Contacts of the helix formed by residues 8 - 24 (chain A) in PDB entry 5XBY
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 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A PRO 3.5 0.2 + - - -
7A PRO* 1.3 73.2 - - - +
9A LEU* 1.3 63.1 + - - +
10A THR* 3.3 3.9 - - - +
11A GLU* 3.3 22.2 + - - +
12A LEU* 3.0 26.3 + - - +
28B LEU* 3.8 7.2 - - - -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 3.6 23.1 - - + -
6A PRO* 3.3 28.4 + - + +
7A PRO 3.3 4.2 + - - -
8A GLY* 1.3 77.2 - - - +
10A THR* 1.3 57.9 + - - +
12A LEU* 3.9 3.7 - - + +
13A LEU* 3.0 49.7 + - + +
16B TYR* 3.7 25.4 - - + +
17B THR* 3.6 29.6 - - + +
20B VAL* 4.5 9.2 - - + -
28B LEU* 3.6 17.0 - - + +
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Residues in contact with THR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.9 11.1 - - + +
6A PRO 4.8 0.4 + - - +
7A PRO* 6.4 0.2 - - + -
8A GLY 5.3 1.6 - - - +
9A LEU* 1.3 78.7 - - - +
11A GLU* 1.3 86.2 + - - +
13A LEU* 4.1 3.5 - - - +
14A GLN* 2.4 66.0 + - - +
3D TRP* 4.0 13.0 + - - -
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY* 3.3 26.9 + - - +
10A THR* 1.3 93.8 - - - +
12A LEU* 1.3 63.0 + - - +
14A GLN* 3.6 10.3 - - - +
15A GLY* 3.0 21.1 + - - -
22C ARG* 6.0 7.2 - - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLY 3.0 18.6 + - - +
9A LEU* 3.9 3.6 - - + +
11A GLU* 1.3 76.9 - - - +
13A LEU* 1.3 62.9 + - + +
15A GLY* 3.1 12.6 + - - -
16A TYR* 3.3 12.0 + - - +
35A TYR* 4.6 1.4 + - - -
36A PHE* 3.6 30.0 - - + -
39A LEU* 3.7 25.1 - - + -
16B TYR* 3.7 30.5 - - + +
28B LEU* 3.7 29.2 - - + +
29B VAL* 3.7 14.6 - - + -
32B ALA* 5.1 0.2 - - + -
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.0 36.2 + - + +
10A THR* 4.1 3.6 - - - +
12A LEU* 1.3 74.5 - - + +
14A GLN* 1.3 59.6 + - - +
16A TYR* 3.7 5.6 + - + +
17A THR* 2.6 34.6 + - - +
36A PHE* 4.7 13.7 - - + -
13B LEU* 3.4 38.1 - - + +
16B TYR* 3.7 25.4 - - + -
17B THR* 3.5 24.5 - - - +
36B PHE* 5.9 0.7 - - + -
3D TRP* 5.1 10.1 - - + -
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Residues in contact with GLN 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 2.4 51.1 + - - +
11A GLU* 3.6 11.1 - - - +
13A LEU* 1.3 76.6 - - - +
15A GLY* 1.3 57.1 + - - +
17A THR* 2.8 23.5 + - - -
18A VAL* 2.9 20.3 + - + +
18C VAL 4.6 0.2 - - - +
21C LEU* 3.9 22.2 + - + +
22C ARG* 3.5 35.4 + - - +
3D TRP* 3.4 33.5 - - + +
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU 3.0 14.5 + - - -
12A LEU 3.1 3.3 + - - -
14A GLN* 1.3 77.2 - - - +
16A TYR* 1.3 62.3 + - - +
18A VAL* 3.3 7.2 + - - +
19A GLU* 3.3 24.4 + - - +
35A TYR* 3.2 17.0 - - - -
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU 3.3 7.4 + - - +
13A LEU* 3.9 5.8 - - - +
15A GLY* 1.3 74.6 - - - +
17A THR* 1.3 66.1 + - - +
19A GLU* 3.3 3.8 + - - +
20A VAL* 3.0 35.9 + - + +
28A LEU* 2.8 40.1 + - - +
31A PHE* 3.7 14.8 - + - -
