Contacts of the helix formed by residues 11 - 24 (chain D) in PDB entry 1ORR
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D GLY 3.1 9.1 + - - -
9D GLY 3.3 0.4 - - - -
10D CYS* 1.3 78.0 - - - +
12D PHE* 1.3 61.4 + - - -
13D LEU 3.6 1.1 - - - -
14D GLY 4.0 0.9 - - - -
15D SER* 2.9 31.9 + - - -
36D ARG* 5.8 2.0 - - - -
39D ALA* 5.6 0.4 - - - -
42D ASN* 3.8 4.9 - - - -
1500D NAD 3.1 32.5 + - - -
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Residues in contact with PHE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLY* 1.3 73.8 - - - +
13D LEU* 1.3 90.5 + - + +
15D SER* 3.6 0.2 + - - -
16D ASN* 2.9 38.5 + - - -
195D MET* 3.8 9.6 - - + -
196D TYR* 3.4 39.5 - - - -
197D GLY* 3.6 11.7 - - - -
198D GLY 3.4 21.3 - - - -
199D ARG 3.7 8.8 + - - -
200D GLN* 3.6 44.0 - - + -
201D PHE 5.0 1.1 - - - +
242D ALA* 4.0 10.3 - - + -
245D MET* 5.0 2.5 - - + -
1500D NAD 2.8 25.8 + - - +
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Residues in contact with LEU 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 1.3 98.0 - - + +
14D GLY* 1.3 58.7 + - - +
16D ASN* 3.2 4.2 + - - +
17D LEU* 2.9 33.1 + - + +
80D LEU* 3.9 17.9 - - + -
192D HIS* 4.4 0.4 - - - +
195D MET* 3.6 38.4 - - + -
245D MET* 3.8 27.4 - - + -
249D TYR* 3.9 22.7 - - + +
1500D NAD 2.8 45.2 + - - +
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Residues in contact with GLY 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.9 5.6 - - - +
8D GLY 3.8 11.5 + - - -
9D GLY* 3.2 15.9 - - - +
11D GLY 3.7 3.0 + - - -
12D PHE 3.3 0.6 - - - -
13D LEU* 1.3 80.1 - - - +
15D SER* 1.3 51.5 + - - +
17D LEU* 3.7 2.3 - - - +
18D ALA* 2.7 36.4 + - - +
80D LEU* 3.5 20.9 - - - +
1500D NAD 4.5 0.8 + - - -
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Residues in contact with SER 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLY 3.1 12.5 + - - -
11D GLY 2.9 25.6 + - - -
12D PHE 3.6 0.5 + - - -
14D GLY* 1.3 71.5 - - - +
16D ASN* 1.3 59.5 + - - +
19D SER* 2.9 27.5 + - - -
42D ASN* 3.7 21.3 + - - -
45D TRP* 3.9 6.5 - - - -
46D LEU* 3.4 22.9 - - - +
199D ARG* 3.3 25.6 - - - +
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Residues in contact with ASN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 2.9 27.4 + - - +
13D LEU 3.2 8.2 + - - +
15D SER* 1.3 81.9 + - - +
17D LEU* 1.3 62.0 + - - +
19D SER* 3.4 6.5 + - - -
20D PHE* 3.3 15.9 + - - +
45D TRP* 5.4 3.5 - - - -
198D GLY 2.8 29.5 + - - +
199D ARG* 3.6 11.7 - - - +
242D ALA* 3.9 17.0 - - - +
245D MET* 3.7 14.4 - - + -
246D ILE* 3.8 24.7 - - + +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 4.0 11.7 - - + -
13D LEU* 2.9 22.1 + - + +
14D GLY 3.8 2.9 - - - +
16D ASN* 1.3 75.9 - - - +
18D ALA* 1.3 58.4 + - - +
20D PHE* 3.3 1.7 + - - +
21D ALA* 2.9 24.4 + - - +
78D PHE* 3.7 20.6 - - + -
80D LEU* 3.8 20.6 - - + -
245D MET* 3.6 23.3 - - - -
246D ILE* 3.9 10.5 - - - -
249D TYR* 3.4 40.2 - - + -
250D PHE* 3.6 26.4 - - + -
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.7 13.2 - - + +
9D GLY 4.5 2.5 - - - +
14D GLY 2.7 22.8 + - - +
15D SER 3.7 4.3 - - - +
17D LEU* 1.3 70.9 - - - +
19D SER* 1.3 66.4 + - - +
21D ALA* 3.1 3.7 + - - +
22D LEU* 2.9 27.5 + - - +
28D LEU* 3.9 21.2 - - + +
30D VAL* 4.5 3.6 - - + -
46D LEU* 3.9 21.5 - - + -
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D SER 2.9 18.1 + - - -
16D ASN* 3.8 5.6 - - - -
17D LEU 3.3 0.2 - - - -
18D ALA* 1.3 75.4 - - - +
20D PHE* 1.3 62.9 + - - +
22D LEU* 3.2 5.7 + - - +
23D SER* 3.0 23.2 + - - -
45D TRP* 3.9 15.4 - - - -
46D LEU* 3.8 1.5 - - - +
49D LEU* 3.5 31.8 - - - +
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Residues in contact with PHE 20 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ASN 3.3 7.1 + - - +
17D LEU 3.3 8.0 + - - +
18D ALA 3.2 0.6 - - - -
19D SER* 1.3 78.0 + - - +
21D ALA* 1.3 65.2 + - - +
23D SER* 2.9 25.8 + - - -
24D GLN* 3.0 49.1 + - + +
246D ILE* 3.7 28.9 - - + -
250D PHE* 3.4 46.0 - + + -
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D LEU* 3.9 25.4 - - + -
17D LEU 2.9 16.8 + - - +
18D ALA* 3.1 6.7 + - - +
20D PHE* 1.3 79.2 - - - +
22D LEU* 1.3 61.7 + - - +
24D GLN* 3.1 10.9 + - - -
26D ILE* 3.1 41.9 + - + +
28D LEU* 4.6 9.9 - - + -
250D PHE* 4.0 7.4 - - + -
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA 2.9 19.1 + - - +
19D SER* 3.6 7.9 - - - +
20D PHE 3.2 0.2 - - - -
21D ALA* 1.3 76.0 - - - +
23D SER* 1.3 62.0 + - - +
25D GLY* 3.2 12.9 + - - +
26D ILE 4.6 5.6 - - - +
28D LEU* 3.7 26.2 - - + -
46D LEU* 3.9 14.8 - - + +
49D LEU* 3.7 43.5 - - + +
50D GLY* 4.0 10.3 - - - +
51D ASN 3.8 22.4 - - - +
52D PHE* 3.9 15.5 - - + -
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 3.0 13.5 + - - -
20D PHE* 2.9 23.3 + - - -
22D LEU* 1.3 77.9 - - - +
24D GLN* 1.3 74.9 + - - +
25D GLY 3.5 0.7 + - - -
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Residues in contact with GLN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.0 51.6 + - + +
21D ALA 3.1 6.0 + - - +
23D SER* 1.3 96.6 + - - +
25D GLY* 1.3 62.3 + - - +
26D ILE* 3.5 20.5 + - + +
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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