Contacts of the helix formed by residues 15 - 29 (chain A) in PDB entry 1SOA
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 GLU 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY 3.6 1.0 + - - -
14A ALA* 1.3 68.7 - - - +
16A GLU* 1.3 67.4 + - - +
17A MET* 2.8 59.9 + - - +
18A GLU* 3.1 43.3 + - - +
19A THR* 3.1 15.8 + - - -
47A SER* 3.6 12.0 + - - +
48A ARG* 3.7 28.5 + - - +
73A PRO* 4.4 0.5 - - - +
74A GLY 2.9 9.1 + - - +
75A GLY* 3.7 13.0 - - - +
106A CSD 4.5 3.6 - - - +
158A PRO* 4.3 7.0 - - + +
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Residues in contact with GLU 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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14A ALA 3.2 2.5 + - - -
15A GLU* 1.3 77.1 + - - +
17A MET* 1.3 65.4 + - + +
19A THR* 3.6 7.1 - - - -
20A VAL* 2.9 34.8 + - + +
46A CYS* 3.4 22.2 - - + +
47A SER* 2.8 26.3 + - - -
48A ARG* 2.9 43.0 + - + +
49A ASP 3.3 0.2 + - - -
50A VAL* 3.1 38.0 + - + +
52A ILE* 4.5 4.0 - - + -
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Residues in contact with MET 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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15A GLU* 2.8 33.6 + - - +
16A GLU* 1.3 78.1 - - + +
18A GLU* 1.3 56.1 + - - +
20A VAL* 4.6 2.2 - - - +
21A ILE* 3.0 54.5 + - + +
158A PRO* 3.5 34.1 - - + +
161A SER* 4.6 0.2 - - - -
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Residues in contact with GLU 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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8A VAL* 5.9 0.2 - - - +
15A GLU* 3.1 21.7 + - + +
17A MET* 1.3 75.4 - - - +
19A THR* 1.3 57.2 + - - +
22A PRO* 3.1 22.8 - - - +
71A VAL* 5.4 1.4 - - - +
73A PRO* 3.9 11.4 - - - +
74A GLY* 2.9 34.3 + - - +
105A ILE* 3.9 17.8 - - + +
106A CSD 2.5 37.4 + - - +
157A GLY 4.3 1.1 - - - -
158A PRO* 3.2 24.6 - - + +
161A SER* 3.6 20.9 - - - +
164A PHE* 5.2 0.2 - - - -
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Residues in contact with THR 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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8A VAL* 4.4 18.9 - - + +
10A LEU* 3.9 33.5 - - + +
14A ALA* 4.0 2.9 - - - +
15A GLU 3.1 12.8 + - - -
16A GLU* 3.6 10.2 - - - -
18A GLU* 1.3 77.8 - - - +
20A VAL* 1.3 67.1 + - + +
22A PRO* 3.4 3.3 - - - +
23A VAL* 3.1 32.6 + - + +
35A VAL* 5.1 3.6 - - + -
52A ILE* 4.4 12.3 - - + -
73A PRO* 3.5 18.3 - - + +
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Residues in contact with VAL 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 GLU* 2.9 21.7 + - + +
17A MET* 4.5 2.2 - - - +
19A THR* 1.3 75.0 - - + +
21A ILE* 1.3 67.6 + - + +
23A VAL* 3.9 5.3 - - + +
24A ASP* 2.9 33.3 + - + +
50A VAL* 6.0 1.8 - - + -
52A ILE* 3.7 26.0 - - + -
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Residues in contact with ILE 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 MET* 3.0 38.5 + - + +
20A VAL* 1.3 78.9 - - + +
22A PRO* 1.3 67.6 - - + +
24A ASP* 3.9 2.4 - - - -
25A VAL* 3.0 27.0 + - + +
158A PRO 4.4 5.8 - - - +
161A SER* 3.6 40.6 - - - +
162A PHE* 3.8 46.9 - - + -
165A ALA* 4.6 0.2 - - + -
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Residues in contact with PRO 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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8A VAL* 5.5 1.3 - - + -
