Contacts of the strand formed by residues 27 - 36 (chain A) in PDB entry 3CJE
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 ARG 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A VAL* 2.9 43.2 + - + +
24A GLY* 5.1 0.4 - - - -
26A MSE 1.3 77.9 - - - +
28A ASN* 1.3 65.9 + - - +
29A GLU* 3.4 25.1 + - - +
45A ALA* 3.6 27.6 - - - +
46A THR 3.3 12.2 + - - +
47A ASP* 3.6 23.6 + - - +
78A ARG* 2.8 17.1 + - - -
167A PO4 3.2 12.0 + - - +
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Residues in contact with ASN 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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21A LYS 3.6 2.9 - - - -
22A ALA* 3.9 0.3 - - - -
26A MSE 3.9 7.3 + - - -
27A ARG* 1.3 73.7 - - - +
29A GLU* 1.3 62.1 + - - +
30A LEU* 3.7 7.1 + - + +
45A ALA* 3.1 7.6 - - - +
46A THR* 2.9 45.8 + - - +
71A GLY* 3.6 10.0 + - - -
74A MSE 3.3 40.0 - - - +
75A THR* 3.4 25.5 + - - +
78A ARG* 3.1 25.6 + - - +
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Residues in contact with GLU 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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19A ASN 3.6 2.9 - - - +
20A GLY* 3.4 1.9 - - - -
21A LYS* 2.9 44.5 + - + +
23A VAL* 3.7 29.4 - - + +
27A ARG* 3.4 35.4 + - - +
28A ASN* 1.3 73.0 - - - +
30A LEU* 1.3 58.6 + - - +
31A ASP* 3.9 1.1 + - - +
44A LEU 3.8 4.3 - - - +
45A ALA* 4.8 0.4 - - + -
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Residues in contact with LEU 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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18A CYS* 3.8 11.9 - - - -
19A ASN 3.8 1.8 - - - -
20A GLY* 3.8 20.4 - - - -
28A ASN* 3.8 8.3 - - + +
29A GLU* 1.3 72.5 - - - +
31A ASP* 1.3 61.3 + - - +
32A VAL* 3.4 5.3 + - + +
42A PHE 3.6 0.2 - - - +
43A ALA* 3.8 1.0 - - - -
44A LEU* 2.8 42.4 + - - +
45A ALA* 4.0 4.5 - - - +
46A THR* 3.7 35.9 - - + +
67A ALA* 3.4 34.8 - - + +
70A THR* 3.9 21.8 - - + -
71A GLY* 4.2 3.4 - - - +
74A MSE 4.0 10.5 - - - -
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Residues in contact with ASP 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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17A THR* 4.0 0.7 + - - +
18A CYS* 3.3 1.7 - - - -
19A ASN* 2.9 48.4 + - + +
29A GLU 3.9 0.8 + - - -
30A LEU* 1.3 68.9 - - - +
32A VAL* 1.3 66.1 + - - +
33A ALA 4.0 0.2 + - - -
41A ARG* 2.9 42.9 + - - +
42A PHE 3.9 6.0 - - - +
43A ALA* 5.0 3.5 - - + +
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Residues in contact with VAL 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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16A PHE* 3.9 10.8 - - + -
17A THR 3.3 4.9 - - - +
18A CYS* 3.8 20.9 - - - -
30A LEU 4.0 7.4 - - - +
31A ASP* 1.3 77.3 - - - +
33A ALA* 1.3 63.8 + - - +
41A ARG* 3.3 3.6 - - - -
42A PHE* 2.8 44.7 + - + +
44A LEU* 4.0 6.5 - - + -
63A ALA* 3.9 22.9 - - + +
66A ILE* 3.6 24.0 - - + -
67A ALA* 4.0 22.7 - - + -
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Residues in contact with ALA 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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16A PHE* 3.2 9.5 - - - -
17A THR* 2.9 48.5 + - - +
31A ASP 4.0 0.4 + - - -
32A VAL* 1.3 75.6 - - - +
34A MSE 1.3 65.0 + - - +
35A VAL* 3.7 5.9 + - + -
40A GLU 3.1 11.9 - - - +
41A ARG* 3.9 28.9 - - + +
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Residues in contact with MSE 34 (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 VAL* 5.1 1.1 - - - -
15A VAL 3.7 2.9 - - - +
16A PHE* 3.7 38.0 - - + -
33A ALA* 1.3 74.7 - - - +
35A VAL* 1.3 58.2 + - - +
36A LYS 3.4 17.3 - - - +
37A PRO* 3.8 20.6 - - - -
38A PHE* 3.1 59.7 - - + +
39A GLU* 3.1 6.8 - - - +
40A GLU* 2.9 43.6 + - + +
42A PHE* 4.3 5.3 - - + -
60A PRO* 5.8 3.8 - - + -
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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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15A VAL* 2.8 21.7 + - + +
17A THR* 4.0 34.3 - - + +
33A ALA* 4.1 8.1 - - + +
34A MSE 1.3 77.2 - - - +
36A LYS* 1.3 73.5 + - + +
37A PRO 4.3 0.5 - - - -
38A PHE* 3.5 16.1 + - - +
39A GLU* 3.9 18.4 - - + +
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Residues in contact with LYS 36 (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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13A GLU* 3.2 40.2 + - + +
14A VAL* 3.4 1.9 - - - +
15A VAL* 2.9 49.9 + - + +
34A MSE 3.4 9.1 - - - +
35A VAL* 1.3 87.8 - - + +
37A PRO* 1.4 70.7 - - + +
38A PHE 3.4 1.8 - - - -
96A ARG* 5.6 4.2 - - - +
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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