Contacts of the helix formed by residues 28 - 39 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ASP* 1.3 70.7 - - - +
29B PRO* 1.3 74.3 - - + +
31B LEU* 3.0 12.3 + - - +
32B LEU* 3.0 38.7 + - + +
54B LEU 5.6 3.8 - - - -
55B ALA 5.1 3.0 + - - -
58B PHE* 3.3 42.2 - - + -
59B GLU* 2.7 39.8 + - - +
67B LYS* 4.8 6.3 + - - +
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP* 2.9 27.4 - - + +
28B LYS* 1.3 92.6 - - + +
30B SER* 1.3 58.6 + - - +
32B LEU* 3.4 12.8 + - + +
33B THR* 3.0 28.4 + - - -
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.6 33.8 + - - -
21B ARG* 5.0 8.3 - - - +
26B ILE* 3.7 5.6 - - - -
27B ASP* 2.5 37.6 + - - -
29B PRO* 1.3 75.4 - - - +
31B LEU* 1.3 56.6 + - - +
33B THR* 3.3 7.6 + - - -
34B MET* 2.9 27.7 + - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 3.4 17.9 - - + +
27B ASP 2.9 15.2 + - - +
28B LYS 3.0 6.7 + - - +
30B SER* 1.3 74.6 - - - +
32B LEU* 1.3 61.0 + - + +
34B MET* 3.1 21.3 + - + +
35B MET* 2.9 31.1 + - + +
57B VAL* 4.0 22.2 - - + -
58B PHE* 3.7 38.8 - - + +
61B LYS* 5.8 1.3 - - + -
69B ILE* 4.4 17.0 - - + -
74B PHE* 5.5 1.8 - - + -
77B LEU* 3.7 24.5 - - + -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 3.0 40.7 + - + +
29B PRO* 3.8 11.9 - - + +
31B LEU* 1.3 80.4 - - + +
33B THR* 1.3 57.4 + - - +
35B MET* 3.3 7.5 + - - +
36B LYS* 3.0 40.0 + - + +
54B LEU* 3.9 40.3 - - + +
57B VAL* 4.0 17.0 - - + -
58B PHE* 5.1 1.1 - - + -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 4.1 8.7 - - + -
29B PRO 3.0 15.8 + - - -
30B SER* 3.4 11.7 - - - -
32B LEU* 1.3 74.2 - - - +
34B MET* 1.3 65.9 + - - +
36B LYS* 3.0 14.1 + - - +
37B GLU* 3.0 48.1 + - + +
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 3.8 21.3 - - + +
16B PHE* 5.7 0.2 - - - -
19B TYR* 3.3 45.5 - - + -
26B ILE* 4.6 6.3 - - - -
30B SER 2.9 14.7 + - - +
31B LEU* 3.3 25.4 - - + +
33B THR* 1.3 76.3 - - - +
35B MET* 1.3 99.4 + - + +
38B ASN* 2.8 35.1 + - - +
39B PHE* 4.4 13.9 - - + -
74B PHE* 3.9 13.9 - - + -
77B LEU* 4.5 5.6 - - + -
78B LEU* 5.3 0.7 - - + -
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Residues in contact with MET 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 2.9 26.0 + - + +
32B LEU* 3.4 10.8 - - - +
34B MET* 1.3 96.4 - - + +
36B LYS* 1.3 57.8 + - - +
39B PHE* 2.8 48.2 + - + +
42B PHE* 4.5 3.6 - - + -
43B LEU* 3.4 23.5 - - + +
53B TYR* 3.9 33.0 - - + -
54B LEU* 3.9 19.7 - - + -
57B VAL* 5.1 4.7 - - + -
77B LEU* 4.1 15.9 - - + -
81B ILE* 4.4 10.8 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.0 23.8 + - - +
33B THR* 3.0 11.3 + - + +
35B MET* 1.3 77.6 - - - +
37B GLU* 1.3 62.5 + - + +
38B ASN 3.6 0.2 + - - -
40B PRO* 3.8 21.7 - - - +
43B LEU* 3.6 16.9 - - + +
54B LEU* 3.5 29.4 - - + +
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Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 4.0 12.8 - - - +
18B LYS* 3.8 14.1 + - - -
19B TYR* 2.3 32.1 + - - -
33B THR* 3.0 34.4 + - + +
36B LYS* 1.3 77.9 - - + +
38B ASN* 1.3 67.1 + - - +
39B PHE 3.8 0.2 - - - -
40B PRO* 4.2 1.5 - - - +
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Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A THR* 2.7 26.3 + - - -
5A ALA* 3.6 16.7 - - + +
6A GLU* 3.6 0.7 - - - +
15B MET* 3.8 21.3 - - - +
18B LYS* 5.0 5.7 + - - -
19B TYR* 2.9 32.3 + - - -
34B MET* 2.8 27.0 + - + +
37B GLU* 1.3 82.2 + - - +
39B PHE* 1.3 82.4 + - + +
40B PRO* 3.3 6.6 - - - +
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 4.0 12.3 - - + -
6A GLU* 3.5 25.4 - - + -
9A ILE* 3.9 24.7 - - + -
15B MET* 4.5 7.0 - - + -
34B MET* 4.4 10.3 - - + -
35B MET* 2.8 37.5 + - + +
38B ASN* 1.3 97.6 - - + +
40B PRO* 1.3 58.7 - - - +
41B ASN 3.3 2.0 - - - -
42B PHE* 4.0 11.4 - - + -
43B LEU* 2.9 28.6 + - - +
78B LEU* 4.1 20.0 - - + -
81B ILE* 3.8 38.1 - - + -
85B TYR* 5.3 0.7 - + - -
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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