Contacts of the strand formed by residues 41 - 47 (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 41 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33X THR* 4.0 28.0 - - + +
35X ASN 3.5 8.3 - - - +
36X GLN* 3.1 43.3 + - + +
40X ASN* 1.3 75.6 - - - +
42X ILE* 1.3 62.6 + - - +
43X ILE* 4.1 14.1 - - + -
54X LEU 3.8 0.2 - - - +
55X LYS* 3.3 3.6 - - - +
56X LYS* 2.6 65.8 + - + +
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Residues in contact with ILE 42 (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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33X THR* 3.5 6.1 - - - -
34X LEU* 2.8 31.6 + - + -
35X ASN* 2.8 49.8 + - + +
40X ASN* 4.3 10.1 - - - +
41X LYS* 1.3 77.3 - - - +
43X ILE* 1.3 63.1 + - - +
53X ALA* 4.2 13.0 - - + -
54X LEU 3.8 7.2 - - - +
55X LYS* 4.1 17.0 - - + +
400X HMD 3.6 64.6 - - + +
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Residues in contact with ILE 43 (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* 4.6 8.3 - - + -
30X ILE* 4.1 22.4 - - + -
32X ARG 3.8 12.3 - - - +
33X THR* 4.3 4.7 - - + +
34X LEU* 4.5 1.8 - - - -
41X LYS* 4.1 19.5 - - + -
42X ILE* 1.3 79.1 - - - +
44X LEU* 1.3 73.2 + - - +
45X CYS* 3.6 16.0 + - - -
53X ALA* 3.2 5.5 - - - -
54X LEU* 2.7 45.5 + - + +
56X LYS* 4.0 25.6 - - + -
114X TYR* 4.3 15.5 - - + -
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Residues in contact with LEU 44 (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* 3.1 43.1 + - + +
32X ARG* 3.0 51.3 + - + +
34X LEU* 3.7 28.9 - - + +
43X ILE* 1.3 72.2 - - - +
45X CYS* 1.3 82.6 + - - +
51X PHE* 3.8 27.8 - - + -
52X TYR 3.4 12.3 - - - +
119X TYR* 4.2 17.9 - - + +
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Residues in contact with CYS 45 (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* 4.9 1.8 - - - -
28X TYR* 3.8 24.2 - - + -
29X ARG 3.1 14.4 - - - +
30X ILE* 4.3 9.2 - - - -
31X ILE* 4.1 4.7 - - - -
43X ILE* 3.9 19.3 - - - -
44X LEU* 1.3 86.0 - - - +
46X GLU* 1.3 61.3 + - - +
51X PHE* 3.4 8.5 - - - -
52X TYR* 2.8 30.4 + - - +
54X LEU* 3.9 31.6 - - + -
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Residues in contact with GLU 46 (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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27X ASP 3.4 3.5 - - - +
28X TYR* 3.5 1.5 - - - -
29X ARG* 2.9 66.7 + - - +
31X ILE* 3.9 14.1 - - + -
45X CYS* 1.3 79.0 - - - +
47X LYS* 1.3 66.7 + - - +
48X ASP 5.0 0.4 - - - +
49X ASN* 4.6 19.3 - - - +
50X LYS 3.4 11.0 - - - +
51X PHE* 4.3 15.4 - - + -
52X TYR* 4.7 0.9 - - - -
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Residues in contact with LYS 47 (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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26X ASN 5.2 0.4 - - - -
27X ASP* 3.9 33.2 - - + +
28X TYR* 3.7 37.3 + - + -
46X GLU* 1.3 76.3 - - - +
48X ASP* 1.3 90.5 + - - +
49X ASN 3.5 0.2 - - - -
50X LYS* 3.0 16.1 + - - +
52X TYR* 3.3 40.5 + - + -
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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