Contacts of the helix formed by residues 18 - 31 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG 4.6 1.1 - - - +
17B SER* 1.3 76.8 - - - +
19B PRO* 1.3 67.9 - - - +
20B ILE* 3.0 22.5 + - - +
21B MET* 3.0 20.9 + - + +
22B ALA 3.0 21.1 + - - -
24B ARG* 4.9 3.5 + - - -
80B LEU* 2.9 30.4 + - + +
161B MET 5.5 0.9 - - - +
162B THR* 5.0 6.9 + - - -
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Residues in contact with PRO 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 4.5 2.7 - - - +
18B ASP* 1.3 85.5 - - - +
20B ILE* 1.3 64.2 + - + +
22B ALA* 3.5 10.1 - - + +
23B ARG* 3.2 24.1 + - - +
80B LEU 3.5 5.8 - - - +
81B LEU* 3.9 12.4 - - + +
82B GLU 6.0 0.4 - - - +
84B ALA* 3.8 28.0 - - + -
85B PRO* 4.5 2.5 - - + -
100B THR* 3.6 30.1 - - + -
104B MET* 3.9 20.6 - - + +
108B HIS* 4.9 1.7 + - - -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 3.0 9.1 + - - +
19B PRO* 1.3 79.1 - - + +
21B MET* 1.3 65.7 + - - +
23B ARG* 3.2 7.2 + - + +
24B ARG* 3.0 49.5 + - + +
99B THR 5.3 0.2 - - - +
100B THR* 3.6 29.4 - - + +
103B GLY* 3.5 37.5 - - - +
104B MET* 3.8 4.0 - - + +
101E MET* 6.0 1.3 - - + -
102E ALA* 6.1 0.7 - - + -
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Residues in contact with MET 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 3.0 32.6 + - + +
20B ILE* 1.3 75.8 - - - +
22B ALA* 1.3 65.1 + - - +
24B ARG* 3.1 27.5 + - - +
25B LEU* 2.9 38.7 + - + +
80B LEU* 4.1 10.3 - - + -
158B LEU* 3.6 47.6 - - + +
161B MET* 3.8 11.4 - - + +
162B THR* 3.8 22.2 - - + +
167B VAL* 4.1 14.4 - - + -
171B LEU* 4.6 0.9 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP 3.0 14.6 + - - +
19B PRO 3.5 9.6 - - - +
20B ILE 3.2 0.2 - - - -
21B MET* 1.3 75.5 - - - +
23B ARG* 1.3 61.9 + - - +
25B LEU* 3.2 12.0 + - - +
26B GLN* 3.3 14.9 + - - +
77B ILE* 3.7 15.8 - - + +
80B LEU* 3.8 22.8 - - + +
81B LEU* 3.6 29.6 - - + -
108B HIS* 4.2 2.9 - - + -
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO 3.2 11.0 + - - +
20B ILE* 3.5 10.8 - - - +
21B MET 3.2 0.2 - - - -
22B ALA* 1.3 79.6 - - - +
24B ARG* 1.3 61.5 + - - +
26B GLN* 3.1 19.8 + - + +
102B ALA 5.0 1.0 + - - -
103B GLY* 2.9 33.9 + - - +
104B MET 4.1 6.0 + - - -
105B ASP* 3.7 23.1 - - + +
106B PRO* 6.3 0.2 - - - -
108B HIS* 4.0 15.0 - - + -
121B PRO* 2.7 32.2 + - + +
122B ASN* 3.2 26.5 + - - +
23E ARG* 5.4 8.7 - - - +
102E ALA 4.5 8.5 + - - -
104E MET 4.8 3.4 + - - -
106E PRO* 3.4 25.4 - - + +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASP* 4.9 3.0 + - - -
20B ILE* 3.0 33.4 + - + +
21B MET* 3.1 33.5 + - - +
23B ARG* 1.3 75.9 - - + +
25B LEU* 1.3 59.1 + - - +
27B GLU* 3.0 28.8 + - - +
121B PRO* 3.8 7.0 - - - +
158B LEU* 3.7 15.1 - - + +
161B MET* 3.4 57.4 + - - +
86E PHE 4.0 5.0 + - - -
87E GLY* 5.2 0.4 - - - -
101E MET* 3.6 29.7 - - - +
106E PRO* 5.2 12.3 - - + +
109E SER* 6.0 0.4 + - - -
