Contacts of the helix formed by residues 16 - 29 (chain D) in PDB entry 1O97
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 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D LEU* 3.6 8.0 - - + +
15D ARG* 1.3 86.9 - - + +
17D VAL* 1.3 66.7 + - - +
18D SER 3.0 2.5 - - - -
19D LEU* 3.0 20.6 + - + +
20D GLU* 3.5 15.7 + - - +
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Residues in contact with VAL 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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8D GLU* 4.5 4.3 - - + -
15D ARG* 3.2 33.6 - - + +
16D PRO* 1.3 80.1 - - - +
18D SER* 1.3 65.5 + - - +
20D GLU* 3.0 30.5 + - + +
21D LEU* 3.0 27.1 + - + +
94D PRO* 3.8 39.0 - - + -
155D ILE* 5.1 1.6 - - + +
156D ARG 5.6 0.2 - - - -
157D PRO* 4.3 23.3 - - + -
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Residues in contact with SER 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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5D VAL* 4.4 2.4 - - - +
7D ALA* 4.2 16.8 - - - +
8D GLU* 3.0 30.1 + - - +
14D LEU* 3.7 16.8 - - - +
15D ARG 2.9 16.7 + - - -
16D PRO 3.0 0.4 - - - -
17D VAL* 1.3 79.9 - - - +
19D LEU* 1.3 62.3 + - - +
21D LEU* 3.3 13.8 + - - +
22D ILE* 3.2 25.4 + - - +
52D LEU* 4.4 5.8 - - - -
94D PRO* 6.4 0.2 - - - -
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Residues in contact with LEU 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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14D LEU* 4.2 10.8 - - + -
16D PRO* 3.0 13.7 + - + +
18D SER* 1.3 79.5 - - - +
20D GLU* 1.3 65.4 + - - +
22D ILE* 3.4 14.3 + - + +
23D GLY 3.1 17.7 + - - -
51D ALA 4.1 11.9 - - - +
52D LEU* 4.1 22.7 - - + -
54D VAL* 3.8 28.5 - - + -
55D ASN 5.7 1.1 - - - +
162D PRO* 3.6 23.1 - - + +
163D LEU* 4.4 20.0 + - + +
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Residues in contact with GLU 20 (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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16D PRO* 3.5 10.8 + - - +
17D VAL* 3.0 29.1 + - + +
19D LEU* 1.3 77.6 - - - +
21D LEU* 1.3 58.1 + - + +
23D GLY* 3.2 2.9 + - - -
24D ALA* 2.9 27.4 + - - +
155D ILE* 6.3 1.3 - - + -
156D ARG 4.5 1.4 - - - +
157D PRO* 3.6 8.1 - - - +
158D SER* 2.7 42.1 + - - -
159D VAL 4.2 2.1 + - - -
160D PHE* 3.5 30.7 + - + +
162D PRO* 4.5 15.3 - - + -
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Residues in contact with LEU 21 (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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5D VAL* 3.5 22.2 - - + -
6D ILE 3.6 14.1 - - - +
17D VAL* 3.0 23.0 + - + +
18D SER* 3.3 8.3 + - - +
20D GLU* 1.3 72.6 - - + +
22D ILE* 1.3 61.0 + - - +
24D ALA* 3.2 6.3 + - + +
25D ALA* 2.9 30.3 + - - +
92D LEU* 3.7 12.2 - - + +
93D LEU 3.9 9.4 - - - +
94D PRO* 3.6 36.1 - - + -
155D ILE* 3.6 42.0 - - + -
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Residues in contact with ILE 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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5D VAL* 4.3 6.3 - - + -
18D SER* 3.2 16.5 + - - +
19D LEU* 3.7 20.2 - - + +
20D GLU 3.3 0.2 - - - -
21D LEU* 1.3 77.2 - - - +
23D GLY* 1.3 61.4 + - - +
25D ALA* 3.3 5.2 + - - +
26D ASN* 2.8 45.0 + - - +
36D VAL* 5.1 1.3 - - + -
