Contacts of the helix formed by residues 18 - 30 (chain A) in PDB entry 5LEZ
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 LEU 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 3.9 13.7 - - + -
11A THR 3.4 29.4 - - - +
12A PHE* 3.6 29.6 - - + +
17A LYS* 1.3 84.8 + - - +
19A VAL* 1.4 63.9 + - - +
20A GLN 3.3 2.5 - - - -
21A ILE* 3.1 41.0 + - + +
22A GLU* 3.3 11.8 + - - +
79B ILE* 4.0 28.5 - - + -
128B ARG* 4.0 22.9 - - - +
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Residues in contact with VAL 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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11A THR 4.2 6.0 + - - +
13A SER* 4.4 22.7 - - - -
17A LYS* 3.5 11.9 + - + -
18A LEU* 1.4 71.8 - - - +
20A GLN* 1.3 62.2 + - + +
22A GLU* 2.9 12.5 + - - +
23A TYR* 2.7 69.3 + - + +
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Residues in contact with GLN 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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9A LEU* 3.6 22.0 - - + +
10A THR* 3.3 25.4 - - - +
11A THR 5.6 0.2 + - - -
18A LEU 3.3 0.8 - - - -
19A VAL* 1.3 84.2 - - + +
21A ILE* 1.3 56.4 + - - +
23A TYR* 3.8 23.5 - - - +
24A ALA* 2.9 26.5 + - - +
127A ARG* 4.3 12.4 - - - +
128A PRO* 4.0 17.4 - - + +
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Residues in contact with ILE 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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10A THR* 4.2 6.3 - - + -
17A LYS* 5.7 3.4 - - - +
18A LEU* 3.1 41.7 + - + +
20A GLN* 1.3 72.9 - - - +
22A GLU* 1.3 69.2 + - + +
23A TYR 3.1 1.1 - - - -
24A ALA* 3.3 7.9 + - - +
25A LEU* 2.9 32.4 + - + +
121A THR* 3.8 35.9 - - + +
128A PRO* 4.1 8.5 - - + -
150A PRO* 4.3 3.8 - - + +
151A SER* 3.9 36.8 - - - +
79B ILE* 5.8 1.8 - - + -
128B ARG* 5.1 0.7 - - - +
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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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17A LYS* 3.1 49.3 - - - +
18A LEU 3.3 4.5 + - - +
19A VAL* 2.9 14.7 + - - +
21A ILE* 1.3 77.6 - - + +
23A TYR* 1.3 68.6 + - + +
25A LEU* 2.9 31.5 + - + +
26A ALA* 2.9 13.3 + - - +
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Residues in contact with TYR 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 VAL* 2.7 51.0 + - + +
20A GLN* 3.9 26.5 - - - +
22A GLU* 1.3 82.4 - - + +
24A ALA* 1.3 60.8 + - - +
26A ALA* 3.2 12.1 + - + +
27A ALA* 3.2 19.1 + - - +
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Residues in contact with ALA 24 (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 GLN 2.9 15.3 + - - +
21A ILE* 3.3 11.0 - - - +
23A TYR* 1.3 77.2 - - - +
25A LEU* 1.3 62.0 + - - +
27A ALA* 3.1 11.1 + - - +
28A VAL* 3.0 22.2 + - - +
128A PRO* 4.3 9.2 - - + +
129A PHE 3.7 22.9 - - - +
130A GLY* 4.2 6.1 - - - -
150A PRO* 3.7 13.0 - - + -
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Residues in contact with LEU 25 (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 ILE* 2.9 25.1 + - + +
22A GLU* 2.9 22.9 + - + +
24A ALA* 1.3 75.5 - - - +
26A ALA* 1.3 56.0 + - - +
28A VAL* 3.2 10.3 + - + +
29A ALA* 2.8 28.4 + - - +
132A SER* 4.6 3.1 - - - +
149A ASP* 4.4 17.0 - - + +
150A PRO* 3.8 24.9 - - + -
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Residues in contact with ALA 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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22A GLU 2.9 10.5 + - - +
23A TYR* 3.5 15.9 - - + +
24A ALA 3.2 0.4 - - - -
25A LEU* 1.3 74.5 - - - +
27A ALA* 1.3 64.3 + - - +
29A ALA* 3.2 8.5 + - - +
30A GLY* 3.1 19.6 + - - -
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Residues in contact with ALA 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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23A TYR 3.2 10.7 + - - +
24A ALA* 3.1 12.2 + - - +
26A ALA* 1.3 75.3 - - - +
28A VAL* 1.3 61.0 + - - +
30A GLY* 3.3 4.4 + - - -
31A GLY* 3.3 15.4 + - - -
77A GLY* 4.0 8.4 - - - -
78A MET* 4.3 26.6 - - + +
130A GLY* 4.4 6.3 - - - +
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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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24A ALA 3.0 14.3 + - - +
25A LEU* 3.4 13.0 - - + +
27A ALA* 1.3 75.0 - - - +
29A ALA* 1.3 59.7 + - - +
31A GLY* 3.0 16.6 + - - -
76A SER* 3.6 19.6 - - - +
77A GLY* 4.0 6.5 - - - -
130A GLY 3.7 0.7 - - - -
131A VAL* 3.5 38.4 - - - +
132A SER* 3.5 23.3 - - - +
150A PRO* 4.1 7.2 - - + -
162A MET* 5.0 3.8 - - + -
163A GLY* 3.3 17.2 - - - +
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Residues in contact with ALA 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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25A LEU 2.8 17.9 + - - +
26A ALA* 3.2 9.8 + - - +
28A VAL* 1.3 74.0 - - - +
30A GLY* 1.3 55.6 + - - +
31A GLY 3.3 0.7 - - - -
163A GLY* 3.3 8.3 - - - +
164A LYS* 3.1 30.2 + - - +
166A TYR* 4.8 17.9 - - + -
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Residues in contact with GLY 30 (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 ALA 3.1 12.2 + - - -
27A ALA* 3.3 5.6 + - - -
28A VAL 3.2 0.2 - - - -
29A ALA* 1.3 73.8 - - - +
31A GLY* 1.3 63.7 + - - +
50A LYS* 4.9 7.3 + - - -
164A LYS* 3.9 18.6 - - - +
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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