Contacts of the strand formed by residues 50 - 58 (chain X) in PDB entry 2PMO
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 50 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46X GLU* 3.4 5.0 - - - +
47X LYS 3.0 37.2 + - - +
48X ASP* 2.9 6.4 + - + +
49X ASN* 1.3 81.3 - - - +
51X PHE* 1.3 75.7 + - - +
52X TYR* 3.4 31.3 + - + +
104X GLU* 5.2 7.7 + - - -
118X GLU* 6.5 0.9 - - - -
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Residues in contact with PHE 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ILE* 3.6 24.9 - - + -
44X LEU* 3.8 11.4 - - + -
45X CYS 3.4 12.8 - - - -
46X GLU* 4.3 16.6 - - + -
49X ASN 6.0 2.0 - - - -
50X LYS* 1.3 90.0 - - - +
52X TYR* 1.3 66.8 + - - +
118X GLU* 5.1 0.3 - - - -
119X TYR* 3.5 47.6 + + + +
121X GLU* 5.7 2.0 - - + -
337X TYR* 5.8 4.3 - - - -
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Residues in contact with TYR 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X TYR* 3.6 24.0 - + + -
44X LEU* 3.4 9.0 - - - +
45X CYS* 2.8 33.6 + - + +
46X GLU 4.7 0.4 - - - -
47X LYS* 3.3 48.2 + - + -
48X ASP* 5.6 0.9 - - - +
50X LYS* 3.4 41.1 + - + +
51X PHE* 1.3 76.4 - - - +
53X ALA* 1.3 58.5 + - - +
54X LEU* 4.1 17.7 - - + -
104X GLU* 4.4 19.5 - - + -
116X ILE* 4.1 17.0 - - + -
117X TYR 3.7 10.5 - - - +
118X GLU* 5.1 2.0 - - - -
119X TYR* 4.0 6.7 - - - +
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Residues in contact with ALA 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34X LEU* 4.1 13.0 - - + -
42X ILE* 4.2 3.1 - - + -
43X ILE 3.2 6.5 - - - +
52X TYR* 1.3 73.7 - - - +
54X LEU* 1.3 63.0 + - - +
55X LYS 3.9 1.2 + - - -
115X ILE 3.4 1.4 - - - +
117X TYR* 2.8 41.2 + - - +
118X GLU 4.0 3.1 - - - +
119X TYR* 4.3 1.7 - - - +
400X HMD 3.5 44.0 - - + +
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Residues in contact with LEU 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X ILE* 4.0 29.6 - - + -
28X TYR* 4.0 30.7 - - + -
42X ILE* 4.4 0.9 - - - -
43X ILE* 2.7 43.0 + - + +
45X CYS* 3.9 29.4 - - + -
52X TYR* 4.1 8.5 - - + -
53X ALA* 1.3 76.3 - - - +
55X LYS* 1.3 63.0 + - - +
56X LYS 3.3 3.3 + - - -
107X ILE* 4.7 3.8 - - + -
114X TYR* 4.2 21.5 - - + -
115X ILE 3.2 9.2 - - - +
116X ILE* 4.3 14.1 - - + -
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Residues in contact with LYS 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ASN* 2.9 37.7 + - - +
41X LYS 3.3 10.5 - - - +
42X ILE* 4.1 10.9 - - + +
53X ALA 3.9 2.0 + - - -
54X LEU* 1.3 69.1 - - - +
56X LYS* 1.3 62.9 + - - +
57X TYR* 2.6 42.3 + - + +
88X GLU* 3.4 9.1 + - - -
113X VAL 3.4 2.1 - - - +
114X TYR* 3.3 5.0 - - - -
115X ILE* 3.0 35.4 + - + +
117X TYR* 4.1 12.1 - - + +
190X ASP* 4.1 12.6 + - - +
400X HMD 3.3 45.3 - - + +
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Residues in contact with LYS 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LYS* 5.6 1.2 - - - +
40X ASN* 3.2 11.1 - - - +
41X LYS* 2.6 58.8 + - + +
43X ILE* 4.0 13.0 - - + -
54X LEU 3.3 2.2 + - - -
55X LYS* 1.3 72.3 - - - +
57X TYR* 1.3 69.5 - - - +
58X GLU* 3.5 34.7 + - + -
112X GLU* 4.0 7.3 + - - -
113X VAL 3.3 3.6 - - - +
114X TYR* 3.3 44.8 + - + -
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Residues in contact with TYR 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X PHE 4.2 9.2 - - - -
40X ASN* 3.6 26.5 - - + +
55X LYS* 2.6 47.5 + - + +
56X LYS* 1.3 77.0 - - - +
58X GLU* 1.3 69.8 + - - +
59X LYS 4.3 0.2 - - - -
62X LEU* 4.2 9.6 - - + -
85X PHE* 3.4 45.3 - + + -
88X GLU* 2.7 25.8 + - - -
92X ILE* 4.0 8.0 - - + +
111X ASP 4.6 0.4 - - - -
112X GLU* 3.5 1.2 - - - -
113X VAL* 2.9 38.7 + - + +
115X ILE* 3.7 23.6 - - + -
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Residues in contact with GLU 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39X PHE 5.2 0.4 + - - -
56X LYS* 3.5 32.7 + - + -
57X TYR* 1.3 80.3 - - - +
59X LYS* 1.3 59.4 + - - +
60X SER* 3.4 8.5 + - - -
61X LEU* 3.2 38.9 + - + +
62X LEU* 2.9 38.1 + - - +
111X ASP* 3.8 6.8 - - - +
112X GLU* 4.3 20.3 - - + +
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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