Contacts of the strand formed by residues 29 - 43 (chain A) in PDB entry 3OAN
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 GLY 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.4 14.3 - - - -
24A ASP* 2.8 30.4 + - - +
27A THR* 3.2 12.7 - - - +
28A LYS* 1.3 78.9 - - - +
30A TYR* 1.3 62.0 + - - -
31A THR* 4.0 1.6 - - - +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 23.4 - - + +
22A ILE 3.5 13.0 - - - -
23A PHE* 3.4 41.7 - + + +
27A THR* 5.5 0.5 - - - +
29A GLY* 1.3 72.9 - - - -
31A THR* 1.3 61.7 - - - +
97A THR* 2.7 42.7 + - - +
99A ILE* 3.5 34.9 - - + +
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Residues in contact with THR 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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21A LEU* 3.9 4.5 - - - -
22A ILE 3.0 24.3 + - - -
24A ASP* 3.8 25.9 + - + +
27A THR* 4.2 15.7 - - + +
29A GLY 4.0 1.8 - - - +
30A TYR* 1.3 80.7 - - - +
32A SER* 1.3 66.7 + - - +
33A ARG* 2.8 38.5 + - - -
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Residues in contact with SER 32 (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 LYS* 3.2 40.2 - - - +
20A LEU 3.4 6.3 - - - -
21A LEU* 3.7 10.5 - - - +
31A THR* 1.3 75.6 - - - +
33A ARG* 1.3 64.5 + - - +
34A GLY* 3.5 9.4 + - - -
35A VAL* 4.8 0.5 - - - +
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Residues in contact with ARG 33 (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 LEU* 2.7 25.3 + - + +
22A ILE* 2.8 62.9 + - + +
23A PHE 3.5 14.5 + - - -
24A ASP* 3.8 9.8 - - - +
31A THR* 2.8 29.7 + - - +
32A SER* 1.3 78.6 - - - +
34A GLY* 1.3 57.4 + - - +
61A HIS* 5.3 0.9 + - - -
63A LEU* 3.3 20.0 - - + +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ALA 4.1 0.2 - - - +
19A LYS* 3.3 4.2 - - - +
20A LEU* 2.9 27.8 + - - +
32A SER* 3.5 8.6 + - - -
33A ARG* 1.3 81.1 - - - +
35A VAL* 1.3 64.5 + - - -
56A SER* 5.7 1.1 - - - -
61A HIS* 6.4 0.2 - - - -
63A LEU* 3.8 14.1 - - - +
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Residues in contact with VAL 35 (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 LYS* 4.4 17.9 - - + -
18A ALA 3.3 10.5 - - - +
19A LYS* 3.6 34.8 - - + -
32A SER* 4.8 1.1 - - - +
34A GLY* 1.3 76.1 - - - +
36A GLY* 1.3 62.0 + - - +
56A SER* 3.4 6.3 - - - -
57A GLU* 2.9 44.3 + - + +
63A LEU* 4.0 4.0 - - - +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.5 5.8 - - - -
18A ALA* 2.8 34.3 + - - +
35A VAL* 1.3 77.2 - - - +
37A GLU* 1.3 61.7 + - - -
38A LEU 3.5 0.5 + - - -
54A MSE 4.2 7.2 - - - +
55A ARG 3.2 15.7 - - - -
56A SER* 4.0 1.1 - - - -
57A GLU* 3.9 12.8 - - - -
63A LEU* 4.6 1.2 - - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A CYS* 3.6 31.2 - - - -
16A GLU 3.7 10.5 - - - +
17A LYS* 4.5 2.0 - - - +
36A GLY* 1.3 70.7 - - - -
38A LEU* 1.3 60.0 + - - +
39A LYS* 3.5 22.8 + - + +
53A LEU 3.6 1.9 - - - +
54A MSE 3.3 4.0 - - - -
55A ARG* 3.2 33.0 + - + +
57A GLU* 5.2 2.0 - - - +
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Residues in contact with LEU 38 (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 PHE* 3.7 16.3 - - + +
15A CYS* 3.2 5.4 - - - -
16A GLU 2.8 38.3 + - - +
18A ALA* 3.9 13.2 - - + -
36A GLY 3.5 1.4 + - - -
37A GLU* 1.3 72.5 - - - +
39A LYS* 1.3 65.6 + - - +
52A VAL* 4.0 29.6 - - + -
53A LEU 3.8 1.8 - - - +
54A MSE 3.9 28.9 - - + -
64A LEU* 4.7 1.6 - - + -
100A ILE* 3.8 34.1 - - + -
102A VAL* 5.4 0.4 - - + -
111A LEU* 3.8 23.3 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.6 15.8 - - + +
14A PHE 3.2 5.2 - - - +
15A CYS* 4.0 22.4 - - + -
37A GLU* 3.5 26.9 + - + +
38A LEU* 1.3 83.4 - - - +
40A LEU* 1.3 60.3 + - - +
41A LEU* 3.8 31.4 + - + +
52A VAL* 3.3 5.4 - - - +
53A LEU* 2.9 42.3 + - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.6 4.2 - - - -
13A LEU* 2.7 58.1 + - + +
14A PHE* 2.9 24.6 + - + +
38A LEU* 4.3 0.4 - - - +
39A LYS* 1.3 73.3 - - - +
41A LEU* 1.3 57.1 - - - +
50A VAL* 3.8 7.2 - - + -
51A ARG 3.6 10.3 - - - +
52A VAL* 3.9 13.7 - - + -
68A VAL* 3.7 29.8 - - + -
111A LEU* 5.2 2.5 - - + -
114A ALA* 3.7 38.6 - - + +
115A VAL* 4.0 13.5 - - + +
118A ALA* 4.5 1.3 - - + -
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Residues in contact with LEU 41 (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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10A GLU* 3.8 35.5 - - + +
11A GLU 3.3 15.5 - - - +
12A VAL* 4.0 21.1 - - + -
13A LEU* 5.1 0.7 - - - -
39A LYS* 4.0 23.3 - - + +
40A LEU* 1.3 76.0 - - - +
42A ARG* 1.3 60.9 + - - +
49A LYS 4.0 0.3 - - - +
50A VAL* 3.4 5.4 - - - +
51A ARG* 2.9 48.7 + - + +
53A LEU* 3.8 35.0 - - + +
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Residues in contact with ARG 42 (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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10A GLU* 3.3 4.2 - - - -
11A GLU* 2.8 66.5 + - + +
13A LEU* 3.7 36.8 - - + +
40A LEU 4.4 0.2 + - - -
41A LEU* 1.3 75.1 - - - +
43A LYS* 1.3 74.4 + - - +
44A LYS 3.2 0.2 + - - -
46A ASP 4.1 3.6 - - - +
47A LYS* 3.9 37.9 - - - +
49A LYS 3.4 12.6 - - - +
50A VAL* 4.0 11.4 - - + -
117A ASP 5.1 0.6 + - - -
118A ALA* 4.4 8.9 - - - +
121A ALA* 3.7 27.3 - - - +
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Residues in contact with LYS 43 (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 GLU* 3.7 18.2 + - - -
9A ASN* 3.4 20.9 + - + +
10A GLU* 3.9 21.4 + - + +
11A GLU* 5.0 0.5 - - - +
42A ARG* 1.3 76.0 - - - +
44A LYS* 1.3 66.4 + - - +
45A ASP* 3.4 18.6 - - - +
46A ASP* 2.9 34.6 + - + +
47A LYS* 4.0 1.7 + - - +
49A LYS* 3.1 30.0 + - + +
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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