Contacts of the helix formed by residues 8 - 23 (chain A) in PDB entry 5OIV
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 THR 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 SER 4.3 1.1 + - - +
7A PHE* 1.3 76.0 - - - +
9A PRO* 1.3 70.9 - - - +
10A THR* 3.4 9.8 + - - -
11A GLN* 2.9 44.5 + - - +
12A LEU* 2.8 27.8 + - - +
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Residues in contact with PRO 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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7A PHE 4.6 0.7 - - - +
8A THR* 1.3 87.2 - - - +
10A THR* 1.3 60.5 + - + +
12A LEU* 4.5 4.5 - - + -
13A ALA* 2.9 30.5 + - - +
445A LEU* 3.6 27.7 - - + +
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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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8A THR* 3.4 9.4 + - - -
9A PRO* 1.3 76.0 - - + +
11A GLN* 1.3 69.1 + - - +
13A ALA* 3.4 5.1 + - - +
14A ALA* 3.0 25.1 + - - +
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Residues in contact with GLN 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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6A SER 4.6 1.6 - - - +
7A PHE* 3.4 27.7 - - + -
8A THR* 2.9 44.4 + - - +
10A THR* 1.3 79.5 + - - +
12A LEU* 1.3 56.5 + - - +
14A ALA* 3.4 5.8 + - - +
15A ARG* 2.9 37.6 + - - +
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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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7A PHE* 4.1 13.6 - - + +
8A THR 2.8 20.6 + - - +
9A PRO* 3.8 5.4 - - + +
11A GLN* 1.3 71.3 - - - +
13A ALA* 1.3 60.1 + - - +
15A ARG* 3.2 3.9 + - + +
16A ALA* 2.9 29.0 + - - +
409A LEU* 4.4 15.0 - - + +
412A ALA* 3.4 25.6 - - + +
413A SER* 4.0 22.7 - - - +
415A GLY* 3.9 13.2 - - - +
417A PHE* 3.8 20.1 - - + -
441A VAL* 3.8 23.6 - - + -
445A LEU* 4.3 7.9 - - + -
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Residues in contact with ALA 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 PRO 2.9 16.7 + - - +
10A THR* 3.9 6.3 - - - +
12A LEU* 1.3 76.7 - - - +
14A ALA* 1.3 62.1 + - - +
16A ALA* 3.3 5.1 + - - -
17A ALA* 3.0 21.7 + - - +
442A LEU* 3.6 18.4 - - + +
445A LEU* 3.6 23.2 - - + +
446A GLY* 5.9 1.3 - - - +
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Residues in contact with ALA 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 3.0 18.4 + - - +
11A GLN* 3.6 7.0 - - - +
13A ALA* 1.3 75.1 - - - +
15A ARG* 1.3 61.5 + - + +
17A ALA* 3.4 6.5 + - - +
18A TYR* 2.9 29.4 + - - +
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Residues in contact with ARG 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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7A PHE* 3.4 51.6 - - - -
11A GLN* 2.9 22.6 + - - +
12A LEU* 3.9 4.7 - - - +
14A ALA* 1.3 80.3 - - + +
16A ALA* 1.3 62.1 + - - +
18A TYR* 3.7 8.8 - - + +
19A LEU* 3.1 22.9 + - - +
415A GLY* 5.0 8.7 + - - -
417A PHE* 3.9 15.8 - - + -
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Residues in contact with ALA 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 2.9 16.6 + - - +
13A ALA 3.6 2.5 - - - +
14A ALA 3.2 0.2 - - - -
15A ARG* 1.3 75.4 - - - +
17A ALA* 1.3 65.1 + - - +
19A LEU* 3.3 4.4 + - - +
20A LEU* 3.1 20.4 + - - +
417A PHE* 3.5 24.0 - - + -
438A ALA* 3.7 18.9 - - + +
441A VAL* 4.2 6.7 - - + -
442A LEU* 3.6 24.2 - - + +
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Residues in contact with ALA 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 ALA 3.0 16.5 + - - +
14A ALA* 3.7 6.5 - - - +
16A ALA* 1.3 76.7 - - - +
18A TYR* 1.3 63.8 + - - +
20A LEU* 3.3 2.2 + - - +
21A ARG* 3.0 25.8 + - - +
54A LEU* 3.9 33.1 - - + +
442A LEU* 3.9 10.5 - - + +
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Residues in contact with TYR 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 ALA 2.9 17.5 + - - +
15A ARG* 3.7 11.2 - - + +
17A ALA* 1.3 77.3 - - - +
19A LEU* 1.3 58.4 + - - +
21A ARG* 3.5 5.3 + - + +
22A GLY* 2.9 24.6 + - - -
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Residues in contact with LEU 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 ARG 3.1 13.6 + - - +
16A ALA 3.5 7.2 - - - +
17A ALA 3.3 0.2 - - - -
18A TYR* 1.3 79.8 - - - +
20A LEU* 1.3 61.6 + - - +
22A GLY* 2.9 17.7 + - - -
23A ASN* 3.0 35.2 + - - +
417A PHE* 3.5 44.0 - - + -
433A GLN* 3.6 28.7 - - + +
434A GLN 4.3 0.2 - - - +
435A SER* 3.9 13.7 - - - -
438A ALA* 3.7 16.6 - - + -
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Residues in contact with LEU 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 ALA 3.1 16.5 + - - +
17A ALA* 3.3 4.5 + - - +
19A LEU* 1.3 77.7 - - + +
21A ARG* 1.3 63.2 + - - +
23A ASN* 3.3 11.7 + - - +
24A ASP* 3.5 11.3 + - - +
29A THR* 4.0 8.6 + - + +
47A VAL* 4.2 18.8 - - + +
50A GLY* 3.8 25.1 - - - -
51A LEU* 4.0 23.6 - - + +
54A LEU* 4.4 2.9 - - + -
435A SER* 3.6 41.3 - - - +
438A ALA* 4.3 5.6 - - + -
439A ALA* 4.7 1.6 - - - -
442A LEU* 3.6 24.9 - - + -
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Residues in contact with ARG 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 ALA 3.0 16.3 + - - +
18A TYR* 4.0 4.7 - - + +
20A LEU* 1.3 77.6 - - - +
22A GLY* 1.3 62.8 + - - +
24A ASP* 3.2 42.7 + - - +
51A LEU* 5.7 2.4 - - - +
54A LEU* 6.0 0.4 - - + +
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Residues in contact with GLY 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 TYR 2.9 12.2 + - - -
19A LEU* 2.9 9.3 + - - -
21A ARG* 1.3 76.9 - - - +
23A ASN* 1.3 63.3 + - - +
24A ASP 3.3 4.6 + - - +
25A LEU* 6.1 0.5 - - - +
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Residues in contact with ASN 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 LEU* 3.0 24.7 + - - +
20A LEU 3.3 1.7 + - - +
21A ARG 3.2 0.6 - - - -
22A GLY* 1.3 78.5 - - - +
24A ASP* 1.3 60.9 + - - +
25A LEU* 3.4 3.7 + - - +
29A THR* 3.4 11.1 - - + -
30A THR* 2.9 46.8 + - - +
32A ALA* 4.3 1.0 - - - +
33A PRO* 3.5 25.3 - - - +
433A GLN* 3.2 24.5 + - - +
435A SER* 2.9 27.7 + - - +
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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