Contacts of the helix formed by residues 265 - 284 (chain A) in PDB entry 3ROT
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 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.0 26.1 + - - +
264A GLN* 1.3 81.7 - - - +
266A PRO* 1.3 69.3 - - - +
267A PHE* 3.3 3.4 - - - -
268A LEU* 3.2 28.6 + - + +
269A MSE 3.1 17.3 + - - +
292A THR* 3.0 23.1 - - - +
293A ALA 4.5 1.0 - - - +
294A MSE 3.9 27.0 + - + +
231B ARG* 6.2 0.4 - - - +
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Residues in contact with PRO 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.5 52.5 - - + +
39A SER* 3.5 21.3 - - - +
40A LEU* 3.1 20.0 - - + +
244A ASP* 5.5 1.8 - - + +
263A ASP* 4.0 7.9 - - - +
264A GLN* 3.6 3.8 - - - +
265A GLN* 1.3 85.7 - - - +
267A PHE* 1.3 57.8 + - - +
269A MSE 3.9 11.2 - - + -
270A GLY 2.8 26.2 + - - -
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Residues in contact with PHE 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 3.5 25.4 + - - +
42A GLN* 3.9 6.3 - - + -
43A GLY* 3.5 30.2 - - - -
46A LYS* 4.3 16.2 - - + -
265A GLN 3.3 1.0 - - - -
266A PRO* 1.3 80.3 - - - +
268A LEU* 1.3 62.6 + - + +
270A GLY 3.3 0.9 + - - -
271A TYR* 2.9 41.0 + + + +
231B ARG* 3.7 67.8 - - + +
232B TYR* 5.9 1.1 - + - -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A GLN* 3.2 40.9 + - + +
267A PHE* 1.3 82.0 - - + +
269A MSE 1.3 61.9 + - - +
271A TYR* 4.4 5.6 - - + -
272A LEU* 2.8 67.2 + - + +
290A ILE* 6.1 0.9 - - + -
292A THR* 4.3 17.0 - - + +
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Residues in contact with MSE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.3 27.1 - - - +
40A LEU* 3.6 13.5 - - + -
111A VAL* 4.6 4.7 - - + -
112A ASP* 3.6 28.0 - - - +
127A LEU* 3.5 28.0 - - + +
128A GLY* 4.0 6.5 - - - -
264A GLN* 3.4 26.7 - - + +
265A GLN 3.1 5.9 + - - +
266A PRO* 3.2 13.7 - - + +
268A LEU* 1.3 76.4 - - - +
270A GLY* 1.3 62.2 - - - +
272A LEU 4.0 0.2 - - - -
273A SER* 3.0 27.7 + - - -
292A THR* 3.4 31.1 - - + +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.5 0.9 - - - -
40A LEU* 3.3 30.9 - - - +
44A ALA* 3.6 19.0 - - - -
266A PRO 2.8 11.3 + - - -
267A PHE 3.7 1.6 - - - -
269A MSE 1.3 76.2 - - - +
271A TYR* 1.3 63.5 + - - +
273A SER* 3.1 20.4 + - - -
274A ILE 3.3 5.5 + - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 3.2 25.3 - - - +
46A LYS* 4.1 7.4 - - + -
47A ALA* 3.5 24.1 - - + +
50A GLU* 2.9 34.8 + - - +
51A LEU* 5.8 2.6 - - + +
267A PHE* 2.9 38.1 + + + +
268A LEU* 3.8 8.7 - - + +
270A GLY* 1.3 72.1 - - - +
272A LEU* 1.3 74.5 + - + +
275A THR* 2.8 44.8 + - + -
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.6 14.1 - - + -
268A LEU* 2.8 52.9 + - + +
271A TYR* 1.3 84.3 - - + +
273A SER* 1.3 64.9 + - - +
275A THR* 3.6 11.4 - - + -
276A GLN* 3.0 30.8 + - + +
290A ILE* 4.1 31.9 - - + -
292A THR* 5.1 1.1 - - + -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.2 3.5 - - - +
44A ALA* 5.4 0.5 - - - +
85A ALA* 4.0 12.0 - - - +
109A ILE* 4.0 5.5 - - - +
111A VAL* 3.6 28.2 - - - +
127A LEU* 3.5 17.4 - - - +
269A MSE 3.0 16.0 + - - -
270A GLY* 3.1 13.2 + - - -
272A LEU* 1.3 74.4 - - - +
274A ILE* 1.3 73.5 + - - +
276A GLN* 3.4 3.3 + - - +
277A LEU* 3.2 26.8 + - - +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.7 14.1 - - + -
26A TYR 4.9 4.5 - - - +
27A LEU* 5.0 3.6 - - + -
44A ALA* 3.7 29.6 - - + +
47A ALA* 4.0 12.6 - - + -
48A ALA* 4.1 26.2 - - + +
51A LEU* 4.9 0.7 - - + -
53A VAL* 4.5 4.9 - - + -
55A LEU* 3.7 17.7 - - + -
85A ALA* 4.8 7.9 - - + -
270A GLY 3.3 4.6 + - - +
273A SER* 1.3 87.1 + - - +
275A THR* 1.3 62.8 + - - +
277A LEU* 3.2 20.3 + - + +
278A VAL* 3.0 35.0 + - + +
