56C SER* 2.8 32.6 + - - +
57C THR* 4.0 11.3 + - - +
58C TRP* 5.0 17.1 - - + +
206C PHE* 4.4 19.7 - - + -
275C ARG* 3.2 23.5 + - - +
276C ILE* 2.8 27.4 + - - +
278C LYS* 1.3 78.5 - - - +
280C ILE* 1.3 64.3 + - - +
282C ALA* 4.1 4.1 - - - +
283C LEU* 3.3 21.6 + - + +
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Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C PHE* 3.7 42.0 - - + -
208C ILE* 4.9 1.6 - - + -
218C LEU* 3.7 28.0 - - + -
220C VAL* 4.1 4.7 - - + -
225C LEU* 5.3 0.4 - - + -
255C PHE* 4.1 15.3 - - + -
269C PHE* 4.3 10.1 - - + -
276C ILE* 2.8 28.9 + - + +
277C ASN* 3.7 20.2 - - - +
278C LYS 3.2 0.2 - - - -
279C ARG* 1.3 74.0 - - - +
281C LEU* 1.3 70.6 + - - +
283C LEU* 2.7 17.5 + - - +
284C CYS* 2.9 27.9 + - - -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 3.5 36.5 - - + +
249C SER* 4.6 2.0 - - - -
250C PHE* 3.7 21.8 - - + -
255C PHE* 4.1 8.6 - - + -
277C ASN 3.0 15.5 + - - +
278C LYS* 3.8 2.9 - - - +
280C ILE* 1.3 78.7 - - - +
282C ALA* 1.3 66.2 + - + +
284C CYS* 3.1 14.3 + - - +
285C MET* 3.2 27.7 + - + +
8F ASP* 3.2 26.9 - - - +
10F THR* 3.5 25.1 - - + +
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Residues in contact with ALA 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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83C LYS* 5.4 10.6 + - - +
84C PHE* 5.3 0.9 - - - -
278C LYS 3.1 16.7 + - - +
279C ARG* 4.1 5.8 - - - +
281C LEU* 1.3 86.1 - - + +
283C LEU* 1.3 62.6 + - - +
285C MET* 3.4 14.4 + - + +
286C GLY* 3.1 19.9 + - - -
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 5.9 1.3 - - - +
83C LYS* 4.0 39.0 - - + +
84C PHE* 3.9 10.0 - - + -
204C ASN* 3.4 42.4 - - + +
206C PHE* 4.1 15.9 - - + -
220C VAL* 4.3 13.4 - - + +
279C ARG* 3.3 12.0 + - + +
280C ILE 2.7 14.3 + - - +
282C ALA* 1.3 75.9 - - - +
284C CYS* 1.3 56.6 + - - +
286C GLY 3.7 0.4 + - - +
287C ASN* 3.0 49.0 + - - +
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Residues in contact with CYS 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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220C VAL* 3.9 9.9 - - - -
225C LEU* 3.6 29.6 - - - -
242C TRP* 3.5 18.2 - - + -
248C ILE* 4.2 22.0 - - + -
255C PHE* 5.2 0.2 - - - -
280C ILE* 2.9 34.8 + - - -
281C LEU* 3.4 8.5 - - - +
283C LEU* 1.3 74.9 - - - +
285C MET* 1.3 66.1 + - - +
287C ASN 3.1 1.6 + - - -
288C HIS* 2.9 26.5 + - - +
12F ILE* 5.0 1.1 - - - -
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Residues in contact with MET 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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28B GLN* 5.0 11.7 - - - +
248C ILE* 5.3 1.1 - - + +
281C LEU* 3.2 24.8 + - + +
282C ALA* 3.6 16.2 - - + +
284C CYS* 1.3 76.6 - - + +
286C GLY* 1.3 66.8 + - - +
288C HIS* 3.2 6.6 + - - +
289C GLU* 2.8 26.7 + - - +
8F ASP* 5.6 0.2 - - - +
10F THR* 3.8 37.0 - - + +
12F ILE* 5.3 3.5 - - + +
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Residues in contact with GLY 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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84C PHE* 3.3 28.3 - - - -
282C ALA 3.1 10.8 + - - -
285C MET* 1.3 80.4 - - - +
287C ASN* 1.3 61.3 + - - +
289C GLU* 3.4 7.2 - - - +
290C LEU* 3.1 25.4 + - - +
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Residues in contact with ASN 287 (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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83C LYS 5.0 0.7 - - - +
