Contacts of the helix formed by residues 265 - 284 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ASP* 2.8 32.1 + - - +
264B GLN* 1.3 82.9 - - - +
266B PRO* 1.3 70.6 - - - +
267B PHE* 3.2 3.8 - - - +
268B LEU* 3.1 31.7 + - + +
269B MSE 3.0 17.5 + - - +
292B THR* 3.0 20.7 + - - +
293B ALA 4.2 7.9 - - - +
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Residues in contact with PRO 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 3.6 51.8 - - + +
39B SER* 3.7 18.6 - - - -
40B LEU* 3.4 19.8 - - + +
244B ASP* 5.6 1.1 - - + +
263B ASP* 4.1 5.4 - - - +
264B GLN* 3.5 3.1 - - + +
265B GLN* 1.3 88.1 - - - +
267B PHE* 1.3 58.2 + - + +
269B MSE 3.1 13.8 + - + +
270B GLY 2.8 25.8 + - - -
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ARG* 3.8 70.9 - - + +
232A TYR* 5.5 0.7 - - - -
39B SER* 3.5 21.7 + - - +
42B GLN* 3.8 7.9 - - + -
43B GLY* 3.5 32.0 - - - -
46B LYS* 4.2 16.4 - - + -
265B GLN* 3.2 1.1 - - - -
266B PRO* 1.3 80.5 - - - +
268B LEU* 1.3 68.0 + - + +
270B GLY 3.2 0.7 + - - -
271B TYR* 3.0 34.5 + + + +
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Residues in contact with LEU 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLN* 3.1 44.4 + - + +
267B PHE* 1.3 83.7 - - + +
269B MSE 1.3 57.8 + - - +
271B TYR* 4.5 5.8 - - + -
272B LEU* 2.9 70.6 + - + +
290B ILE* 6.4 0.2 - - + -
292B THR* 4.6 12.1 - - + +
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Residues in contact with MSE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B TYR* 3.4 26.5 - - - +
40B LEU* 4.1 15.5 - - + -
111B VAL* 4.7 5.8 - - + -
112B ASP* 3.7 26.5 - - - +
127B LEU* 3.6 28.1 - - + +
128B GLY* 4.2 4.9 - - - -
264B GLN* 3.2 39.3 - - + +
265B GLN 3.0 6.6 + - - +
266B PRO* 3.1 14.8 - - + +
268B LEU* 1.3 76.9 - - - +
270B GLY* 1.3 61.9 + - - +
273B SER* 3.1 26.0 + - - -
292B THR* 3.4 20.6 - - + +
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Residues in contact with GLY 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.6 31.6 - - - +
44B ALA* 3.4 18.5 - - - -
111B VAL* 6.2 0.2 - - - -
266B PRO 2.8 15.1 + - - -
267B PHE 3.7 0.7 - - - -
269B MSE 1.3 75.1 - - - +
271B TYR* 1.3 61.9 + - - +
273B SER* 2.8 20.1 + - - -
274B ILE* 3.4 6.1 + - - +
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Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLY* 3.3 27.4 - - - +
46B LYS* 4.0 15.5 - - + -
47B ALA* 3.4 25.9 - - + +
50B GLU* 3.5 31.0 + - - +
51B LEU* 5.9 2.4 - - + +
267B PHE* 3.0 30.0 + + + +
268B LEU* 3.8 9.4 - - + +
270B GLY* 1.3 76.6 - - - +
272B LEU* 1.3 73.9 + - + +
275B THR* 2.8 44.2 + - + -
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.5 15.0 - - + -
268B LEU* 2.9 50.2 + - + +
271B TYR* 1.3 86.7 - - + +
273B SER* 1.3 60.1 + - - +
275B THR* 3.5 10.2 - - + -
276B GLN* 2.9 34.9 + - + +
290B ILE* 4.0 33.4 - - + -
292B THR* 5.0 2.2 - - + -
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 5.2 3.3 - - - +
44B ALA* 5.2 0.2 - - - +
85B ALA* 4.3 9.3 - - - +
109B ILE* 3.9 10.5 - - - +
111B VAL* 3.7 28.2 - - - +
127B LEU* 3.4 14.1 - - - +
269B MSE 3.1 15.6 + - - -
270B GLY* 2.8 23.4 + - - -
272B LEU* 1.3 77.7 - - - +
274B ILE* 1.3 66.5 + - - +
276B GLN* 3.4 1.0 + - - -
277B LEU* 3.2 27.4 + - - +
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Residues in contact with ILE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 4.7 10.3 - - + -
26B TYR 4.8 1.8 - - - +
27B LEU* 5.0 2.5 - - + -
44B ALA* 3.7 22.7 - - + +
47B ALA* 3.9 11.9 - - + -
48B ALA* 4.1 25.8 - - + +
53B VAL* 4.4 5.2 - - + -
55B LEU* 3.7 24.7 - - + -
85B ALA* 4.6 9.2 - - + -
