Contacts of the strand formed by residues 25 - 29 (chain A) in PDB entry 1MSG
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 SER 25 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 4.4 0.3 - - - +
24A GLN* 1.3 73.8 - - - +
26A VAL* 1.3 53.6 + - - +
27A ASN* 5.1 1.5 + - - -
42A ALA* 3.1 7.3 - - - +
43A THR* 2.6 50.2 + - - +
66A MET* 2.9 16.1 - - - +
27B ASN* 6.0 1.6 - - - -
28B VAL 2.8 22.2 - - - -
29B LYS* 3.1 33.9 - - - +
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Residues in contact with VAL 26 (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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25A SER* 1.3 79.7 + - - +
27A ASN* 1.3 82.7 + - - +
28A VAL* 5.4 3.1 - - + -
40A VAL* 4.3 5.8 - - + +
41A ILE 2.9 20.9 - - - +
42A ALA* 3.6 9.2 - - + +
43A THR 3.8 1.3 - - - +
52A LEU* 5.2 6.3 - - + -
62A ILE* 5.4 4.3 - - + +
63A ILE* 5.5 12.1 - - + -
66A MET* 3.4 23.8 - - + -
26B VAL 3.9 0.5 - - - +
27B ASN* 3.3 0.9 - - - -
28B VAL* 3.0 53.4 + - + +
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Residues in contact with ASN 27 (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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25A SER* 5.1 1.0 + - - -
26A VAL* 1.3 85.8 + - - +
28A VAL* 1.3 61.6 + - - +
29A LYS 4.2 0.2 - - - -
39A GLU* 3.8 8.8 - - - +
40A VAL* 3.1 6.2 + - - -
41A ILE* 2.5 69.5 + - + +
43A THR* 3.6 15.3 + - - -
25B SER* 6.0 1.8 - - - -
26B VAL 3.3 4.7 - - - -
27B ASN* 3.4 27.9 - - - +
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Residues in contact with VAL 28 (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 VAL* 5.4 3.1 - - + -
27A ASN* 1.3 76.3 - - - +
29A LYS* 1.3 64.7 + - - +
38A THR* 5.1 7.0 - - + -
39A GLU 3.0 15.5 - - - +
40A VAL* 4.1 12.6 - - + -
63A ILE* 6.5 0.2 - - + -
25B SER* 2.8 22.5 - - - -
26B VAL* 3.0 33.8 + - + +
63B ILE* 5.7 1.1 - - + +
66B MET* 3.9 22.7 - - + +
67B LEU* 4.5 23.8 - - + -
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Residues in contact with LYS 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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27A ASN* 6.3 0.2 - - + -
28A VAL* 1.3 75.5 - - - +
30A SER* 1.3 71.7 + - - +
38A THR* 3.1 8.4 - - - +
39A GLU* 2.7 71.9 + - + +
24B GLN* 3.4 45.3 + - - +
25B SER* 3.1 33.9 - - - +
43B THR* 6.0 0.7 - - - -
44B LEU 6.0 0.4 - - - -
66B MET 6.1 1.1 - - - -
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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