Contacts of the helix formed by residues 11 - 24 (chain B) in PDB entry 3LRB
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 GLY 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B LYS 4.1 0.2 + - - -
10B VAL* 1.3 85.7 - - - +
12B LEU* 1.3 68.3 + - - -
13B ILE 3.3 2.0 - - - -
14B PRO* 2.9 19.2 - - - +
15B VAL* 3.0 17.4 - - - +
217B VAL* 4.9 1.3 - - - -
218B LYS* 3.7 22.9 - - - +
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Residues in contact with LEU 12 (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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11B GLY* 1.3 68.2 - - - -
13B ILE* 1.3 67.5 - - + +
15B VAL* 2.9 6.6 + - - +
16B THR* 2.9 47.5 + - + +
218B LYS* 5.2 0.8 - - - +
223B ASN* 3.2 57.7 + - - +
226B ILE* 3.5 37.2 - - + -
227B ALA* 4.5 0.9 - - + -
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Residues in contact with ILE 13 (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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12B LEU* 1.3 86.9 - - + +
14B PRO* 1.3 69.5 - - + +
16B THR* 3.7 7.3 + - - +
17B LEU* 3.3 36.9 + - + +
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Residues in contact with PRO 14 (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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10B VAL* 3.7 12.3 - - + -
11B GLY* 2.9 22.0 - - - +
13B ILE* 1.3 90.0 - - + +
15B VAL* 1.3 59.4 + - - +
17B LEU* 3.8 2.5 + - - +
18B MET* 3.3 17.2 + - - +
148B THR* 3.1 38.1 + - - +
149B ARG* 5.2 11.7 - - + +
151B GLN* 5.2 0.2 - - - +
152B ALA* 4.4 13.9 - - + -
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Residues in contact with VAL 15 (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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10B VAL* 3.6 15.9 - - + -
11B GLY 3.0 17.0 - - - +
12B LEU* 2.9 6.3 + - - +
14B PRO* 1.3 74.2 - - - +
16B THR* 1.3 62.2 + - - +
17B LEU 3.0 1.8 - - - -
18B MET* 2.9 13.8 + - + +
19B VAL* 2.8 36.9 + - + +
148B THR* 5.8 0.9 - - - -
209B SER 5.8 0.4 - - - +
210B ALA* 4.7 8.7 - - + -
213B ALA* 5.0 3.6 - - + -
217B VAL* 3.5 43.3 - - + -
224B VAL* 5.9 0.7 - - - -
227B ALA* 4.1 17.0 - - + -
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Residues in contact with THR 16 (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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12B LEU* 2.9 34.9 + - + +
13B ILE* 3.7 10.4 + - - +
15B VAL* 1.3 74.5 - - - +
17B LEU* 1.3 60.4 + - - +
19B VAL* 3.8 3.8 - - - +
20B SER* 2.9 30.0 + - - -
226B ILE* 4.4 3.8 - - + +
227B ALA* 3.3 37.5 - - + +
230B GLY* 5.0 3.4 - - - -
231B GLY* 3.8 8.8 - - - -
234B ILE* 5.0 7.8 - - - +
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Residues in contact with LEU 17 (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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13B ILE* 3.3 29.0 + - + +
14B PRO 3.9 4.9 - - - +
15B VAL 3.0 0.8 - - - -
16B THR* 1.3 82.4 + - - +
18B MET* 1.3 54.1 + - - +
20B SER* 3.5 8.6 + - - -
21B GLY* 2.7 32.4 + - - -
151B GLN* 4.9 1.3 - - - -
152B ALA* 3.7 37.5 - - + +
155B THR* 3.6 25.0 + - - +
156B VAL* 4.3 20.9 - - + +
159B LEU* 5.7 8.1 - - + -
234B ILE* 5.7 6.1 - - + -
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Residues in contact with MET 18 (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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14B PRO 3.3 9.7 + - - +
15B VAL* 2.9 17.0 + - + +
17B LEU* 1.3 78.1 - - - +
19B VAL* 1.3 61.1 + - + +
21B GLY 2.9 7.7 + - - +
