Contacts of the helix formed by residues 18 - 31 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.8 2.4 + - + +
17A SER* 1.3 76.2 - - - +
19A PRO* 1.3 65.2 - - - +
20A ILE* 3.1 13.3 + - - +
21A MET* 3.0 34.1 + - + +
22A ALA 3.0 21.1 + - - -
24A ARG* 4.8 4.0 + - - -
80A LEU* 2.9 26.6 + - + +
161A MET 5.2 2.1 - - - +
162A THR* 4.8 7.6 + - - -
164A ASP* 6.1 1.8 - - + +
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Residues in contact with PRO 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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17A SER* 4.4 4.9 - - - +
18A ASP* 1.3 86.3 - - - +
20A ILE* 1.3 63.4 + - + +
22A ALA* 3.5 8.9 - - + +
23A ARG* 3.1 24.3 + - - +
80A LEU 3.9 8.3 - - - +
81A LEU* 3.9 10.4 - - + +
84A ALA* 3.8 26.2 - - + -
85A PRO* 4.3 1.8 - - + -
100A THR* 3.6 30.3 - - + -
104A MET* 3.8 21.9 - - + +
108A HIS* 4.8 1.7 + - - -
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Residues in contact with ILE 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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18A ASP* 3.1 9.3 + - - +
19A PRO* 1.3 78.7 - - + +
21A MET* 1.3 64.3 + - - +
23A ARG* 3.2 8.1 + - + +
24A ARG* 3.0 49.5 + - + +
99A THR 5.2 0.2 - - - +
100A THR* 3.5 29.8 - - + +
103A GLY* 3.5 39.0 - - - +
104A MET* 3.8 3.4 - - + +
101D MET* 6.0 0.7 - - + -
102D ALA* 6.1 0.7 - - + -
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Residues in contact with MET 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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18A ASP* 3.0 33.5 + - + +
20A ILE* 1.3 73.6 - - - +
22A ALA* 1.3 66.6 + - - +
24A ARG* 3.1 28.4 + - - +
25A LEU* 2.9 31.7 + - + +
80A LEU* 4.0 16.4 - - + -
158A LEU* 3.6 46.9 - - + +
161A MET 3.7 11.4 - - - +
162A THR* 3.9 20.4 - - + -
167A VAL* 4.1 15.0 - - + -
171A LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 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 ASP 3.0 13.0 + - - +
19A PRO 3.5 10.1 - - - +
20A ILE 3.2 0.2 - - - -
21A MET* 1.3 75.1 - - - +
23A ARG* 1.3 62.4 + - - +
25A LEU* 3.3 4.7 + - - +
26A GLN* 3.2 22.5 + - - +
77A ILE* 3.8 16.2 - - + +
80A LEU* 3.8 19.6 - - + +
81A LEU* 3.8 31.0 - - + -
108A HIS* 4.1 3.5 - - + -
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Residues in contact with ARG 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 PRO 3.1 10.4 + - - +
20A ILE* 3.5 10.5 - - - +
21A MET 3.2 0.2 - - - -
22A ALA* 1.3 80.6 - - - +
24A ARG* 1.3 63.1 + - + +
26A GLN* 3.1 19.9 + - + +
102A ALA 4.9 1.4 + - - -
103A GLY* 2.9 33.4 + - - +
104A MET 3.9 7.1 + - - -
105A ASP* 3.7 23.2 - - + +
108A HIS* 4.0 14.1 - - + -
121A PRO* 2.8 40.2 + - + +
122A ASN* 3.3 19.6 + - - +
23C ARG* 5.4 9.1 - - - +
122C ASN* 5.4 2.6 + - - -
23D ARG* 5.6 6.7 - - - +
102D ALA 4.7 6.5 + - - -
104D MET 4.8 3.0 + - - -
106D PRO* 3.5 30.1 - - + +
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Residues in contact with ARG 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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18A ASP* 4.8 2.8 + - - -
20A ILE* 3.0 35.3 + - + +
21A MET* 3.1 33.5 + - - +
23A ARG* 1.3 76.1 - - - +
25A LEU* 1.3 58.7 + - - +
27A GLU* 3.0 29.5 + - - +
121A PRO* 3.8 6.9 - - - +
158A LEU* 3.7 14.1 - - + +
161A MET* 3.4 59.5 + - - +
86D PHE* 3.9 6.3 + - - +
87D GLY* 5.1 0.6 - - - -
91D LEU* 6.0 0.4 - - - +
101D MET* 3.6 28.9 - - - +
106D PRO* 5.1 12.7 - - + +
109D SER* 5.9 0.4 + - - -
110D LEU* 3.6 11.0 - - + +
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Residues in contact with LEU 25 (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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21A MET* 2.9 29.3 + - + +