38D VAL* 3.7 24.0 - - + -
52D LEU* 4.3 11.7 - - + -
54D VAL* 4.0 13.5 - - + -
55D ASN 3.7 20.0 - - - +
56D GLY 4.1 1.3 - - - +
57D VAL* 3.5 26.7 - - + -
163D LEU* 4.3 3.6 - - + -
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Residues in contact with GLY 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 LEU 3.1 12.1 + - - -
20D GLU 3.2 1.5 + - - -
22D ILE* 1.3 71.4 - - - +
24D ALA* 1.3 66.6 + - - +
26D ASN* 3.2 2.3 + - - +
27D GLY* 2.9 21.1 + - - -
160D PHE* 5.1 0.7 - - - -
161D LYS 3.4 21.5 - - - -
163D LEU* 3.0 23.8 - - - +
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Residues in contact with ALA 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 GLU 2.9 13.3 + - - +
21D LEU* 3.2 11.4 + - - +
23D GLY* 1.3 75.6 - - - +
25D ALA* 1.3 57.8 + - - +
27D GLY* 3.3 1.6 + - - -
28D LEU* 2.9 30.6 + - + +
92D LEU* 4.0 13.5 - - + -
121D VAL* 5.5 6.1 - - + +
155D ILE* 5.1 5.8 - - + -
160D PHE* 3.6 40.1 - - + +
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Residues in contact with ALA 25 (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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3D ILE* 3.7 19.3 - - + +
5D VAL* 3.8 11.4 - - + -
21D LEU 2.9 17.3 + - - +
22D ILE 3.7 4.5 - - - +
24D ALA* 1.3 76.2 - - - +
26D ASN* 1.3 58.5 + - - +
28D LEU* 3.2 4.4 + - - +
29D LYS* 3.1 32.8 + - - +
36D VAL* 3.8 26.9 - - + -
92D LEU* 3.8 7.5 - - + +
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Residues in contact with ASN 26 (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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22D ILE* 2.8 31.6 + - - +
23D GLY 3.2 3.3 + - - +
25D ALA* 1.3 78.2 - - - +
27D GLY* 1.3 61.1 + - - +
28D LEU 3.4 0.3 + - - -
29D LYS* 3.7 35.9 + - - +
36D VAL* 3.7 8.4 - - - +
56D GLY* 2.9 44.5 + - - +
58D ASP* 5.4 0.9 - - - +
163D LEU* 4.1 16.1 - - + +
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Residues in contact with GLY 27 (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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23D GLY 2.9 14.8 + - - -
24D ALA* 3.7 3.8 - - - -
26D ASN* 1.3 76.9 - - - +
28D LEU* 1.3 60.8 + - - +
29D LYS 4.3 3.0 - - - +
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Residues in contact with LEU 28 (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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3D ILE* 4.0 15.7 - - + -
24D ALA 2.9 16.8 + - - +
25D ALA 3.2 4.9 + - - +
27D GLY* 1.3 78.2 - - - +
29D LYS* 1.3 68.1 + - - +
30D LYS* 4.3 1.0 - - - -
90D VAL* 4.1 15.7 - - + -
92D LEU* 4.8 9.6 - - + -
121D VAL* 4.0 27.8 - - + +
122D GLU* 3.7 30.1 - - - +
123D TYR* 3.5 37.6 + - + +
128D LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 29 (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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3D ILE* 4.0 17.3 - - + -
25D ALA 3.1 18.7 + - - +
26D ASN* 3.7 35.7 + - - +
27D GLY 3.6 4.5 - - - +
28D LEU* 1.3 78.8 - - - +
30D LYS* 1.3 62.8 + - - +
31D SER* 3.3 15.3 + - - +
32D GLY* 3.3 22.0 + - - -
34D ASP* 3.0 42.7 + - + +
35D LYS 5.8 0.4 - - - +
36D VAL* 4.3 13.9 - - + -
58D ASP* 5.2 2.8 + - - -
123D TYR* 5.1 2.2 - - - -
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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