Contacts of the helix formed by residues 276 - 293 (chain C) in PDB entry 2Y05
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 GLN 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A SER* 5.4 1.4 + - - +
28A GLU* 3.6 41.7 + - - +
29A LEU 4.6 0.9 - - - -
30A PRO* 4.2 20.3 - - + +
273C TYR* 2.7 42.0 + - - +
274C ARG 3.5 6.2 + - - +
275C TRP* 1.3 76.5 + - - +
277C GLY* 1.3 68.7 + - - +
279C ALA* 3.5 4.0 + - - +
280C ARG* 3.4 29.6 + - - +
1330C EDO 3.5 11.8 + - - -
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Residues in contact with GLY 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 5.9 1.2 + - - -
276C GLN* 1.3 78.4 + - - +
278C ASP* 1.3 59.0 + - - -
280C ARG* 3.3 5.2 + - - +
281C GLN* 3.1 26.1 + - - +
1330C EDO 3.6 14.1 - - - -
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Residues in contact with ASP 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LYS* 3.5 27.9 - - - +
72B VAL* 6.0 1.2 - - - +
82B GLY* 6.5 0.2 - - - -
277C GLY* 1.3 70.0 - - - -
279C ALA* 1.3 57.4 + - - +
281C GLN* 4.2 12.9 - - - +
282C LYS* 2.7 51.8 + - - +
285C LYS* 5.8 1.2 + - - -
1330C EDO 3.4 23.9 + - - +
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C PHE* 3.6 10.2 - - + -
275C TRP* 4.6 20.0 - - + -
276C GLN 3.8 5.8 - - - +
278C ASP* 1.3 76.8 - - - +
280C ARG* 1.3 62.3 + - - +
282C LYS* 3.6 10.0 + - - +
283C ALA* 3.1 23.0 + - - +
1330C EDO 3.3 14.6 + - - +
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Residues in contact with ARG 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLN* 6.1 0.6 - - - +
86C LEU* 5.3 1.6 - - - +
103C GLU* 3.2 40.3 + - - -
123C GLY* 6.3 0.4 - - - -
127C LEU* 4.0 27.0 - - + +
131C PHE* 4.4 9.6 - - + -
273C TYR* 6.4 0.4 - - - -
275C TRP 3.5 25.1 - - - +
276C GLN* 3.4 26.0 + - - +
277C GLY 3.3 10.4 + - - +
278C ASP 3.2 0.2 - - - -
279C ALA* 1.3 77.8 - - - +
281C GLN* 1.3 68.0 + - - +
283C ALA* 3.2 4.4 + - - +
284C LEU* 2.9 46.7 + - + +
1331C EDO 4.8 4.2 + - - -
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Residues in contact with GLN 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 3.9 23.6 - - - +
277C GLY 3.1 14.3 + - - +
278C ASP* 3.7 13.5 - - - +
280C ARG* 1.3 85.0 + - - +
282C LYS* 1.3 63.4 - - - +
284C LEU* 3.3 13.5 + - - +
285C LYS* 3.0 47.9 + - - +
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Residues in contact with LYS 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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40B GLU* 3.1 28.5 + - - +
41B ALA 5.7 0.2 + - - -
42B LEU* 3.8 29.3 - - + +
70B LYS* 5.8 2.2 - - - -
130C TYR* 5.1 3.8 - - - +
278C ASP* 2.7 37.7 + - - +
279C ALA* 3.8 8.5 - - - +
281C GLN* 1.3 73.6 - - - +
283C ALA* 1.3 50.4 + - - +
285C LYS* 3.3 10.3 + - - +
286C ASP* 2.8 53.7 + - - +
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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
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127C LEU* 3.5 18.4 - - + -
130C TYR* 3.6 37.8 + - + -
131C PHE* 3.7 7.0 - - + -
279C ALA 3.1 15.6 + - - +
280C ARG 3.2 7.6 + - - +
282C LYS* 1.3 75.9 - - - +
284C LEU* 1.3 58.1 + - - +
286C ASP* 3.2 2.1 + - - +
287C LEU* 2.9 35.9 + - - +
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Residues in contact with LEU 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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103C GLU* 4.6 0.2 - - - +
106C LEU* 4.0 15.9 - - + +
122C VAL* 3.8 24.0 - - + +
123C GLY 3.9 0.7 - - - +
127C LEU* 3.8 28.7 - - + -
280C ARG* 2.9 43.0 + - - +
281C GLN* 3.3 17.5 + - - +
283C ALA* 1.3 74.4 - - - +
285C LYS* 1.3 59.1 + - - +
287C LEU* 3.4 6.1 + - + +
288C LEU* 2.9 29.5 + - - +
1331C EDO 3.6 37.9 - - - +
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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