17A MET 3.9 0.2 - - - +
18A GLU* 3.1 31.6 - - - +
19A THR* 3.4 6.1 - - - +
21A ILE* 1.3 93.7 - - + +
23A VAL* 1.3 61.4 + - + +
26A MET* 2.9 43.3 + - + +
71A VAL* 4.6 8.7 - - + -
161A SER* 4.7 3.6 - - - +
164A PHE* 4.0 30.5 - - + -
165A ALA* 3.9 18.2 - - + -
168A ILE* 5.0 2.2 - - + -
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Residues in contact with VAL 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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8A VAL* 3.9 23.3 - - + -
19A THR* 3.1 24.9 + - + +
20A VAL* 3.3 6.0 + - - +
22A PRO* 1.3 75.6 - - - +
24A ASP* 1.3 58.4 + - - +
26A MET* 3.9 7.2 - - - +
27A ARG* 3.0 65.0 + - - +
33A VAL* 4.1 4.8 - - + +
35A VAL* 3.7 25.4 - - + -
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Residues in contact with ASP 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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20A VAL* 2.9 27.5 + - + +
21A ILE* 4.0 2.9 - - - +
23A VAL* 1.3 76.3 - - + +
25A VAL* 1.3 62.2 + - + +
27A ARG* 3.1 9.0 + - - +
28A ARG* 2.9 59.6 + - - +
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Residues in contact with VAL 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 ILE* 3.0 22.9 + - + +
24A ASP* 1.3 77.5 - - + +
26A MET* 1.3 62.4 + - - +
28A ARG* 3.2 11.7 + - - +
29A ALA* 3.1 19.6 + - - +
162A PHE* 4.1 30.5 - - + -
165A ALA* 3.7 22.0 - - + -
166A LEU* 4.0 26.5 - - + -
169A VAL* 4.1 9.4 - - + -
181A VAL* 4.0 6.9 - - + +
185A LEU* 4.3 13.7 - - + -
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Residues in contact with MET 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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6A ALA* 3.7 25.8 - - + -
8A VAL* 3.7 30.1 - - + -
22A PRO* 2.9 36.2 + - + +
23A VAL 4.2 0.4 - - - +
25A VAL* 1.3 74.4 - - - +
27A ARG* 1.3 62.3 + - - +
29A ALA* 3.1 10.6 + - - +
31A ILE* 3.1 40.5 + - + +
33A VAL* 3.7 15.7 - - + -
69A VAL* 4.4 2.2 - - - -
71A VAL* 4.1 9.6 - - + -
165A ALA* 4.9 4.3 - - + +
168A ILE* 3.8 30.5 - - + -
169A VAL* 4.3 9.2 - - + -
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Residues in contact with ARG 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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23A VAL* 3.0 43.8 + - - +
24A ASP* 3.1 6.9 + - - +
26A MET* 1.3 72.3 - - - +
28A ARG* 1.3 65.7 + - - +
30A GLY* 3.0 14.2 + - - -
31A ILE 3.9 10.5 - - - +
33A VAL* 2.9 45.7 + - + +
35A VAL* 4.3 4.9 - - - +
55A ASP* 2.9 27.1 + - - -
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Residues in contact with ARG 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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24A ASP* 2.9 40.6 + - - +
25A VAL* 3.2 14.8 + - - +
27A ARG* 1.3 76.2 - - - +
29A ALA* 1.3 58.6 + - - +
30A GLY 3.2 1.3 + - - -
181A VAL* 3.8 23.8 + - + +
184A PRO* 4.6 18.4 + - - +
185A LEU* 3.6 35.2 - - - +
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Residues in contact with ALA 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 VAL 3.1 4.9 + - - +
26A MET 3.1 11.9 + - - +
28A ARG* 1.3 75.0 - - - +
30A GLY* 1.3 56.5 + - - +
31A ILE* 4.2 2.5 - - + -
169A VAL* 3.6 42.4 - - + -
173A ASN* 2.9 25.7 + - - +
177A VAL* 4.1 7.9 - - + +
181A VAL* 3.7 13.0 - - + +
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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