Contacts of the strand formed by residues 44 - 48 (chain A) in PDB entry 1L9W
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 ILE 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.6 24.2 - - + -
11A ILE* 3.8 24.0 - - + -
17A LYS* 4.4 9.2 - - + -
18A ILE 3.1 2.9 + - - +
19A ILE* 3.3 53.5 - - + -
20A VAL 3.4 5.9 + - - -
42A PHE* 3.8 7.1 - - - -
43A ASP* 1.3 82.6 - - + +
45A LEU* 1.3 73.4 + - - +
75A ILE* 4.1 0.2 - - - -
76A PRO* 3.9 14.1 - - + +
78A LEU* 4.2 8.3 - - + -
112A MET* 3.7 24.2 - - + -
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Residues in contact with LEU 45 (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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20A VAL* 3.7 13.7 - - + +
22A LEU* 3.9 18.6 - - + -
37A TYR* 3.8 27.8 - - + -
42A PHE* 4.0 14.8 - - + -
44A ILE* 1.3 74.9 - - - +
46A GLU* 1.3 63.6 + - - +
47A TRP* 5.7 0.2 - - + -
68A ILE* 3.5 32.8 - - + -
72A MET* 3.7 23.8 - - + -
75A ILE* 3.5 9.4 - - + +
76A PRO 3.0 11.1 + - - +
77A LEU* 3.5 12.6 - - + +
78A LEU* 2.9 26.0 + - - +
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Residues in contact with GLU 46 (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 ILE* 3.9 12.3 - - + -
20A VAL 2.8 16.3 + - - +
21A SER* 3.0 12.7 + - - +
22A LEU* 2.8 27.4 + - - +
44A ILE 3.9 0.8 + - - -
45A LEU* 1.3 74.4 - - - +
47A TRP* 1.3 64.1 + - - +
48A ARG* 3.3 5.3 - - + -
78A LEU* 3.4 22.8 - - + +
80A THR* 2.8 36.7 + - - +
114A ASP* 4.5 1.6 - - - +
170A LYS* 4.3 2.9 + - - -
225A PHE* 3.6 9.1 - - - -
301A DHS 2.5 40.6 + - - -
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Residues in contact with TRP 47 (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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22A LEU* 3.6 28.9 - - + +
23A MET* 5.3 0.2 - - - -
24A GLY 5.1 3.0 + - - +
30A VAL* 4.0 13.9 - - + +
45A LEU* 4.0 1.0 + - + -
46A GLU* 1.3 72.0 - - - +
48A ARG* 1.4 70.4 + - - +
49A VAL* 3.3 22.2 + - + +
52A PHE* 4.1 22.6 - + + +
61A VAL* 3.3 37.9 - - + -
64A ALA* 3.6 21.5 - - + -
65A ALA* 3.9 16.8 - - + -
68A ILE* 3.5 23.8 - - + -
77A LEU* 4.3 13.6 - - + +
78A LEU 2.9 12.6 + - - +
79A PHE* 3.8 27.8 - + - -
80A THR* 3.1 27.2 + - - +
110A VAL* 5.9 0.9 - - + -
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Residues in contact with ARG 48 (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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21A SER* 3.8 18.6 - - - -
22A LEU 2.9 16.5 + - - +
23A MET* 4.1 13.0 - - + -
24A GLY 5.2 0.3 + - - -
46A GLU* 3.3 24.9 + - - +
47A TRP* 1.4 80.1 + - - +
49A VAL* 1.3 63.1 + - - +
50A ASP* 2.8 37.5 + - - +
51A HIS* 3.4 29.6 + - + +
52A PHE 4.3 0.7 + - - -
80A THR* 3.3 12.1 - - - -
82A ARG* 3.6 17.2 - - - +
87A GLY 4.5 4.0 + - - -
88A GLY* 3.9 9.5 - - - -
89A GLU* 4.5 2.0 + - - +
232A SER* 3.4 22.6 + - - -
301A DHS 3.1 27.4 + - - +
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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