22B ASN* 2.8 42.6 + - - +
147B ILE* 4.9 0.2 - - + -
148B THR* 3.7 30.1 - - - +
151B GLN* 4.1 18.1 - - + +
209B SER* 4.9 6.5 - - - +
213B ALA* 6.0 3.4 - - - -
292B GLY* 3.7 21.1 - - - -
295B LEU* 3.5 33.0 - - + -
296B LEU* 4.0 15.9 - - - -
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Residues in contact with VAL 19 (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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15B VAL* 2.8 23.3 + - + +
16B THR 3.8 4.3 - - - +
17B LEU 3.3 0.2 - - - -
18B MET* 1.3 74.5 - - + +
20B SER* 1.3 64.2 + - - +
21B GLY 3.4 0.2 + - - -
23B ILE* 2.8 37.3 + - + +
207B VAL* 4.6 8.5 - - - +
209B SER* 3.5 16.6 - - - +
210B ALA* 3.4 35.7 - - + +
227B ALA* 3.8 15.9 - - + +
228B THR* 3.7 28.9 - - - +
231B GLY* 4.2 2.8 - - - -
232B VAL* 4.8 1.8 - - + +
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Residues in contact with SER 20 (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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16B THR 2.9 17.7 + - - -
17B LEU* 3.9 10.5 - - - -
19B VAL* 1.3 76.6 - - - +
21B GLY* 1.3 57.3 + - - +
23B ILE* 3.6 3.2 + - - +
24B MET* 2.8 40.4 + - - +
159B LEU* 6.0 0.5 - - - +
231B GLY* 3.5 22.8 + - - -
234B ILE* 2.9 34.8 - - - +
235B ALA* 4.0 2.7 + - - -
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Residues in contact with GLY 21 (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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17B LEU 2.7 19.2 + - - -
18B MET 2.9 2.8 + - - -
20B SER* 1.3 77.4 - - - +
22B ASN* 1.3 69.6 + - - +
24B MET* 4.1 9.4 - - - +
25B GLY* 4.4 3.5 - - - -
151B GLN* 4.0 3.3 + - - -
155B THR* 3.8 28.3 - - - +
285B GLY 4.4 2.1 - - - +
289B SER* 4.1 11.8 - - - -
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Residues in contact with ASN 22 (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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18B MET* 2.8 36.4 + - - +
21B GLY* 1.3 80.6 + - - +
23B ILE* 1.3 73.6 + - + +
24B MET 3.1 2.1 + - - -
25B GLY* 3.9 8.3 - - - -
26B SER* 4.4 4.5 + - - -
151B GLN* 3.8 12.5 + - - +
205B ILE 4.6 2.7 - - - +
206B GLY* 5.4 0.2 - - - -
209B SER* 3.8 15.8 - - - +
289B SER* 4.4 7.1 + - - -
292B GLY* 4.1 6.2 - - - -
293B TRP* 2.9 45.7 + - + +
296B LEU* 4.0 8.0 - - - +
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Residues in contact with ILE 23 (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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19B VAL* 2.8 31.2 - - + +
20B SER 3.9 1.3 - - - +
22B ASN* 1.3 82.5 - - + +
24B MET* 1.3 65.6 + - - +
25B GLY 3.4 0.9 + - - -
203B SER 4.7 1.9 - - - +
204B PHE* 4.0 21.9 - - + +
205B ILE 3.4 19.7 - - - +
206B GLY* 3.0 34.8 - - - +
207B VAL* 3.4 17.0 - - + +
209B SER* 4.0 3.6 - - - +
232B VAL* 5.5 2.9 - - + -
235B ALA* 3.3 31.2 - - + -
239B TYR* 3.0 16.1 + - - +
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Residues in contact with MET 24 (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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20B SER* 2.8 25.3 + - - +
21B GLY* 4.3 7.2 - - - +
22B ASN 3.1 3.8 + - - -
23B ILE* 1.3 82.2 - - - +
25B GLY* 1.3 58.1 + - - +
28B VAL* 2.8 27.3 + - + +
155B THR* 6.1 3.6 - - + -
158B ALA* 5.6 3.4 - - + +
159B LEU* 3.6 24.9 - - + -
162B ILE* 3.8 18.8 - - + -
234B ILE* 5.0 1.1 - - + -
235B ALA* 4.2 16.2 - - - +
238B CYS* 3.2 44.2 - - + -
239B TYR* 3.1 17.9 + - - -
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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