Contacts of the helix formed by residues 245 - 260 (chain B) in PDB entry 1B8I
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 VAL 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B GLU 5.4 1.8 - - - +
234B LYS* 3.8 30.4 - - + +
235B GLU* 4.5 13.0 - - + +
238B ALA* 3.4 11.0 - - + +
244B THR* 1.3 78.8 - - + +
246B SER* 1.3 59.5 + - - +
248B VAL* 3.0 15.3 + - - +
249B SER* 2.9 31.8 + - - +
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Residues in contact with SER 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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158A LYS* 4.0 28.6 - - - +
244B THR* 3.5 16.2 - - - +
245B VAL* 1.3 83.7 - - - +
247B GLN* 1.3 59.3 + - - +
249B SER* 3.0 11.5 + - - -
250B ASN* 2.9 35.8 + - - +
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Residues in contact with GLN 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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208B PHE* 2.7 43.1 - - + -
243B ILE* 3.7 20.4 - - + +
244B THR* 3.0 28.9 + - - +
246B SER* 1.3 77.5 - - - +
248B VAL* 1.3 57.2 + - - +
250B ASN* 3.7 4.7 - - - +
251B TRP* 2.9 27.5 + - - +
20D G 3.9 1.2 + - - -
21D A 3.1 36.5 + - - +
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Residues in contact with VAL 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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216B LEU* 3.8 19.7 - - + -
234B LYS* 3.7 26.5 - - + +
237B LEU* 4.2 15.9 - - + -
238B ALA* 3.8 5.8 - - + +
243B ILE* 3.4 18.8 - - + -
244B THR 2.8 18.6 - - - +
245B VAL* 3.1 16.6 - - - +
247B GLN* 1.3 75.1 - - - +
249B SER* 1.3 60.6 + - - +
251B TRP* 3.2 5.3 + - - +
252B PHE* 2.9 48.8 + - + -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LYS* 3.0 30.5 - - - +
245B VAL* 2.9 15.7 + - - +
246B SER* 3.2 12.3 - - - -
248B VAL* 1.3 73.1 - - - +
250B ASN* 1.3 63.4 + - - +
252B PHE* 3.4 4.5 + - - +
253B GLY* 2.8 27.9 + - - -
256B ARG* 5.3 0.9 + - - -
8C T 5.8 1.3 - - - -
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Residues in contact with ASN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER* 2.9 21.7 + - - +
247B GLN* 3.7 10.7 - - - +
249B SER* 1.3 76.3 - - - +
251B TRP* 1.3 53.9 + - - +
253B GLY* 3.1 1.7 + - - -
254B ASN* 2.7 49.5 + - - +
20D G 5.1 0.9 - - + -
21D A 3.2 49.5 + - + +
22D T 3.7 23.2 + - + +
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Residues in contact with TRP 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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208B PHE* 3.6 28.8 - + + -
213B SER* 5.3 3.6 + - - +
216B LEU* 3.6 53.5 - - + +
217B ASN* 3.9 14.5 + - - -
220B PHE* 3.7 12.3 - - + -
247B GLN 2.9 19.5 + - - +
248B VAL* 3.4 8.1 - - - +
249B SER 3.2 0.2 - - - -
250B ASN* 1.3 77.2 - - - +
252B PHE* 1.3 72.0 + + - +
254B ASN* 3.7 4.9 - - - +
255B LYS* 2.6 90.6 + - + +
20D G 3.9 21.9 + - + -
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Residues in contact with PHE 252 (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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216B LEU* 4.1 9.6 - - + -
219B TYR* 3.3 34.3 - + + -
220B PHE* 3.5 46.4 - + + -
227B PRO 3.6 21.3 - - - -
229B PRO* 3.8 20.9 - - + -
234B LYS* 5.8 0.7 - - + +
237B LEU* 4.6 5.4 - - + -
248B VAL* 2.9 40.2 + - + +
249B SER* 4.1 3.8 - - - +
251B TRP* 1.3 86.7 - + - +
253B GLY* 1.3 60.8 + - - +
255B LYS* 4.2 1.6 - - - -
256B ARG* 2.8 51.5 + - - +
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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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249B SER 2.8 16.7 + - - -
250B ASN* 3.5 3.4 - - - -
