Contacts of the helix formed by residues 18 - 31 (chain D) in PDB entry 1O9I
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 ASP 18 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ARG* 3.8 3.0 + - + +
17D SER* 1.3 77.2 - - - +
19D PRO* 1.3 65.3 - - - +
20D ILE* 3.0 14.6 + - - +
21D MET* 3.0 29.0 + - + +
22D ALA 3.0 21.5 + - - -
24D ARG* 4.9 3.6 + - - -
80D LEU* 2.9 30.0 + - + +
161D MET 5.5 0.9 - - - +
162D THR* 4.9 7.8 + - - -
164D ASP* 6.0 1.3 - - + +
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Residues in contact with PRO 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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17D SER* 4.5 3.1 - - - -
18D ASP* 1.3 86.2 - - - +
20D ILE* 1.3 63.6 + - + +
22D ALA* 3.5 9.7 - - + +
23D ARG* 3.1 24.1 + - - +
80D LEU 3.5 7.4 - - - +
81D LEU* 3.9 10.0 - - + +
82D GLU 6.0 0.2 - - - +
84D ALA* 3.8 25.6 - - + -
85D PRO* 4.4 3.4 - - + -
100D THR* 3.6 29.4 - - + -
104D MET* 3.8 22.9 - - + +
108D HIS* 4.9 2.1 + - - -
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Residues in contact with ILE 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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101C MET* 6.1 0.4 - - + -
102C ALA* 6.1 1.1 - - + -
18D ASP* 3.0 9.6 + - - +
19D PRO* 1.3 79.5 - - + +
21D MET* 1.3 62.8 + - - +
23D ARG* 3.2 8.6 + - + +
24D ARG* 3.0 50.2 + - + +
99D THR 5.2 0.4 - - - +
100D THR* 3.5 29.6 - - + +
103D GLY* 3.5 38.4 - - - +
104D MET* 3.8 3.1 - - + +
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Residues in contact with MET 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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18D ASP* 3.0 32.4 + - + +
20D ILE* 1.3 75.5 - - - +
22D ALA* 1.3 65.9 + - - +
24D ARG* 3.2 27.5 + - - +
25D LEU* 2.9 40.2 + - + +
80D LEU* 4.1 9.6 - - + -
158D LEU* 3.6 47.3 - - + +
161D MET 3.8 11.2 - - - +
162D THR* 3.9 20.9 - - + +
167D VAL* 4.1 15.3 - - + -
171D LEU* 4.7 0.4 - - + -
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Residues in contact with ALA 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 ASP 3.0 13.1 + - - +
19D PRO 3.5 10.3 - - - +
20D ILE 3.2 0.2 - - - -
21D MET* 1.3 77.5 - - - +
23D ARG* 1.3 62.4 + - - +
25D LEU* 3.3 2.9 + - - +
26D GLN* 3.2 23.2 + - - +
77D ILE* 3.9 16.1 - - + +
80D LEU* 3.8 19.6 - - + +
81D LEU* 3.7 32.3 - - + -
108D HIS* 4.2 3.1 - - + -
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Residues in contact with ARG 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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23A ARG* 5.6 6.3 - - - +
122A ASN* 5.4 4.3 + - - -
23C ARG* 5.4 10.1 - - - +
102C ALA 4.6 6.5 + - - -
104C MET 4.7 4.4 + - - -
105C ASP* 5.3 0.2 - - - +
106C PRO* 3.3 28.5 - - + +
19D PRO 3.1 11.2 + - - +
20D ILE* 3.5 10.8 - - - +
21D MET 3.2 0.4 - - - -
22D ALA* 1.3 80.6 - - - +
24D ARG* 1.3 62.6 + - + +
26D GLN* 3.2 19.3 + - + +
102D ALA 5.1 1.0 + - - -
103D GLY* 2.9 33.8 + - - +
104D MET 4.1 5.7 + - - -
105D ASP* 3.8 21.2 - - + +
108D HIS* 4.0 13.8 - - + -
121D PRO* 2.8 33.2 + - + +
122D ASN* 2.9 27.1 + - - +
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Residues in contact with ARG 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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86C PHE 4.0 5.5 + - - -
87C GLY* 5.3 0.4 - - - -
101C MET* 3.6 28.7 - - - +
106C PRO* 5.0 14.1 - - + +
110C LEU* 3.6 10.1 - - + +
18D ASP* 4.9 3.0 + - - -
20D ILE* 3.0 42.6 + - + +
21D MET* 3.2 27.5 + - - +
23D ARG* 1.3 76.8 - - + +
25D LEU* 1.3 58.0 + - - +
27D GLU* 3.0 29.5 + - - +
121D PRO* 3.8 6.6 - - - +
158D LEU* 3.8 15.2 - - + +
161D MET* 3.4 58.8 + - - +
