Contacts of the helix formed by residues 245 - 262 (chain B) in PDB entry 3BRS
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 LYS 245 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B THR* 5.1 0.4 + - - -
226B SER* 5.3 0.7 - - - -
227B MET* 6.5 0.9 - - - -
243B VAL* 5.6 0.4 - - + +
244B GLN* 1.3 81.2 - - - +
246B PRO* 1.3 63.2 - - - +
247B PHE* 3.2 3.8 - - - -
248B ASN* 3.0 32.6 + - + +
249B ILE* 3.2 10.6 + - - +
272B SER* 3.3 28.4 + - - +
273B GLY* 3.7 30.5 + - - +
274B CYS* 4.0 12.2 + - - +
275B ALA* 5.3 4.2 - - - +
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Residues in contact with PRO 246 (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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21B PHE* 3.5 44.4 - - + +
24B VAL* 3.9 11.7 - - + -
25B LEU* 3.4 16.2 - - + +
225B SER 3.2 21.3 - - - +
226B SER* 3.9 14.6 - - - +
244B GLN* 3.2 14.3 - - + +
245B LYS* 1.3 85.9 - - - +
247B PHE* 1.3 66.4 + - - +
249B ILE* 3.2 8.2 + - + +
250B GLY 3.2 17.7 + - - -
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Residues in contact with PHE 247 (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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24B VAL* 3.5 30.1 - - + +
27B GLU* 3.7 16.2 - - + -
28B GLY* 3.4 35.1 - - - -
31B MET* 3.9 26.5 - - + -
245B LYS 3.2 1.7 - - - -
246B PRO* 1.3 79.1 - - - +
248B ASN* 1.3 68.1 + - - +
250B GLY 3.4 0.5 + - - -
251B TYR* 3.0 40.6 + + + +
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Residues in contact with ASN 248 (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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245B LYS* 3.0 34.8 + - + +
247B PHE* 1.3 85.0 - - - +
249B ILE* 1.3 66.2 + - - +
250B GLY 3.1 1.3 - - - -
251B TYR* 4.4 6.4 - - - +
252B LEU* 3.0 40.0 + - + +
272B SER* 3.8 13.2 + - - +
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Residues in contact with ILE 249 (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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21B PHE* 3.6 33.7 - - + -
25B LEU* 3.8 9.6 - - + -
96B ILE* 3.6 25.2 - - + +
97B ASP* 3.7 9.0 - - - +
109B VAL* 3.4 31.2 - - - +
110B ALA* 4.6 2.2 - - - -
111B THR* 4.2 21.1 - - - +
245B LYS 3.2 6.5 + - - +
246B PRO* 3.2 9.6 + - + +
248B ASN* 1.3 76.3 - - - +
250B GLY* 1.3 58.6 - - - +
252B LEU 4.0 0.2 - - - -
253B GLY* 3.0 26.7 + - - -
272B SER* 3.2 24.0 - - - +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.6 31.8 - - - +
29B ALA* 3.4 21.9 - - - +
70B LEU* 5.3 0.7 - - - +
96B ILE* 5.5 2.5 - - - -
246B PRO 3.2 6.5 + - - -
247B PHE 3.7 1.3 - - - -
248B ASN 3.1 0.6 - - - -
249B ILE* 1.3 78.9 - - - +
251B TYR* 1.3 63.0 + - - +
253B GLY* 3.5 1.4 + - - -
254B VAL* 3.3 16.5 + - - +
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Residues in contact with TYR 251 (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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28B GLY* 3.2 25.0 - - - +
31B MET* 3.9 23.8 - - + -
32B ALA* 3.5 30.8 - - + +
35B GLU* 3.7 24.3 + - + +
36B TYR* 4.0 2.9 + + - -
247B PHE* 3.0 28.1 + + + +
248B ASN* 4.3 6.7 - - - +
250B GLY* 1.3 74.0 - - - +
252B LEU* 1.3 62.4 + - + +
254B VAL 3.4 1.6 + - - -
255B GLU* 3.0 60.7 + - + +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 4.1 23.4 - - + +
248B ASN* 3.0 36.2 + - + +
251B TYR* 1.3 78.4 - - + +
253B GLY* 1.3 64.3 + - - +
254B VAL 3.1 1.6 - - - -
255B GLU* 3.5 22.7 - - - +
256B LYS* 3.1 49.8 + - + +
270B LEU* 4.4 11.4 - - + -
271B ASP 5.3 2.7 - - - +
272B SER* 5.2 7.9 - - - -
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Residues in contact with GLY 253 (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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70B LEU* 3.4 19.7 - - - +
94B ILE* 4.0 9.7 - - - +
96B ILE* 4.3 2.7 - - - -
109B VAL* 3.9 16.1 - - - +
249B ILE 3.0 19.1 + - - -
250B GLY 4.1 0.9 - - - -
252B LEU* 1.3 76.7 - - - +
254B VAL* 1.3 57.9 + - - +
256B LYS* 4.0 0.8 - - - +
257B ALA* 3.1 28.6 + - - +
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Residues in contact with VAL 254 (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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8B MET* 3.8 13.3 - - - +
