Contacts of the helix formed by residues 28 - 39 (chain A) in PDB entry 3PSR
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 LYS 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP* 1.3 72.6 - - - +
29A PRO* 1.3 74.1 - - + +
31A LEU* 2.9 12.1 + - - +
32A LEU* 2.9 36.3 + - + +
54A LEU 5.3 4.0 - - - -
55A ALA 4.8 4.6 + - - -
58A PHE* 3.4 55.5 - - + -
59A GLU* 3.0 26.5 + - - +
67A LYS 4.7 1.0 + - - -
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Residues in contact with PRO 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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21A ARG* 6.0 0.2 - - - +
27A ASP* 3.4 17.7 - - + +
28A LYS* 1.3 99.2 - - + +
30A SER* 1.3 55.5 + - - +
32A LEU* 3.5 10.6 + - + +
33A THR* 3.0 30.7 + - - -
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Residues in contact with SER 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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19A TYR* 4.0 22.0 + - - -
21A ARG* 3.6 13.5 + - - -
26A ILE* 3.9 12.3 - - - -
27A ASP* 2.7 29.3 + - - -
29A PRO* 1.3 77.9 - - - +
31A LEU* 1.3 60.7 + - - +
33A THR* 3.2 8.3 + - - -
34A MET* 2.8 30.3 + - - +
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Residues in contact with LEU 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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26A ILE* 3.5 15.7 - - + +
27A ASP 2.8 14.0 + - - +
28A LYS 2.9 7.6 + - - +
30A SER* 1.3 77.6 - - - +
32A LEU* 1.3 62.3 + - + +
34A MET* 3.4 17.9 - - + +
35A MET* 3.1 25.6 + - + +
57A VAL* 4.7 14.8 - - + -
58A PHE* 3.3 44.2 - - + +
61A LYS* 5.6 1.1 - - + -
69A ILE* 3.8 26.9 - - + -
74A PHE* 5.4 1.3 - - + -
77A LEU* 4.0 24.0 - - + -
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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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28A LYS* 2.9 44.8 + - + +
29A PRO* 3.8 10.8 - - + +
31A LEU* 1.3 75.8 - - + +
33A THR* 1.3 65.5 + - - +
35A MET* 3.3 7.0 + - + +
36A LYS* 3.0 35.1 + - - +
54A LEU* 3.8 40.0 - - + +
57A VAL* 4.2 16.8 - - + -
58A PHE* 5.1 3.8 - - + -
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Residues in contact with THR 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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19A TYR* 4.1 9.0 - - + -
29A PRO 3.0 16.0 + - - -
30A SER* 3.3 11.8 - - - -
32A LEU* 1.3 76.7 - - - +
34A MET* 1.3 63.0 + - - +
36A LYS* 3.3 8.1 + - - +
37A GLU* 2.9 56.0 + - + +
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Residues in contact with MET 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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15A MET* 4.5 9.9 - - + +
16A PHE* 5.9 0.2 - - - -
19A TYR* 3.3 46.4 - - + -
26A ILE* 4.7 6.1 - - - -
30A SER 2.8 17.1 + - - +
31A LEU* 3.4 18.4 - - - +
33A THR* 1.3 76.1 - - - +
35A MET* 1.3 72.9 + - + +
38A ASN* 2.9 39.7 + - - +
39A PHE* 3.8 26.0 - - + -
74A PHE* 3.9 26.5 - - + -
77A LEU* 4.8 7.2 - - + -
78A LEU* 5.5 0.7 - - + -
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Residues in contact with MET 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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31A LEU* 3.1 19.7 + - + +
32A LEU* 3.4 9.2 - - - +
34A MET* 1.3 93.8 - - + +
36A LYS* 1.3 58.2 + - - +
39A PHE* 2.8 49.3 + - + +
42A PHE* 4.2 5.2 - - + -
43A LEU* 3.8 16.7 - - + +
53A TYR* 4.1 27.8 - - + -
54A LEU* 3.7 21.5 - - + -
57A VAL* 5.2 5.6 - - + -
77A LEU* 4.1 20.9 - - + -
81A ILE* 3.9 22.7 - - + -
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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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32A LEU* 3.0 24.7 + - - +
33A THR* 3.7 8.3 - - - +
35A MET* 1.3 77.7 - - - +
37A GLU* 1.3 63.2 + - + +
40A PRO* 3.8 21.1 - - - +
43A LEU* 4.0 10.3 - - + +
54A LEU* 3.3 31.6 - - + +
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Residues in contact with GLU 37 (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 TYR* 2.6 32.8 + - - +
33A THR* 2.9 34.4 + - + +
36A LYS* 1.3 79.8 - - + +
38A ASN* 1.3 69.2 + - - +
40A PRO* 4.2 2.0 - - - +
3B THR* 4.0 12.3 - - - +
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Residues in contact with ASN 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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15A MET* 3.8 18.2 - - - +
19A TYR* 2.8 35.7 + - - -
34A MET* 2.9 28.2 + - + +
37A GLU* 1.3 80.5 - - - +
39A PHE* 1.3 76.0 + - + +
40A PRO* 3.3 5.6 - - - -
3B THR* 2.5 30.0 + - - -
5B ALA* 3.5 20.6 + - + +
6B GLU* 3.7 0.7 - - - +
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Residues in contact with PHE 39 (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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12A MET* 5.3 1.1 - - + -
15A MET* 4.1 7.2 - - + -
34A MET* 3.8 21.5 - - + -
35A MET* 2.8 38.5 + - + +
38A ASN* 1.3 91.3 - - + +
40A PRO* 1.3 64.1 - - - +
42A PHE* 3.4 12.0 + - + -
43A LEU* 3.1 23.4 + - - +
78A LEU* 3.4 27.1 - - + -
81A ILE* 4.1 20.4 - - + -
85A TYR* 5.5 0.2 - + - -
5B ALA* 4.0 27.4 - - + -
6B GLU* 3.2 21.5 - - + -
9B ILE* 4.2 21.8 - - + -
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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