22A ALA 3.8 4.7 - - - +
23A ARG 3.2 0.4 - - - -
24A ARG* 1.3 72.0 - - - +
26A GLN* 1.3 64.9 + - - +
27A GLU 3.0 1.8 - - - -
28A SER* 2.9 27.3 + - - +
29A LEU 3.3 7.4 + - - -
73A ILE* 3.6 11.9 - - + +
76A MET* 3.7 18.4 - - + -
77A ILE* 3.9 12.8 - - + -
80A LEU* 3.5 31.9 - - + -
158A LEU* 3.9 23.6 - - + -
167A VAL* 4.7 5.2 - - + -
170A MET* 4.5 9.0 - - + -
171A LEU* 4.5 15.3 - - + -
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Residues in contact with GLN 26 (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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22A ALA 3.2 13.0 + - - +
23A ARG* 3.1 14.1 + - + +
24A ARG 3.1 0.8 - - - -
25A LEU* 1.3 77.9 - - - +
27A GLU* 1.3 55.6 + - - +
29A LEU* 3.7 9.6 - - - +
30A GLY 2.8 27.5 + - - -
31A GLY 3.5 1.7 + - - -
77A ILE* 3.6 10.7 - - - +
105A ASP* 5.4 2.7 - - - +
108A HIS* 2.8 29.9 + - + +
116A ALA* 3.5 6.8 - - - -
117A SER* 2.9 47.0 + - - +
119A ASN 2.9 26.5 + - - +
120A ASN* 3.7 13.2 - - - +
121A PRO* 4.1 2.2 - - + -
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Residues in contact with GLU 27 (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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24A ARG 3.0 14.7 + - - +
25A LEU 3.0 0.4 - - - -
26A GLN* 1.3 78.6 - - - +
28A SER* 1.3 58.2 + - - +
31A GLY* 2.9 45.5 + - - +
32A GLN* 3.9 8.7 + - - +
33A TRP 5.1 0.2 + - - -
34A GLY* 3.8 7.1 + - - -
120A ASN* 4.3 0.5 + - - +
121A PRO* 3.1 16.7 - - + +
154A GLN* 3.5 27.6 + - + +
158A LEU* 5.9 0.4 - - + -
107D GLU* 2.4 37.1 - - - +
110D LEU* 3.6 19.9 - - + +
111D VAL* 3.3 14.6 - - + +
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Residues in contact with SER 28 (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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25A LEU* 2.9 12.8 + - - +
27A GLU* 1.3 78.2 - - - +
29A LEU* 1.3 57.5 + - - +
34A GLY* 4.1 6.3 - - - -
35A GLU* 2.8 38.4 + - - +
73A ILE* 4.2 24.2 - - - +
154A GLN* 5.2 5.6 + - - +
155A VAL* 4.7 10.1 - - - +
158A LEU* 3.5 26.7 - - - +
171A LEU* 6.0 0.2 - - - +
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Residues in contact with LEU 29 (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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25A LEU 3.3 4.4 + - - +
26A GLN* 3.2 11.1 + - - +
28A SER* 1.3 81.7 - - - +
30A GLY* 1.3 61.0 + - - +
31A GLY 3.6 1.0 + - - -
34A GLY 4.8 0.3 - - - -
35A GLU* 4.4 0.8 + - - -
36A THR* 2.8 35.0 + - - +
70A VAL* 3.8 31.2 - - + +
73A ILE* 3.8 12.6 - - + -
74A SER* 3.5 30.3 - - - +
77A ILE* 4.0 7.9 - - + -
116A ALA* 3.9 16.2 - - + -
117A SER 3.3 25.8 - - - +
118A LEU* 4.2 14.1 - - + +
126A TRP* 4.5 0.2 - - - -
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Residues in contact with GLY 30 (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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26A GLN 2.8 11.7 + - - -
29A LEU* 1.3 76.4 - - - +
31A GLY* 1.3 63.9 + - - +
118A LEU* 3.9 16.6 - - - -
119A ASN 3.6 17.6 + - - -
120A ASN* 4.0 5.4 + - - +
124A ALA 4.4 0.9 - - - +
126A TRP* 3.4 32.4 + - - +
130A TYR* 3.9 2.4 + - - -
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Residues in contact with GLY 31 (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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26A GLN 3.5 1.6 + - - -
27A GLU* 2.9 32.3 + - - -
29A LEU 3.6 0.8 - - - -
30A GLY* 1.3 81.9 - - - +
32A GLN* 1.3 67.8 + - - +
33A TRP 3.2 2.9 - - - -
34A GLY* 3.1 13.1 + - - -
37A THR* 3.4 8.7 + - - -
120A ASN* 3.9 11.4 - - - -
126A TRP* 3.7 3.6 - - - -
130A TYR* 3.8 2.5 - - - -
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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