Contacts of the strand formed by residues 37 - 41 (chain A) in PDB entry 1LGP
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 GLU 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LYS* 4.0 11.0 + - - +
36A ARG* 1.3 84.2 - - + +
38A TRP* 1.3 59.2 + - - +
39A THR* 3.7 15.0 + - + +
47A ASP* 3.9 6.1 - - - +
62A ARG* 2.9 43.6 + - + -
63A ILE 3.7 3.6 - - - -
64A VAL* 3.8 7.2 - - + -
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Residues in contact with TRP 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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16A TRP* 5.3 6.1 - - + -
19A LEU* 4.5 5.2 - - + +
31A VAL* 3.4 26.9 - - + -
32A LEU 3.9 14.4 - - - -
33A LEU* 3.7 34.0 - - + +
34A ARG 5.3 0.9 - - - -
35A LYS* 4.5 21.5 - - + +
37A GLU* 1.3 71.5 - - - +
39A THR* 1.3 61.5 + - - +
40A ILE* 3.8 22.0 - - + +
47A ASP* 3.5 50.9 - - + -
48A LEU* 3.8 19.9 - - + +
61A CYS 4.1 0.2 - - - +
62A ARG* 3.2 5.9 - - - -
63A ILE* 3.0 43.3 + - + +
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Residues in contact with THR 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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37A GLU* 4.2 21.1 - - + +
38A TRP* 1.3 76.0 + - - +
40A ILE* 1.3 64.5 + - - +
45A GLY 4.3 2.1 + - - -
46A CYS* 3.3 16.1 - - - -
47A ASP* 2.9 46.7 + - - +
48A LEU 3.1 8.3 + - - -
59A ASP* 5.3 6.1 - - - +
61A CYS 3.9 4.3 - - - -
62A ARG* 4.7 6.5 - - + -
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Residues in contact with ILE 40 (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 LEU* 4.8 5.4 - - + -
38A TRP* 3.8 24.5 - - + +
39A THR* 1.3 81.1 - - - +
41A GLY* 1.3 62.6 + - - +
46A CYS* 3.9 3.5 - - - -
48A LEU* 3.3 24.5 - - + +
50A PHE* 4.0 17.7 - - + -
56A VAL* 5.6 2.5 - - + -
59A ASP* 4.0 2.1 - - - -
60A HIS* 3.0 24.2 + - + +
61A CYS* 3.1 41.0 + - - +
63A ILE* 4.4 17.0 - - + -
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Residues in contact with GLY 41 (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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40A ILE* 1.3 78.1 - - - +
42A ARG* 1.3 60.1 + - - -
43A ARG 3.5 1.3 - - - -
46A CYS* 3.5 6.8 - - - -
48A LEU 3.0 7.5 + - - +
49A SER* 2.9 7.8 - - - -
50A PHE* 2.9 23.7 + - - -
56A VAL* 3.9 14.6 - - - -
57A SER 3.5 11.9 - - - -
58A GLY 3.6 8.3 - - - -
60A HIS 4.0 0.2 - - - -
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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