29B ALA* 3.9 22.4 - - + +
32B ALA* 3.4 21.5 - - + -
33B ALA* 3.9 7.9 - - + +
36B TYR* 5.2 0.2 - - + -
38B ILE* 3.5 28.3 - - + -
40B LEU* 4.3 13.0 - - + -
70B LEU* 3.7 12.5 - - + +
250B GLY 3.3 12.8 + - - +
251B TYR 3.6 6.5 - - - +
252B LEU 3.1 0.4 - - - -
253B GLY* 1.3 73.0 - - - +
255B GLU* 1.3 68.3 + - - +
257B ALA* 2.9 24.3 + - - +
258B LEU* 3.3 3.6 + - - +
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Residues in contact with GLU 255 (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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32B ALA* 4.3 0.4 - - - +
36B TYR* 2.6 39.4 + - + +
251B TYR* 3.0 47.4 + - + +
252B LEU* 3.5 23.5 - - - +
254B VAL* 1.3 73.6 - - - +
256B LYS* 1.3 73.0 + - + +
258B LEU* 2.8 31.8 - - - +
259B LYS* 3.7 5.3 + - + +
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Residues in contact with LYS 256 (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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94B ILE* 4.8 2.5 - - + -
107B ILE* 4.6 9.9 - - + +
252B LEU* 3.1 36.8 + - - +
253B GLY* 4.6 0.9 - - - +
255B GLU* 1.3 90.5 + - + +
257B ALA* 1.3 61.4 + - - +
258B LEU 2.9 6.0 + - - -
259B LYS* 3.4 36.9 + - + +
260B LEU* 3.4 15.8 + - - +
266B VAL* 3.9 28.2 - - + +
267B PRO* 5.9 0.4 - - + -
270B LEU* 3.7 31.2 - - + -
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Residues in contact with ALA 257 (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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8B MET* 3.4 26.0 - - + -
68B VAL* 4.2 9.1 - - + +
70B LEU* 4.8 0.7 - - + -
94B ILE* 3.9 23.7 - - + +
253B GLY 3.1 17.8 + - - +
254B VAL 2.9 14.8 + - - +
256B LYS* 1.3 75.2 - - - +
258B LEU* 1.3 60.2 + - - +
260B LEU* 3.6 7.8 - - - +
261B LEU* 3.2 25.3 + - - +
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Residues in contact with LEU 258 (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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6B TYR* 3.7 36.3 - - + -
8B MET* 4.2 4.3 - - + -
36B TYR* 3.6 35.2 - - + +
38B ILE* 3.6 31.0 - - + -
254B VAL 4.2 1.1 - - - +
255B GLU 2.8 18.0 + - - +
256B LYS 2.9 0.4 - - - -
257B ALA* 1.3 79.1 - - - +
259B LYS* 1.3 64.1 + - - +
261B LEU* 3.0 8.6 + - + +
262B LYS* 2.9 42.3 + - + +
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Residues in contact with LYS 259 (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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255B GLU* 3.7 3.9 + - + +
256B LYS* 3.4 41.9 + - + +
258B LEU* 1.3 77.3 - - - +
260B LEU* 1.3 63.0 + - - +
262B LYS* 3.2 3.1 + - - +
263B LYS 2.9 17.8 + - - -
264B GLU* 3.0 42.0 + - + +
265B TYR* 2.8 28.9 + - - +
266B VAL* 4.1 20.2 - - + +
267B PRO* 4.5 6.5 - - - +
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Residues in contact with LEU 260 (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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92B LYS* 3.5 41.2 + - + +
94B ILE* 3.3 35.0 - - + -
106B ASP* 3.9 26.0 - - + +
107B ILE* 3.7 6.7 - - + -
256B LYS 3.4 7.0 + - - +
257B ALA* 3.6 9.9 - - - +
258B LEU 3.2 0.6 - - - -
259B LYS* 1.3 76.1 - - - +
261B LEU* 1.3 65.7 + - - +
263B LYS* 3.0 16.9 + - - +
264B GLU 4.5 6.3 + - - +
266B VAL* 3.8 20.4 - - + +
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Residues in contact with LEU 261 (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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6B TYR* 3.5 51.9 + - + -
8B MET* 4.1 10.5 - - + -
67B ASP* 3.9 16.4 - - + +
68B VAL* 3.8 20.4 - - + -
92B LYS* 3.8 32.8 + - + +
257B ALA 3.2 13.8 + - - +
258B LEU* 3.0 9.7 + - - +
260B LEU* 1.3 82.7 - - - +
262B LYS* 1.3 57.0 + - - +
263B LYS* 3.0 12.0 + - - +
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Residues in contact with LYS 262 (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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6B TYR* 4.3 16.4 - - + +
258B LEU* 2.9 33.5 + - + +
259B LYS* 3.3 2.2 - - - +
261B LEU* 1.3 72.0 - - + +
263B LYS* 1.3 63.5 + - - +
264B GLU* 3.0 46.9 + - - +
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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