Contacts of the strand formed by residues 27 - 35 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 3.4 32.5 - - + -
20A CYS 3.4 8.5 - - - +
21A GLU* 4.2 19.7 - - + +
25A GLY 3.9 9.2 - - - +
26A GLU* 1.3 81.1 - - - +
28A TYR* 1.3 63.2 - - - +
29A ARG* 5.7 0.9 - - + -
47A THR 3.5 2.8 - - - +
48A VAL* 3.3 2.4 - - - -
49A THR* 2.8 50.0 + - + +
65B ARG* 5.7 4.7 - - - +
19K ILE* 4.4 15.7 - - + -
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Residues in contact with TYR 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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18A VAL 3.6 2.1 - - - +
19A THR* 3.3 3.4 - - - -
20A CYS* 2.9 40.9 + - + +
22A THR* 3.6 22.5 - - + +
26A GLU* 3.5 25.0 + - + +
27A VAL* 1.3 76.7 - - - +
29A ARG* 1.3 60.0 + - - +
43A MET* 3.7 10.8 - - - +
46A ILE* 3.8 24.7 - - + -
47A THR 4.1 0.4 - - - -
48A VAL* 3.7 23.6 - - + +
50A TYR* 5.4 0.5 - - - -
58A LEU* 4.5 6.7 - - + -
61A VAL* 4.8 5.2 - - + -
63A ILE* 4.1 22.0 - - + -
20G LYS* 3.5 27.7 + - - -
68G ILE* 5.7 0.3 - - - +
69G MET* 3.5 31.4 - - + +
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Residues in contact with ARG 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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17A ILE* 3.9 21.7 - - + +
18A VAL 3.5 4.0 - - - +
19A THR* 3.5 27.4 + - + +
27A VAL* 5.7 0.9 - - + -
28A TYR* 1.3 74.3 - - - +
30A GLY* 1.3 60.7 + - - +
45A ASN 3.6 1.7 - - - +
46A ILE* 3.1 6.8 - - - +
47A THR* 2.9 51.3 + - - +
15K PRO* 3.4 17.0 - - - +
16K ARG 2.4 32.3 + - - -
17K ASP* 3.6 0.8 - - - +
18K PRO* 3.4 42.3 - - + +
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Residues in contact with GLY 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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17A ILE* 3.3 13.9 - - - +
18A VAL 2.9 32.3 + - - +
29A ARG* 1.3 77.6 - - - +
31A LYS* 1.3 64.5 + - - -
32A LEU 3.5 0.2 + - - -
43A MET* 3.6 5.9 - - - +
45A ASN 3.6 14.1 - - - -
46A ILE* 3.7 8.5 - - - -
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Residues in contact with LYS 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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15A GLY* 3.2 33.9 - - - +
16A HIS 3.4 8.3 - - - +
17A ILE* 3.7 13.5 - - + +
30A GLY* 1.3 71.0 - - - -
32A LEU* 1.3 62.8 + - - +
33A ILE* 3.2 22.7 + - + +
43A MET* 3.2 5.9 - - - -
44A SER* 2.9 45.6 + - - +
45A ASN* 4.5 13.4 + - + +
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Residues in contact with LEU 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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10A LEU* 3.8 26.0 - - + +
13A ALA* 3.6 19.5 - - + +
14A GLU* 3.7 17.5 - - + +
15A GLY* 2.6 35.9 + - - -
16A HIS 2.8 16.8 + - - +
18A VAL* 3.9 22.9 - - + -
30A GLY 3.5 2.4 + - - -
31A LYS* 1.3 69.4 - - - +
33A ILE* 1.3 55.4 + - - +
34A GLU 3.2 28.7 - - - +
35A ALA* 4.3 1.3 - - + -
41A CYS* 3.9 23.6 - - + -
42A GLN 3.5 9.2 - - - +
43A MET* 4.2 7.2 - - + -
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Residues in contact with ILE 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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14A GLU* 4.1 9.4 - - - +
15A GLY* 4.3 3.6 + - - +
31A LYS* 3.2 27.1 + - + +
32A LEU* 1.3 74.5 - - - +
34A GLU* 1.3 65.6 + - + +
42A GLN* 3.1 39.8 + - - +
44A SER* 3.3 34.5 - - - +
60A GLN* 5.9 0.4 - - - +
11G LYS* 5.8 2.2 - - - -
3K GLN* 5.4 2.8 + - - +
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Residues in contact with GLU 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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11A HIS* 5.5 0.2 - - - -
14A GLU* 3.9 15.8 - - - +
32A LEU* 3.2 11.6 - - - +
33A ILE* 1.3 91.3 - - + +
35A ALA* 1.3 74.8 + - - +
36A GLU* 5.0 8.1 - - + +
40A ASN 4.3 0.2 - - - +
41A CYS* 3.7 0.2 - - - -
42A GLN* 3.1 30.7 + - + -
8G GLU* 2.7 33.3 - - + +
11G LYS* 3.6 17.0 + - - +
22L LYS* 4.1 23.8 + - - +
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Residues in contact with ALA 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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10A LEU* 3.8 37.2 - - + +
11A HIS* 2.8 23.5 + - + +
14A GLU* 3.0 20.3 + - + +
32A LEU* 4.3 7.9 - - + -
34A GLU* 1.3 83.1 - - - +
36A GLU* 1.3 65.5 + - - +
40A ASN 3.6 8.1 - - - +
41A CYS* 4.4 2.5 - - - -
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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