Contacts of the helix formed by residues 8 - 28 (chain C) in PDB entry 1BRR
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 PRO 8 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 3.8 9.2 - - - +
6C GLY 4.3 1.1 - - - +
7C ARG* 1.3 93.5 - - + +
9C GLU* 1.3 70.3 + - - +
10C TRP* 2.8 18.1 + - + -
11C ILE* 4.0 8.5 + - - +
202C ASN* 4.2 20.2 + - + +
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Residues in contact with GLU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 2.8 29.1 + - - -
6C GLY 3.7 0.3 - - - -
7C ARG* 3.3 17.0 + - - -
8C PRO* 1.3 83.0 - - - +
10C TRP* 1.3 63.6 + - - +
11C ILE 3.2 2.6 + - - -
12C TRP* 3.3 9.7 + - + +
13C LEU* 3.1 27.2 + - + +
79C TYR* 2.9 24.8 + - - +
201C LEU* 3.6 12.1 - - - +
202C ASN* 3.7 25.1 + - - +
205C THR* 3.5 35.7 - - + +
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Residues in contact with TRP 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLY 5.5 0.2 - - - +
7C ARG* 3.0 66.1 + - - +
8C PRO* 2.8 17.7 + - + -
9C GLU* 1.3 78.4 - - - +
11C ILE* 1.3 81.0 + - + +
13C LEU* 3.5 8.9 + - - +
14C ALA* 2.8 46.1 + - + +
61C LEU* 3.5 19.9 - - + +
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Residues in contact with ILE 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C PRO 4.0 13.2 - - - +
10C TRP* 1.3 107.1 - - + +
12C TRP* 1.3 103.3 + - + +
14C ALA* 3.0 3.2 + - + +
15C LEU* 2.6 43.1 + - + +
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Residues in contact with TRP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C GLU* 3.3 15.1 + - + +
11C ILE* 1.3 107.6 - - + +
13C LEU* 1.3 52.3 + - - +
15C LEU* 3.4 17.2 + - + -
16C GLY 2.7 29.8 + - - -
202C ASN* 3.1 45.2 - - - +
203C ILE* 5.3 0.2 - - - +
205C THR* 4.3 8.3 - - + +
206C LEU* 3.6 54.0 - - + +
209C MET* 3.4 16.8 - - + +
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLY 6.5 0.2 - - - -
9C GLU* 3.1 22.8 + - + +
10C TRP* 3.8 7.2 - - - +
12C TRP* 1.3 72.5 - - - +
14C ALA* 1.3 54.7 + - - +
16C GLY 3.6 0.2 - - - -
17C THR* 2.5 40.6 + - - -
57C TYR* 3.7 11.7 - - + +
60C MET* 3.4 60.3 - - + +
61C LEU* 4.1 15.7 - - - +
79C TYR* 3.7 21.1 - - + +
82C ARG* 4.5 0.4 - - - +
205C THR* 3.3 25.1 - - + -
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C TRP* 2.8 33.9 + - + +
11C ILE* 3.0 10.1 + - + +
13C LEU* 1.3 74.0 - - - +
15C LEU* 1.3 54.6 + - - +
17C THR* 3.0 10.2 + - - -
18C ALA* 2.7 35.4 + - - +
61C LEU* 4.1 17.7 - - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 2.6 27.5 + - + +
12C TRP* 3.7 16.8 - - + +
14C ALA* 1.3 72.2 - - - +
16C GLY* 1.3 57.4 + - - +
18C ALA* 3.1 11.2 - - + +
19C LEU* 2.9 48.5 + - + +
209C MET* 3.2 26.5 - - + -
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C TRP 2.7 18.3 + - - -
13C LEU 3.6 1.6 - - - -
15C LEU* 1.3 74.9 - - - +
17C THR* 1.3 63.9 + - - +
19C LEU* 4.3 0.3 - - - +
20C MET* 3.0 30.0 + - - +
57C TYR* 3.8 18.6 - - - -
209C MET* 3.8 15.9 - - - +
213C VAL* 4.8 6.1 - - - -
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU 2.5 30.3 + - - -
14C ALA* 3.0 9.3 + - - -
16C GLY* 1.3 74.0 - - - +
18C ALA* 1.3 63.7 + - - +
20C MET* 3.8 1.2 - - - +
21C GLY* 3.1 18.0 + - - -
54C PHE* 3.6 32.9 - - + +
57C TYR* 3.7 22.9 + - - -
58C LEU* 3.8 29.3 + - + +
61C LEU* 4.2 8.0 - - + +
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ALA 2.7 12.9 + - - +
15C LEU* 3.1 22.2 - - + +
17C THR* 1.3 76.1 - - - +
19C LEU* 1.3 65.6 + - + +
21C GLY* 3.0 4.3 + - - -
22C LEU* 3.0 31.9 + - + +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 2.9 25.9 + - + +