270B GLY 3.4 13.5 + - - +
273B SER* 1.3 82.1 + - - +
275B THR* 1.3 64.1 + - - +
277B LEU* 3.3 18.0 + - + +
278B VAL* 3.0 41.6 + - + +
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Residues in contact with THR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 3.8 4.7 - - - +
51B LEU* 3.8 18.9 - - + +
271B TYR* 2.8 42.9 + - + -
272B LEU* 3.5 15.3 - - + +
273B SER 3.2 0.2 - - - -
274B ILE* 1.3 77.0 - - - +
276B GLN* 1.3 60.2 + - + +
278B VAL* 3.3 2.4 + - - +
279B LEU* 2.9 53.2 + - + +
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.0 5.4 - - + -
125B VAL* 4.4 1.4 - - - +
127B LEU* 3.8 16.4 - - - +
272B LEU* 2.9 20.2 + - + +
273B SER 4.0 3.4 - - - +
275B THR* 1.3 78.7 - - + +
277B LEU* 1.3 62.1 + - - +
279B LEU* 3.4 10.5 + - + +
280B MSE 3.0 24.9 + - - +
287B PRO* 3.1 22.7 - - + +
288B VAL* 2.8 52.4 + - - +
290B ILE* 3.4 24.5 - - + +
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.8 19.7 - - + -
26B TYR 5.0 0.9 - - - +
83B GLY* 3.9 12.3 - - - +
84B ILE 3.8 27.8 - - - +
85B ALA* 4.1 12.1 - - + +
107B PRO* 4.1 20.6 - - + +
109B ILE* 3.5 25.1 - - + -
273B SER 3.2 14.7 + - - +
274B ILE* 3.6 15.7 - - + +
276B GLN* 1.3 77.8 - - - +
278B VAL* 1.3 62.7 + - - +
280B MSE 3.4 20.8 + - + +
281B ASN* 3.1 27.0 + - - -
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Residues in contact with VAL 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B TYR* 3.6 28.0 - - + +
51B LEU* 3.6 24.5 - - + -
53B VAL* 4.0 17.3 - - + -
274B ILE* 3.0 24.6 + - + +
275B THR 3.6 4.3 - - - +
277B LEU* 1.3 73.5 - - - +
279B LEU* 1.3 61.2 + - + +
281B ASN* 3.2 2.1 + - - +
282B ARG* 2.9 71.7 + - + +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.6 4.3 - - + -
275B THR* 2.9 39.1 + - + +
276B GLN* 3.9 10.3 - - + +
278B VAL* 1.3 77.3 - - + +
280B MSE 1.3 57.9 + - - +
282B ARG* 5.1 7.6 - - - +
283B TYR* 3.0 59.2 + - + +
284B GLN 3.7 0.9 + - - -
285B LEU* 3.8 23.8 + - + +
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Residues in contact with MSE 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 3.7 22.2 - - + -
109B ILE* 4.4 0.9 - - + -
124B LEU* 3.7 19.3 - - + -
276B GLN 3.0 10.5 + - - +
277B LEU* 3.5 36.8 - - + +
278B VAL 3.1 0.2 - - - -
279B LEU* 1.3 78.8 - - - +
281B ASN* 1.3 59.9 + - - +
284B GLN* 2.7 33.2 + - - +
285B LEU* 3.2 26.4 - - - +
286B ASN* 5.9 0.2 - - - +
287B PRO* 3.1 29.8 - - + -
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Residues in contact with ASN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP* 4.8 7.0 - - - +
25B TYR* 2.7 30.6 + - - +
82B SER* 2.8 39.9 + - - +
107B PRO* 4.5 9.1 - - - +
277B LEU 3.1 6.7 + - - +
278B VAL 3.7 1.1 - - - +
280B MSE 1.3 85.1 - - - +
282B ARG* 1.3 60.7 + - + +
284B GLN* 2.9 17.5 - - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP* 4.8 10.8 - - - +
25B TYR* 5.4 0.4 - - - +
51B LEU* 3.0 49.9 + - - +
53B VAL* 4.8 4.6 - - - +
278B VAL* 2.9 38.6 + - + +
279B LEU* 5.1 2.6 - - - +
281B ASN* 1.3 78.4 - - + +
283B TYR* 1.3 104.2 + - + +
284B GLN* 3.9 8.2 + - - -
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B LEU* 3.0 45.1 + - + +
282B ARG* 1.3 119.2 + - + +
284B GLN* 1.3 80.1 + - - +
285B LEU* 3.1 25.0 + - + +
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Residues in contact with GLN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B MSE 2.7 23.6 + - - +
281B ASN* 2.9 25.8 - - - +
282B ARG 3.9 5.7 + - - -
283B TYR* 1.3 83.0 + - - +
285B LEU* 1.3 63.3 + - - +
286B ASN* 4.2 4.2 + - - +
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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