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Residues in contact with THR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.9 5.4 - - - +
51A LEU* 3.8 20.4 - - + +
271A TYR* 2.8 42.5 + - + -
272A LEU* 3.6 16.8 - - + -
273A SER 3.2 0.2 - - - -
274A ILE* 1.3 77.5 - - - +
276A GLN* 1.3 58.3 + - + +
278A VAL* 3.3 2.6 + - - +
279A LEU* 2.9 48.6 + - + +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 4.1 5.6 - - + -
125A VAL* 4.4 2.2 - - - +
127A LEU* 3.8 16.4 - - - +
272A LEU* 3.0 22.0 + - + +
273A SER 3.9 3.8 - - - +
274A ILE 3.3 0.2 - - - -
275A THR* 1.3 75.9 - - + +
277A LEU* 1.3 67.0 + - - +
279A LEU* 3.9 11.2 - - + +
280A MSE 2.9 26.2 + - - +
286A ASN 4.9 0.3 - - - +
287A PRO* 3.3 17.8 - - + +
288A VAL* 2.8 52.2 + - - +
290A ILE* 3.3 23.3 - - + +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.8 17.7 - - + -
26A TYR 4.9 0.7 - - - +
83A GLY* 4.1 10.3 - - - -
84A ILE* 3.8 34.3 - - - +
85A ALA* 4.0 12.8 - - + +
107A PRO* 4.2 24.0 - - + +
109A ILE* 3.5 30.7 - - + -
273A SER 3.2 11.2 + - - +
274A ILE* 3.2 16.4 + - + +
276A GLN* 1.3 79.0 - - - +
278A VAL* 1.3 61.3 + - - +
280A MSE 3.4 8.6 - - - +
281A ASN* 3.1 29.5 + - - -
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Residues in contact with VAL 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.5 32.5 - - + +
51A LEU* 3.8 22.4 - - + -
53A VAL* 4.0 16.8 - - + -
274A ILE* 3.0 19.5 + - + +
275A THR 3.7 3.6 - - - +
277A LEU* 1.3 72.8 - - - +
279A LEU* 1.3 64.5 + - + +
280A MSE 3.0 1.3 - - - -
281A ASN* 3.0 4.2 + - - +
282A ARG* 2.9 67.6 + - + +
283A TYR* 6.1 0.2 - - + -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 5.8 7.0 - - + -
275A THR* 2.9 40.1 + - + +
276A GLN* 3.9 11.2 - - + +
278A VAL* 1.3 77.9 - - + +
280A MSE 1.3 57.0 + - - +
283A TYR* 2.9 63.7 + - + +
284A GLN 3.8 1.4 + - - -
285A LEU* 3.9 20.8 + - + +
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Residues in contact with MSE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A PRO* 3.7 25.8 - - + -
124A LEU* 3.2 40.6 - - + -
276A GLN 2.9 17.9 + - - +
277A LEU* 3.4 12.3 - - - +
278A VAL 3.0 0.2 - - - -
279A LEU* 1.3 80.1 - - - +
281A ASN* 1.3 61.8 + - - +
284A GLN* 3.1 25.3 + - - -
285A LEU 3.3 23.6 - - - +
286A ASN* 5.2 5.8 - - - +
287A PRO* 3.7 21.5 - - + -
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Residues in contact with ASN 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 4.5 9.9 - - - +
25A TYR* 2.7 32.9 + - - +
82A SER* 3.1 34.3 + - - +
107A PRO* 4.5 10.4 - - - +
277A LEU* 3.1 13.5 + - - +
278A VAL 3.0 2.7 + - - +
280A MSE 1.3 81.4 - - - +
282A ARG* 1.3 61.3 + - + +
284A GLN* 3.3 15.1 + - - -
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Residues in contact with ARG 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 5.6 6.1 + - - +
25A TYR* 5.9 0.2 - - - +
51A LEU* 2.4 44.2 + - - +
52A LYS* 4.0 12.1 + - - +
53A VAL* 3.5 16.2 - - - +
278A VAL* 2.9 40.0 + - + +
281A ASN* 1.3 76.1 - - + +
283A TYR* 1.3 99.1 + - + +
284A GLN* 3.7 9.4 + - - +
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Residues in contact with TYR 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A VAL* 6.1 0.2 - - + -
279A LEU* 2.9 48.0 + - + +
282A ARG* 1.3 113.0 + - + +
284A GLN* 1.3 80.6 + - - +
285A LEU* 3.2 22.6 + - + +
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Residues in contact with GLN 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A MSE 3.1 13.8 + - - +
281A ASN 3.3 24.9 + - - -
282A ARG 3.7 9.0 + - - +
283A TYR* 1.3 90.2 - - - +
285A LEU* 1.3 62.7 + - - +
286A ASN* 4.3 4.8 + - - -
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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