16C GLY 4.4 0.2 - - - +
18C ALA* 1.3 76.1 - - + +
20C MET* 1.3 53.9 + - - +
22C LEU* 3.3 12.4 + - + +
23C GLY* 2.8 33.6 + - - -
209C MET* 3.8 22.4 - - + -
213C VAL* 3.7 44.0 - - + -
217C VAL* 4.6 6.2 - - + +
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Residues in contact with MET 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY* 3.0 23.9 + - - +
17C THR 3.8 3.1 - - - +
18C ALA 3.2 0.8 - - - -
19C LEU* 1.3 76.2 - - - +
21C GLY* 1.3 60.0 + - - +
23C GLY* 4.0 0.2 - - - -
24C THR* 2.9 28.4 + - - -
50C PRO* 3.8 12.6 - - - +
53C ALA* 3.6 22.7 - - + -
54C PHE* 4.2 18.2 - - - -
57C TYR* 4.3 10.8 - - + -
212C ASP* 3.4 46.9 - - + +
213C VAL* 3.5 15.3 - - + +
216C LYS* 3.7 13.2 - - + -
217C VAL* 4.0 16.4 - - - -
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR 3.1 6.8 + - - -
18C ALA 3.0 6.2 + - - -
20C MET* 1.3 73.0 - - - +
22C LEU* 1.3 67.7 + - - +
24C THR* 3.2 4.8 + - - -
25C LEU* 3.0 33.8 + - - +
54C PHE* 3.7 27.1 - - - -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA* 3.0 24.7 + - + +
19C LEU* 3.8 10.8 - - + +
21C GLY* 1.3 76.6 - - - +
23C GLY* 1.3 52.7 + - - +
24C THR 3.0 0.3 + - - -
25C LEU* 3.0 9.6 + - + +
26C TYR* 2.7 37.3 + - - +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU 2.8 21.0 + - - -
20C MET 4.0 2.2 - - - -
22C LEU* 1.3 73.2 - - - +
24C THR* 1.3 55.4 + - - +
26C TYR* 3.5 8.6 - - - +
27C PHE* 3.0 38.4 + - - -
50C PRO* 4.8 2.7 - - - -
217C VAL* 4.0 22.7 - - - -
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A ARC 5.1 5.4 - - + -
20C MET 2.9 18.1 + - - -
21C GLY* 3.2 10.1 + - - -
22C LEU 3.0 0.8 - - - -
23C GLY* 1.3 73.0 - - - +
25C LEU* 1.3 66.5 + - + +
26C TYR 3.0 1.6 - - - -
27C PHE* 3.1 6.3 + - - +
28C LEU* 2.8 40.2 + - + +
47C THR* 4.0 16.8 - - + +
50C PRO* 3.0 20.4 - - - +
51C ALA* 3.2 30.2 + - + -
54C PHE* 5.1 0.4 - - - +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A ARC 6.3 3.6 - - + -
21C GLY* 3.0 27.1 + - - +
22C LEU* 3.0 14.2 + - + +
24C THR* 1.3 81.4 - - + +
26C TYR* 1.3 53.5 + - - +
28C LEU* 4.1 16.6 - - + -
29C VAL* 2.8 52.5 + - + +
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU 2.7 17.3 + - - +
23C GLY* 3.5 9.4 - - - +
25C LEU* 1.3 77.9 - - - +
27C PHE* 1.3 76.9 + + - +
28C LEU 3.4 0.3 + - - -
29C VAL* 3.6 4.5 + - - -
30C LYS* 3.0 49.6 + - + +
221C LEU* 3.7 28.3 - - + +
225C ARG* 5.3 6.8 + - - -
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Residues in contact with PHE 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1000A ARC 4.4 1.4 - - - +
23C GLY 3.0 19.2 + - - +
24C THR* 3.1 4.7 + - - +
26C TYR* 1.3 100.7 - + - +
28C LEU* 1.3 59.4 + - - +
30C LYS* 4.0 6.2 - - + +
31C GLY* 3.4 16.5 + - - -
43C TYR* 4.1 6.6 - - - -
46C THR* 3.5 25.6 - - + -
47C THR* 3.9 24.6 + - - +
50C PRO* 4.2 16.2 - - + -
216C LYS 4.8 0.2 - - - -
217C VAL* 3.6 33.0 - - + -
220C GLY* 3.7 22.9 - - - -
221C LEU* 3.6 17.5 - - + -
224C LEU* 3.8 21.1 - - + -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A TYR* 4.5 8.7 - - + -
1000A ARC 3.7 73.1 - - + +
24C THR* 2.8 25.4 + - + +
25C LEU* 3.5 22.0 - - + +
27C PHE* 1.3 75.5 - - - +
29C VAL* 1.3 62.0 + - + +
30C LYS 2.9 10.2 + - - -
31C GLY* 3.2 10.6 + - - -
32C MET* 3.7 13.3 + - - +
47C THR* 4.0 9.6 - - + -
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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
------------------------------------------------------------
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