Contacts of the strand formed by residues 38 - 46 (chain Q) 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 THR 38 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17Q ILE* 4.0 22.9 - - + -
29Q ILE* 4.6 3.8 - - + -
31Q GLY 3.5 2.2 - - - +
32Q VAL* 3.7 19.8 - - + +
36Q MET 2.8 21.1 + - - -
37Q ASN* 1.3 75.7 + - - +
39Q HIS* 1.3 73.6 + - - +
40Q LEU* 4.3 7.4 - - + +
58Q LEU 3.8 0.9 - - - +
59Q SER* 3.2 3.8 - - - -
60Q ILE* 2.8 38.0 + - - +
65Q ILE* 3.7 10.3 - - - +
68Q PHE* 3.7 18.4 - - + -
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Residues in contact with HIS 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P LYS* 4.1 33.3 + - + +
9P MET* 3.7 23.7 - - + +
12P HIS* 5.6 0.8 - - - -
38P MET* 5.9 0.4 - - - -
29Q ILE* 3.4 7.6 - - - +
30Q THR* 3.0 37.5 + - - +
31Q GLY 2.8 24.7 + - - +
32Q VAL* 5.1 0.7 - - - -
33Q ASP* 4.9 8.0 + - + +
37Q ASN* 4.2 16.4 + - + +
38Q THR* 1.3 79.3 - - - +
40Q LEU* 1.3 65.3 + - - +
58Q LEU 3.4 4.3 - - - +
59Q SER* 2.9 34.1 + - - +
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Residues in contact with LEU 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q VAL* 4.1 9.9 - - + -
17Q ILE* 4.0 9.0 - - + -
25Q VAL* 3.5 28.0 - - + -
27Q GLY* 3.7 28.3 - - - +
28Q THR 3.2 13.5 - - - +
29Q ILE* 3.9 18.4 - - + -
30Q THR* 4.1 5.5 + - - +
38Q THR* 4.3 4.9 - - + -
39Q HIS* 1.3 79.5 - - - +
41Q LYS* 1.3 62.2 + - - +
43Q VAL* 3.6 15.3 - - + -
57Q THR* 3.4 6.8 + - - -
58Q LEU* 2.7 33.4 + - + +
60Q ILE* 3.8 20.6 - - + -
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Residues in contact with LYS 41 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q HIS* 4.8 13.7 + - - -
27Q GLY* 3.8 0.3 - - - -
28Q THR* 2.8 56.7 + - - +
30Q THR* 3.7 20.6 - - + -
40Q LEU* 1.3 74.1 - - - +
42Q ALA* 1.3 70.8 + - + +
43Q VAL* 3.5 3.1 - - - -
56Q GLU 3.5 14.1 - - - +
57Q THR* 5.7 0.4 - - - -
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Residues in contact with ALA 42 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q HIS* 3.7 5.9 - - - +
27Q GLY* 3.5 11.1 - - - -
28Q THR* 4.5 8.4 + - - +
41Q LYS* 1.3 83.8 - - + +
43Q VAL* 1.3 61.8 + - - +
44Q LYS* 5.5 0.2 - - - +
55Q LEU 3.8 3.4 - - - -
56Q GLU* 3.5 12.7 + - - +
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Residues in contact with VAL 43 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Q VAL* 4.0 14.1 - - + -
26Q HIS 3.2 9.9 - - - +
27Q GLY* 4.4 0.7 - - - -
40Q LEU* 3.6 33.9 - - + +
41Q LYS* 3.8 9.9 - - - +
42Q ALA* 1.3 80.0 - - - +
44Q LYS* 1.3 72.1 - - - +
45Q MET* 3.8 7.4 - - + +
53Q VAL 3.9 0.2 - - - +
54Q GLN* 3.3 7.7 - - - +
55Q LEU* 2.8 48.5 + - + +
57Q THR 4.5 0.2 - - - -
58Q LEU* 4.0 26.2 - - + +
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Residues in contact with LYS 44 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Q GLN 3.6 4.0 - - - +
26Q HIS* 2.8 48.6 + - + +
42Q ALA 4.1 0.4 + - - +
43Q VAL* 1.3 76.3 - - - +
45Q MET* 1.3 57.8 + - - +
46Q THR* 3.9 7.9 + - - +
52Q PRO* 3.9 30.3 - - + -
53Q VAL 3.5 5.2 - - - +
54Q GLN* 3.5 26.5 - - + +
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Residues in contact with MET 45 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P ILE* 4.5 16.4 - - + -
79P SER* 4.5 8.1 - - - +
19Q LEU* 6.5 0.2 - - - -
23Q THR* 3.7 20.0 - - + -
24Q GLN 3.4 2.9 - - - -
25Q VAL* 4.0 8.1 - - + +
43Q VAL* 3.8 11.3 - - + +
44Q LYS* 1.3 70.4 - - - +
46Q THR* 1.3 65.2 + - - +
47Q LEU* 3.9 30.6 + - + -
52Q PRO* 3.5 0.9 - - - +
53Q VAL* 2.9 47.2 + - + +
55Q LEU* 4.2 13.7 - - + -
58Q LEU* 3.9 33.0 - - - -
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Residues in contact with THR 46 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q GLY 4.2 2.1 - - - +
23Q THR* 3.6 1.5 - - - -
24Q GLN* 2.8 42.7 + - - +
44Q LYS* 3.9 11.3 + - - +
45Q MET* 1.3 76.6 + - - +
47Q LEU* 1.3 69.1 + - - +
50Q ARG 3.6 20.4 - - - +
51Q GLU 4.8 0.4 - - - -
52Q PRO* 3.8 27.6 - - + +
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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