Contacts of the strand formed by residues 27 - 35 (chain O) in PDB entry 4PJO
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 VAL 27 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19N ILE* 4.5 16.2 - - + -
21N TYR* 6.3 0.4 - - + -
19O THR* 3.4 30.3 - - + -
20O CYS 3.4 12.6 - - - +
21O GLU* 4.1 13.9 - - + +
25O GLY 4.7 2.7 - - - +
26O GLU* 1.3 77.0 - - - +
28O TYR* 1.3 62.1 + - - +
29O ARG* 4.1 0.4 - - - -
47O THR 3.4 3.1 - - - +
48O VAL* 3.3 2.1 - - - -
49O THR* 2.8 56.2 + - + +
70O PHE* 5.9 1.1 - - + -
65P ARG* 6.4 0.2 - - - +
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Residues in contact with TYR 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O VAL 3.6 2.1 - - - +
19O THR* 3.4 3.0 - - - -
20O CYS* 2.9 40.3 + - + +
22O THR* 3.5 23.3 - - + +
26O GLU* 3.4 25.0 + - + +
27O VAL* 1.3 76.0 - - - +
29O ARG* 1.3 58.8 + - - +
43O MET* 3.7 11.7 - - - +
46O ILE* 3.9 22.0 - - + -
47O THR 4.0 3.1 - - - -
48O VAL* 3.6 22.7 - - + +
50O TYR* 5.4 0.2 - - - -
58O LEU* 4.5 4.0 - - + -
61O VAL* 4.8 7.4 - - + -
63O ILE* 4.1 21.5 - - + -
20U LYS* 3.4 28.4 - - - -
69U MET* 3.5 35.1 - - + +
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Residues in contact with ARG 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N PRO* 3.4 17.8 - - - +
16N ARG 2.5 31.1 + - - -
17N ASP* 3.6 1.0 - - - +
18N PRO* 3.4 44.3 - - + +
17O ILE* 3.9 22.0 - - + +
18O VAL 3.5 3.8 - - - +
19O THR* 3.5 26.6 + - + +
28O TYR* 1.3 73.5 - - - +
30O GLY* 1.3 59.2 + - - +
43O MET* 4.2 0.9 - - - -
45O ASN 3.6 1.2 - - - +
46O ILE* 3.1 5.6 - - - +
47O THR* 2.8 53.2 + - - +
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Residues in contact with GLY 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O ILE* 3.3 14.3 - - - +
18O VAL 2.9 34.0 + - - +
29O ARG* 1.3 77.5 - - - +
31O LYS* 1.3 64.0 + - - -
32O LEU 3.5 0.2 + - - -
43O MET* 3.6 5.4 - - - +
44O SER 3.7 2.9 - - - -
45O ASN 3.6 13.9 - - - -
46O ILE* 3.8 5.8 - - - -
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Residues in contact with LYS 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O GLY* 3.4 22.9 + - - +
16O HIS 3.4 6.5 - - - +
17O ILE* 3.4 20.6 - - + +
30O GLY* 1.3 72.2 - - - -
32O LEU* 1.3 64.1 + - - +
33O ILE* 3.4 19.4 + - + +
43O MET* 3.2 6.4 - - - -
44O SER* 2.9 39.2 + - - +
45O ASN* 4.2 21.3 + - + +
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Residues in contact with LEU 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O LEU* 3.8 25.6 - - + +
13O ALA 3.6 19.7 - - - +
14O GLU* 3.6 18.8 - - + +
15O GLY* 2.6 36.2 + - - -
16O HIS 2.8 16.2 + - - +
18O VAL* 3.9 23.8 - - + -
30O GLY 3.5 2.4 + - - -
31O LYS* 1.3 71.2 - - - +
33O ILE* 1.3 56.3 + - - +
34O GLU 3.8 17.7 - - - +
35O ALA* 4.3 1.8 - - + -
41O CYS* 3.9 23.6 - - + -
42O GLN 3.5 17.7 - - - +
43O MET* 4.2 7.0 - - + -
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Residues in contact with ILE 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14O GLU* 3.6 15.9 - - - +
15O GLY* 3.9 4.1 + - - -
31O LYS* 4.0 23.1 - - + +
32O LEU* 1.3 78.3 - - - +
34O GLU* 1.3 66.3 + - + +
42O GLN* 3.0 40.4 + - - +
44O SER* 3.5 35.0 - - - +
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Residues in contact with GLU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22M LYS* 4.3 24.2 + - - +
11O HIS* 5.6 0.2 - - - -
14O GLU* 3.8 11.9 - - - +
32O LEU* 3.8 3.9 - - - +
33O ILE* 1.3 89.2 - - + +
35O ALA* 1.3 76.7 + - - +
36O GLU* 5.0 5.4 - - + +
40O ASN 4.1 0.3 - - - +
41O CYS* 3.6 1.6 - - - -
42O GLN* 2.9 38.7 + - + +
62O TYR* 5.8 0.6 - - + -
8U GLU* 2.9 38.5 - - + +
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Residues in contact with ALA 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O LEU* 3.8 34.8 - - + -
11O HIS* 2.9 26.9 - - - +
14O GLU* 3.1 14.0 + - + +
32O LEU* 4.3 10.1 - - + -
34O GLU* 1.3 81.9 - - - +
36O GLU* 1.3 63.8 + - - +
40O ASN 3.4 9.0 - - - +
41O CYS* 4.1 8.1 - - - +
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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