32A ALA* 3.6 27.3 - - + +
35A TYR* 3.4 33.5 + + + -
36A PHE* 3.6 29.8 - + + -
9B LEU* 3.7 17.0 - - + -
12B LEU* 4.1 8.3 - - + +
13B LEU* 4.0 22.2 - - + -
36B PHE* 5.6 0.7 - + - -
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 2.6 20.0 + - - -
14A GLN* 2.8 18.5 + - - -
16A TYR* 1.3 77.9 - - - +
18A VAL* 1.3 61.1 + - - -
20A VAL* 3.3 6.3 + - - +
21A LEU* 3.1 27.4 + - + +
9B LEU* 3.8 21.1 - - + -
13B LEU* 3.7 19.5 - - + +
21C LEU* 4.4 7.0 - - + -
3D TRP* 4.4 6.6 - - + -
5D ILE* 3.9 27.6 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN* 2.9 12.9 + - + +
15A GLY* 3.3 9.4 + - - +
17A THR* 1.3 76.5 - - - +
19A GLU* 1.3 52.9 + - - +
21A LEU* 3.1 10.9 + - - +
22A ARG* 2.7 78.0 + - + +
14C GLN* 4.8 4.5 - - + +
17C THR* 4.7 6.9 - - + +
18C VAL* 3.8 30.7 - - + +
21C LEU* 3.4 26.5 - - + -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 3.3 5.6 + - - +
16A TYR 3.3 7.7 + - - +
18A VAL* 1.3 75.1 - - + +
20A VAL* 1.3 60.4 + - - +
22A ARG* 2.5 43.0 + - - +
23A GLN* 2.9 56.7 + - - +
31A PHE* 4.0 18.4 - - + -
35A TYR* 3.5 28.5 - - + +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 3.0 56.9 + - + +
17A THR* 3.5 9.9 - - - +
18A VAL 3.3 0.2 - - - -
19A GLU* 1.3 76.0 - - - +
21A LEU* 1.3 58.6 + - - +
24A GLN* 2.9 30.8 + - - -
25A PRO* 4.0 12.3 - - + -
28A LEU* 3.7 14.6 - - + -
31A PHE* 4.1 9.6 - - + -
6B PRO* 3.3 34.5 - - + -
9B LEU* 4.6 5.6 - - + -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR* 3.1 29.7 + - + +
18A VAL* 3.6 7.6 - - - +
20A VAL* 1.3 79.7 - - + +
22A ARG* 1.3 64.3 + - - +
23A GLN 3.4 0.3 + - - -
24A GLN* 3.6 14.3 + - - +
3B TRP* 3.3 33.9 + - + +
4B GLN 3.2 27.8 - - - +
5B ILE* 3.7 24.0 - - + -
6B PRO* 3.9 11.4 - - + -
9B LEU* 5.5 1.6 - - + -
17C THR* 3.9 26.7 - - + -
21C LEU* 5.4 2.5 - - + -
5D ILE* 4.9 3.8 - - + -
9D LEU* 4.2 14.4 - - + -
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Residues in contact with ARG 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 2.7 44.7 + - + +
19A GLU* 2.5 46.9 + - - +
21A LEU* 1.3 75.5 - - - +
23A GLN* 1.3 64.7 + - + +
24A GLN* 4.8 2.4 - - - +
3B TRP* 4.5 12.5 - - + -
10C THR* 5.4 3.8 + - - +
14C GLN* 2.4 65.4 + - + +
15C GLY* 4.8 0.8 - - - +
18C VAL* 4.0 12.5 - - - +
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU* 2.9 37.9 + - - +
22A ARG* 1.3 81.8 - - + +
24A GLN* 1.3 73.2 + - - +
25A PRO* 3.3 9.3 - - + +
31A PHE* 3.5 31.2 - - - -
34A GLU* 5.5 2.7 + - - +
35A TYR* 6.0 0.2 - - - -
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 2.9 19.9 + - - -
21A LEU* 3.6 21.4 + - - +
22A ARG 4.8 1.6 - - - +
23A GLN* 1.3 78.9 - - - +
25A PRO* 1.3 72.5 - - - +
26A PRO* 3.6 2.6 - - - +
2B PRO* 3.4 35.4 - - + +
3B TRP 3.9 0.2 - - - -
4B GLN* 2.9 47.8 + - - +
6B PRO* 4.9 7.3 - - - +
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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