Contacts of the helix formed by residues 16 - 23 (chain A) in PDB entry 1LIE
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 PHE 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A SER* 3.3 10.3 - - - +
14A GLU 3.1 2.2 + - - -
15A ASN* 1.3 77.4 - - - +
17A ASP* 1.3 63.9 + - - +
19A TYR* 3.1 16.8 + + - +
20A MET* 2.9 60.0 + - + +
33A ALA* 4.3 17.5 - - + -
34A GLY* 5.3 4.0 - - - -
117A OCS 4.3 1.6 - - - -
124A SER* 3.1 19.1 - - - +
126A ARG* 3.2 37.7 - - - -
133A PLM 3.8 42.2 - - + -
134A PPI 3.0 18.8 + - - +
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Residues in contact with ASP 17 (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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15A ASN 3.4 0.2 - - - -
16A PHE* 1.3 75.8 - - - +
18A ASP* 1.3 59.3 + - - +
20A MET* 3.3 15.0 + - + +
21A LYS* 2.2 74.5 + - - +
30A ARG* 3.2 22.6 + - - +
31A LYS* 3.1 26.9 + - - -
134A PPI 3.1 15.8 + - - +
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Residues in contact with ASP 18 (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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15A ASN* 3.2 29.1 + - + +
16A PHE 3.2 0.4 - - - -
17A ASP* 1.3 77.8 - - - +
19A TYR* 1.3 62.7 + - - +
21A LYS* 3.3 26.1 + - - +
22A GLU* 3.0 24.6 + - - +
122A VAL* 3.9 17.0 - - + +
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Residues in contact with TYR 19 (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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15A ASN 3.0 13.1 + - - +
16A PHE* 3.1 22.4 + + - +
18A ASP* 1.3 76.5 - - - +
20A MET* 1.3 61.6 + - + +
22A GLU* 3.1 5.8 + - - +
23A VAL* 2.9 42.3 + - + +
78A ARG* 5.1 2.2 + - - -
95A GLN* 4.9 0.7 + - - -
102A THR* 2.7 39.2 + - - +
104A ILE* 4.2 8.0 - - - +
117A OCS 3.4 48.9 + - + +
118A VAL 3.7 4.0 - - - -
119A MET* 3.6 23.1 - - + -
122A VAL* 3.8 12.9 - - + +
124A SER* 3.7 11.2 - - - -
133A PLM 4.4 16.9 - - + +
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Residues in contact with MET 20 (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 PHE* 2.9 55.4 + - + +
17A ASP* 3.7 21.1 - - - +
19A TYR* 1.3 77.3 - - + +
21A LYS* 1.3 66.3 + - - +
23A VAL* 3.2 3.9 + - - -
24A GLY 2.9 5.5 + - - -
25A VAL* 2.9 37.8 + - + +
30A ARG* 3.7 43.1 - - + +
33A ALA* 3.7 9.4 - - + -
34A GLY* 4.7 2.9 - - - +
133A PLM 3.7 26.5 - - + -
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Residues in contact with LYS 21 (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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17A ASP* 2.2 47.8 + - - +
18A ASP* 3.3 27.3 + - - +
20A MET* 1.3 76.1 - - - +
22A GLU* 1.3 58.8 + - - +
24A GLY* 3.0 19.2 + - - -
25A VAL 4.8 1.3 - - - +
30A ARG* 3.7 36.7 - - - +
31A LYS* 5.3 1.6 - - - +
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Residues in contact with GLU 22 (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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18A ASP 3.0 12.9 + - - +
19A TYR* 3.3 9.9 - - - +
21A LYS* 1.3 75.4 - - - +
23A VAL* 1.3 63.7 + - - +
24A GLY* 3.4 0.9 + - - -
119A MET* 3.5 49.2 - - + +
120A LYS* 4.3 20.1 + - + +
122A VAL* 3.5 21.0 - - + +
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Residues in contact with VAL 23 (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 TYR* 2.9 52.1 + - + +
20A MET* 3.2 7.8 + - - +
22A GLU* 1.3 76.5 - - - +
24A GLY* 1.3 57.1 + - - +
25A VAL* 4.0 13.7 - - + -
78A ARG* 3.5 42.7 - - - +
97A TRP* 4.1 15.7 + - + -
100A LYS* 4.6 8.7 + - - +
102A THR* 4.7 0.7 - - - +
119A MET* 3.9 21.5 - - + +
133A PLM 6.3 0.4 - - + -
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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