252B PHE* 1.3 79.9 - - - +
254B ASN* 1.3 61.2 + - - +
256B ARG* 3.7 15.5 - - - +
257B ILE* 3.2 28.7 + - - +
8C T 6.2 0.4 - - - -
9C A 4.5 3.8 - - - -
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Residues in contact with ASN 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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250B ASN* 2.7 25.8 + - - +
251B TRP* 3.7 4.7 - - - +
253B GLY* 1.3 71.8 - - - +
255B LYS* 1.3 64.9 + - - +
257B ILE* 4.1 1.7 - - - +
258B ARG* 3.0 58.1 + - - +
11C A 4.3 6.5 - - - +
12C T 5.0 0.2 + - - -
20D G 3.9 13.1 - - + +
21D A 2.8 51.3 - - - +
22D T 4.8 1.4 + - - +
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Residues in contact with LYS 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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217B ASN* 3.0 22.2 - - - +
220B PHE* 3.3 41.7 - - + -
221B TYR* 2.9 29.9 + - - +
251B TRP* 2.6 52.4 + - + +
252B PHE 4.1 2.0 - - - +
254B ASN* 1.3 72.8 - - - +
256B ARG* 1.3 52.4 + - - +
258B ARG* 3.7 2.4 - - - +
259B TYR* 2.7 48.1 + - + +
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Residues in contact with ARG 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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91A TRP* 3.5 25.8 - - + -
220B PHE* 4.3 10.5 - - + -
227B PRO* 3.2 29.0 + - + -
228B TYR* 3.5 34.4 - - - +
229B PRO* 4.2 5.9 - - - +
234B LYS* 5.5 3.0 - - - +
249B SER 5.3 0.8 + - - -
252B PHE* 2.8 49.0 + - - +
253B GLY* 3.7 12.7 - - - +
255B LYS* 1.3 79.8 - - - +
257B ILE* 1.3 63.2 + - + +
259B TYR* 3.3 11.5 - - - +
260B LYS* 3.2 23.8 - - - +
8C T 3.9 13.3 + - - +
9C A 2.8 46.6 + - - -
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Residues in contact with ILE 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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253B GLY 3.2 19.1 + - - +
254B ASN* 4.2 2.7 - - - +
256B ARG* 1.3 76.7 - - + +
258B ARG* 1.3 64.0 + - + +
259B TYR 3.0 4.9 - - - -
260B LYS* 3.4 15.2 + - + +
261B LYS* 3.2 34.8 + - + +
9C A 3.9 34.8 - - + +
10C A 3.2 56.1 - - + +
11C A 5.3 2.9 - - - +
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Residues in contact with ARG 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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254B ASN* 3.0 41.7 + - - +
255B LYS* 4.3 2.7 - - - +
257B ILE* 1.3 78.1 - - + +
259B TYR* 1.3 62.2 + - - +
261B LYS* 3.4 37.5 - - - +
262B ASN* 3.7 7.4 - - - +
12C T 3.6 9.9 + - - +
13C C 4.4 0.4 - - - +
19D T 3.6 35.0 + - - +
20D G 2.5 53.8 + - - -
21D A 3.5 11.1 - - - +
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Residues in contact with TYR 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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88A PHE* 4.5 10.4 - - - -
91A TRP* 3.7 16.4 - + - -
92A MET* 3.6 28.4 - - - -
220B PHE* 3.6 29.2 - + + -
221B TYR* 4.9 12.1 - + - -
224B LEU* 3.5 22.6 - - + +
255B LYS* 2.7 28.9 + - + +
256B ARG* 3.3 6.7 - - - +
257B ILE 3.0 0.4 - - - -
258B ARG* 1.3 75.0 - - - +
260B LYS* 1.3 68.5 + - + +
261B LYS 3.1 2.1 + - - -
262B ASN 3.3 22.2 - - - +
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Residues in contact with LYS 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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91A TRP* 3.8 25.7 + - + -
92A MET* 4.0 13.5 - - + -
93A ALA* 3.1 45.6 - - + +
256B ARG 3.2 18.6 - - - +
257B ILE* 3.4 18.5 + - + +
259B TYR* 1.3 80.5 - - - +
261B LYS* 1.3 58.5 + - + +
262B ASN 3.1 7.4 + - - +
9C A 4.8 1.8 + - - -
10C A 3.2 29.0 + - - +
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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