84C PHE* 3.2 28.3 - - - +
85C PHE 5.1 3.8 + - - +
204C ASN* 5.5 0.9 - - - +
220C VAL* 4.7 4.3 - - + +
221C ASP 3.2 9.8 + - - +
222C ALA* 3.0 37.8 - - - +
242C TRP* 3.6 21.5 - - + -
283C LEU* 3.0 37.2 + - - +
284C CYS* 3.1 0.4 + - - -
286C GLY* 1.3 74.4 - - - +
288C HIS* 1.3 56.5 + - - +
290C LEU* 3.4 7.6 + - - +
291C TYR* 2.9 26.3 + - - +
294C ARG* 5.0 1.3 + - - +
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Residues in contact with HIS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C TRP* 3.7 22.6 - - + -
284C CYS 2.9 16.7 + - - +
285C MET* 3.5 5.4 - - - +
287C ASN* 1.3 72.9 - - - +
289C GLU* 1.3 58.7 + - - +
291C TYR* 2.7 43.9 + + - +
292C MET* 2.7 52.6 + - + +
11F ASP 4.9 3.1 + - - -
12F ILE* 2.6 52.1 + - + +
13F ASN* 5.2 6.1 - - - -
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Residues in contact with GLU 289 (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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28B GLN* 5.7 4.3 + - - +
31B ASP* 5.7 1.4 - - - +
285C MET 2.8 21.7 + - - +
286C GLY* 3.4 7.6 - - - +
288C HIS* 1.3 73.1 - - - +
290C LEU* 1.3 61.7 - - + +
292C MET* 3.1 23.7 + - - +
293C ARG* 2.8 61.9 + - - +
296C LYS* 4.9 3.5 + - - -
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Residues in contact with LEU 290 (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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43C TRP* 3.7 45.1 - - + +
44C PHE* 4.7 3.8 - - + -
84C PHE* 4.6 25.6 - - + -
286C GLY* 3.1 17.8 + - - +
287C ASN* 3.5 11.7 - - - +
289C GLU* 1.3 82.9 - - + +
291C TYR* 1.3 61.2 + - - +
293C ARG* 3.5 18.4 + - + +
294C ARG* 3.2 52.0 + - - +
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Residues in contact with TYR 291 (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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87C GLU* 3.8 12.8 - - - -
222C ALA 4.0 7.4 - - - +
223C LEU* 5.1 7.6 - - + -
242C TRP* 3.4 44.0 - + + +
243C SER* 4.2 19.4 + - - -
287C ASN 2.9 14.0 + - - +
288C HIS* 2.7 31.4 + + - +
290C LEU* 1.3 72.7 - - - +
292C MET* 1.3 64.8 + - + -
294C ARG* 3.9 6.2 + - - +
295C ARG* 3.1 78.2 + - - +
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Residues in contact with MET 292 (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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35B LYS* 4.5 12.1 - - - +
288C HIS* 2.7 55.6 + - + +
289C GLU* 3.6 28.9 - - - +
291C TYR* 1.3 77.5 - - + +
293C ARG* 1.3 65.8 + - - +
294C ARG 3.3 0.4 - - - -
295C ARG* 3.1 15.5 + - - +
296C LYS* 3.3 44.3 + - - +
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 3.8 51.6 - - - +
289C GLU* 2.8 41.9 + - - +
290C LEU* 3.8 16.9 - - + +
291C TYR 3.5 0.2 - - - -
292C MET* 1.3 78.6 - - - +
294C ARG* 1.3 57.5 + - - +
295C ARG 3.2 4.0 + - - -
296C LYS* 3.5 23.1 + - + +
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Residues in contact with ARG 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 4.2 13.1 - - - -
85C PHE 4.0 13.5 + - - -
87C GLU* 2.6 44.4 + - - +
92C GLU* 2.7 49.0 + - - +
222C ALA* 4.0 10.7 + - - +
287C ASN* 5.0 1.0 + - - +
290C LEU* 3.2 44.0 + - + +
291C TYR* 3.9 9.4 - - - +
292C MET 3.3 0.2 - - - -
293C ARG* 1.3 74.9 - - + +
295C ARG* 1.3 62.0 + - - +
296C LYS 3.6 0.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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