----------------------------------------------------------
106C LEU* 4.5 9.4 - - + -
108C GLU* 3.2 34.8 - - + +
278C ASP* 5.8 1.6 + - - -
281C GLN* 3.0 47.1 + - - +
282C LYS* 3.7 10.1 - - - +
284C LEU* 1.3 75.2 - - - +
286C ASP* 1.3 66.2 + - - +
288C LEU* 3.8 6.5 - - - +
289C LYS* 3.0 26.7 + - - +
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Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 6.0 0.7 - - - -
328B LYS* 3.4 35.5 + - - +
130C TYR* 2.6 37.4 + - + -
282C LYS* 2.8 35.8 + - - +
283C ALA 3.2 7.2 + - - +
285C LYS* 1.3 75.8 - - - +
287C LEU* 1.3 57.7 + - - +
289C LYS* 3.5 3.9 + - - +
290C TRP* 3.0 36.9 + - + -
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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
----------------------------------------------------------
121C THR* 3.6 25.1 - - + +
122C VAL* 4.5 4.9 - - + -
126C GLY 3.7 32.5 - - - +
127C LEU* 3.9 18.2 - - + +
130C TYR* 4.2 10.1 - - + -
157C VAL* 3.9 19.5 - - + -
161C ILE* 4.3 7.9 - - + -
283C ALA 2.9 22.2 + - - +
284C LEU* 3.7 9.2 - - + +
286C ASP* 1.3 74.5 - - - +
288C LEU* 1.3 66.1 + - - +
290C TRP* 3.3 8.7 + - + +
291C VAL* 3.0 29.7 + - - +
296C ILE* 4.0 14.2 - - + +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.1 11.9 - - + -
108C GLU* 3.7 43.3 - - + +
109C TRP* 4.7 4.5 - - + -
110C PRO* 4.0 11.2 - - + -
113C ILE* 3.7 31.2 - - + -
122C VAL* 4.1 19.6 - - + +
284C LEU 2.9 17.5 + - - +
285C LYS* 3.8 6.7 - - - +
287C LEU* 1.3 75.9 - - - +
289C LYS* 1.3 64.4 + - - +
291C VAL* 3.0 6.8 + - + +
292C LEU* 2.9 41.7 + - + +
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Residues in contact with LYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PRO* 3.7 31.5 - - + +
298B TYR* 4.6 11.3 + - - -
300B GLU* 4.6 3.3 + - - -
302B ILE* 4.5 11.2 - - + -
328B LYS* 6.0 2.9 - - - +
285C LYS 3.0 15.8 + - - +
286C ASP* 3.8 4.9 - - - +
288C LEU* 1.3 78.9 - - - +
290C TRP* 1.3 60.9 + - + +
292C LEU* 3.1 17.5 + - + +
293C GLU* 2.9 62.9 + - + +
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Residues in contact with TRP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 3.1 31.4 + - - -
328B LYS* 3.1 28.9 - - - +
130C TYR* 3.7 36.3 - + - -
134C LEU* 4.5 6.1 - - + -
161C ILE* 4.2 21.1 - - + -
164C LEU* 3.7 29.9 - - + +
165C LYS* 4.7 7.0 - - - -
286C ASP* 3.0 23.7 + - + +
287C LEU* 3.6 7.0 - - + +
288C LEU 3.3 0.2 - - - -
289C LYS* 1.3 77.9 - - + +
291C VAL* 1.3 60.5 + - - +
293C GLU* 3.4 18.4 + - - -
294C GLY 3.2 2.8 + - - -
295C LYS* 3.0 33.7 + - + +
296C ILE* 3.1 33.9 + - + +
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Residues in contact with VAL 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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113C ILE* 4.5 16.6 - - + -
117C LEU* 4.5 6.7 - - + -
121C THR* 3.9 26.0 - - + -
122C VAL* 4.2 10.5 - - + -
287C LEU 3.0 20.0 + - - +
288C LEU* 3.4 8.7 - - + +
290C TRP* 1.3 72.3 - - - +
292C LEU* 1.3 67.9 + - + +
294C GLY* 3.0 14.0 + - - -
296C ILE* 3.2 23.9 - - + +
298C TYR* 3.9 29.2 - - + -
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLU 5.6 0.9 - - - +
110C PRO* 4.0 27.6 - - + -
112C THR* 4.4 7.0 - - - +
113C ILE* 4.2 18.2 - - + -
288C LEU* 2.9 38.2 + - + +
289C LYS* 3.6 20.2 - - + +
291C VAL* 1.3 75.8 - - - +
293C GLU* 1.3 61.1 + - + +
294C GLY 3.5 0.2 + - - -
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B GLU 5.4 1.6 - - - +
302B ILE* 3.0 30.4 - - - +
304B GLU* 4.8 1.9 - - - +
289C LYS* 2.9 40.5 + - - +
290C TRP* 3.6 28.0 + - - +
291C VAL 3.2 0.2 - - - -
292C LEU* 1.3 77.8 - - - +
294C GLY* 1.3 58.2 + - - +
295C LYS* 3.0 38.1 + - + +
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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
------------------------------------------------------------
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