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Residues in contact with LEU 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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21D MET* 2.9 31.1 + - + +
22D ALA 3.8 4.3 - - - +
23D ARG 3.3 0.4 - - - -
24D ARG* 1.3 71.5 - - - +
26D GLN* 1.3 65.3 + - - +
27D GLU 3.0 2.2 - - - -
28D SER* 2.9 26.6 + - - +
29D LEU 3.3 7.4 + - - -
73D ILE* 3.6 11.1 - - + +
76D MET* 3.8 15.9 - - + -
77D ILE* 3.9 13.2 - - + -
80D LEU* 3.5 31.4 - - + -
158D LEU* 3.8 23.8 - - + -
167D VAL* 4.6 6.1 - - + -
170D MET* 4.5 10.1 - - + -
171D LEU* 4.4 15.0 - - + -
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Residues in contact with GLN 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 ALA 3.2 13.7 + - - +
23D ARG* 3.3 13.0 - - + +
24D ARG 3.1 0.6 - - - -
25D LEU* 1.3 78.1 - - - +
27D GLU* 1.3 54.5 + - - +
29D LEU* 3.9 8.8 - - - +
30D GLY 2.8 27.9 + - - -
31D GLY 3.5 1.2 + - - -
77D ILE* 3.6 10.9 - - - +
105D ASP* 5.5 1.8 - - - +
108D HIS* 2.8 30.2 + - + +
116D ALA* 3.6 6.2 - - - -
117D SER* 2.8 46.2 + - - +
119D ASN 2.9 26.4 + - - +
120D ASN* 3.7 12.7 - - - +
121D PRO* 4.0 2.7 - - + -
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Residues in contact with GLU 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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107C GLU* 2.5 36.6 - - - +
110C LEU* 3.6 19.8 - - + +
111C VAL* 3.3 15.0 - - + +
24D ARG 3.0 16.8 + - - +
26D GLN* 1.3 79.0 - - - +
28D SER* 1.3 59.6 + - - +
31D GLY* 3.0 44.0 + - - +
32D GLN* 3.9 8.8 + - - +
33D TRP 5.0 0.7 + - - -
34D GLY* 3.8 7.3 + - - -
120D ASN* 4.8 0.3 + - - -
121D PRO* 3.0 17.7 - - + +
154D GLN* 3.4 25.6 + - + +
158D LEU* 5.9 0.2 - - + -
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Residues in contact with SER 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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25D LEU* 2.9 12.8 + - - +
27D GLU* 1.3 78.3 - - - +
29D LEU* 1.3 57.8 + - - +
34D GLY* 4.1 5.6 - - - -
35D GLU* 2.8 38.6 + - - +
73D ILE* 4.2 23.5 - - - +
154D GLN* 5.2 6.4 + - - +
155D VAL* 4.6 11.0 - - - +
158D LEU* 3.6 25.6 - - - +
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Residues in contact with LEU 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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25D LEU 3.3 3.7 + - - +
26D GLN* 3.2 11.3 + - - +
28D SER* 1.3 78.5 - - - +
30D GLY* 1.3 60.7 + - - +
31D GLY 3.6 0.6 + - - -
34D GLY 4.8 0.7 - - - -
35D GLU 4.4 0.7 + - - -
36D THR* 2.8 38.7 + - - +
70D VAL* 3.8 31.4 - - + +
73D ILE* 3.8 13.9 - - + -
74D SER* 3.4 30.5 - - - +
77D ILE* 4.0 7.4 - - + -
116D ALA* 3.9 16.6 - - + -
117D SER 3.2 25.6 - - - +
118D LEU* 4.2 13.5 - - + -
126D TRP* 4.5 0.3 - - - -
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Residues in contact with GLY 30 (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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26D GLN 2.8 13.6 + - - -
29D LEU* 1.3 76.8 - - - +
31D GLY* 1.3 60.5 + - - -
118D LEU* 3.8 16.4 - - - -
119D ASN 3.6 16.3 + - - -
120D ASN* 3.9 7.2 + - - +
124D ALA 4.4 0.7 - - - +
126D TRP* 3.4 31.5 + - - +
130D TYR* 3.9 2.6 + - - -
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Residues in contact with GLY 31 (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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26D GLN 3.5 2.4 + - - -
27D GLU* 3.0 31.7 + - - -
29D LEU 3.6 0.8 - - - +
30D GLY* 1.3 81.0 - - - +
32D GLN* 1.3 68.0 + - - +
33D TRP 3.2 2.9 - - - -
34D GLY* 3.1 12.1 + - - -
37D THR* 3.4 8.3 + - - -
120D ASN* 3.9 10.8 - - - -
126D TRP* 3.7 4.2 - - - -
130D TYR* 3.8 3.4 - - - -
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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