110E LEU* 3.6 11.4 - - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B MET* 2.9 30.9 + - + +
22B ALA 3.7 5.8 - - - +
23B ARG 3.2 0.4 - - - -
24B ARG* 1.3 72.8 - - - +
26B GLN* 1.3 66.8 + - - +
27B GLU 3.0 2.0 - - - -
28B SER* 2.9 27.5 + - - +
29B LEU 3.3 7.3 + - - -
73B ILE* 3.6 10.5 - - + +
76B MET* 3.8 17.5 - - + -
77B ILE* 3.9 13.9 - - + -
80B LEU* 3.5 31.4 - - + -
158B LEU* 3.9 24.0 - - + -
167B VAL* 4.6 5.8 - - + -
170B MET* 4.5 15.9 - - + -
171B LEU* 4.5 8.3 - - + -
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA 3.3 12.8 + - - +
23B ARG* 3.1 14.0 + - + +
24B ARG 3.0 0.8 - - - -
25B LEU* 1.3 77.7 - - - +
27B GLU* 1.3 56.9 + - - +
29B LEU* 3.9 8.8 - - - +
30B GLY 2.8 27.7 + - - -
31B GLY 3.5 1.6 + - - -
77B ILE* 3.7 11.0 - - - +
105B ASP* 5.5 2.2 - - - +
108B HIS* 2.8 31.1 + - + +
116B ALA* 3.5 6.2 - - - -
117B SER* 2.8 47.3 + - - +
119B ASN 2.9 26.2 + - - +
120B ASN* 3.7 12.7 - - - +
121B PRO* 3.8 2.2 - - + -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG 3.0 16.2 + - - +
26B GLN* 1.3 79.0 - - - +
28B SER* 1.3 59.4 + - - +
31B GLY* 3.0 45.2 + - - +
32B GLN* 3.8 8.8 + - - +
33B TRP 5.0 0.3 + - - -
34B GLY* 3.8 7.1 + - - -
120B ASN* 4.9 0.2 + - - -
121B PRO* 3.1 19.7 - - + +
154B GLN* 3.5 26.0 + - + +
158B LEU* 5.9 0.2 - - + -
107E GLU* 2.4 37.6 - - - +
110E LEU* 3.5 21.1 - - + +
111E VAL* 3.4 15.0 - - + +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 2.9 13.4 + - - +
27B GLU* 1.3 77.1 - - - +
29B LEU* 1.3 57.4 + - - +
34B GLY* 4.2 5.4 - - - -
35B GLU* 2.8 39.4 + - - +
73B ILE* 4.2 23.3 - - - -
154B GLN* 5.3 5.8 + - - +
155B VAL* 4.7 9.8 - - - +
158B LEU* 3.6 26.2 - - - +
174B LEU* 6.2 0.9 - - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU 3.3 4.6 + - - +
26B GLN* 3.2 11.3 + - - +
28B SER* 1.3 79.9 - - - +
30B GLY* 1.3 60.5 + - - +
31B GLY 3.6 0.8 + - - -
34B GLY 4.7 0.3 - - - -
35B GLU* 4.3 1.4 + - - -
36B THR* 2.8 36.8 + - - +
70B VAL* 3.8 30.3 - - + +
73B ILE* 3.8 13.9 - - + -
74B SER* 3.5 29.2 - - - +
77B ILE* 4.0 7.9 - - + -
116B ALA* 3.9 17.3 - - + -
117B SER 3.2 25.8 - - - +
118B LEU* 4.1 13.7 - - + -
126B TRP* 4.5 0.2 - - - -
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN 2.8 13.3 + - - -
29B LEU* 1.3 76.7 - - - +
31B GLY* 1.3 61.4 + - - +
118B LEU* 3.8 16.4 - - - -
119B ASN 3.6 17.8 + - - -
120B ASN* 3.9 5.7 + - - +
124B ALA 4.4 0.5 - - - +
126B TRP* 3.4 31.9 + - - +
130B TYR* 4.0 2.4 - - - -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B GLN 3.5 2.0 + - - -
27B GLU* 3.0 32.2 + - - -
29B LEU 3.6 0.6 - - - -
30B GLY* 1.3 81.4 - - - +
32B GLN* 1.3 66.3 + - - +
33B TRP 3.3 2.5 - - - -
34B GLY* 3.0 13.0 + - - -
37B THR* 3.4 8.5 + - - -
120B ASN* 3.9 11.2 - - - -
126B TRP* 3.7 3.8 - - - -
130B TYR* 3.8 3.1 - - - -
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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