Contacts of the helix formed by residues 7 - 20 (chain O) in PDB entry 2LPZ
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 GLY 7 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LYS* 4.2 7.9 - - - -
39D SER* 4.3 1.6 - - - -
53I GLU* 3.3 13.0 - - - -
5O TRP* 3.5 21.5 - - - -
6O SER* 1.3 76.3 - - - +
8O TYR* 1.3 62.1 + - - -
9O LEU 3.4 2.0 - - - -
10O ASP* 3.0 12.3 + - - -
11O ASP* 2.9 29.0 + - - -
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Residues in contact with TYR 8 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LYS* 4.0 12.8 - - + +
39D SER* 3.1 37.7 + - - +
40D ASP* 3.5 32.5 - - + +
41D PRO* 3.4 16.7 - - + +
54J TYR* 4.6 4.7 + - - -
58J ARG* 5.9 0.3 + - - -
7O GLY* 1.3 71.5 - - - -
9O LEU* 1.3 64.1 + - + +
11O ASP* 2.9 15.9 + - + +
12O VAL* 2.8 50.3 + - + +
15O LYS* 5.9 7.2 - - - -
68O PHE* 3.4 35.0 - + + -
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Residues in contact with LEU 9 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D SER* 3.2 24.2 + - - +
49I SER* 4.0 6.1 + - - +
52I SER* 3.5 25.6 - - - +
53I GLU* 3.5 14.8 - - + +
56I LEU* 5.8 0.4 - - + -
8O TYR* 1.3 78.8 - - + +
10O ASP* 1.3 66.3 + - - +
12O VAL* 3.4 6.1 - - + +
13O SER* 3.0 23.0 + - - -
65O VAL* 3.4 36.4 - - + +
68O PHE* 3.5 26.0 - - + +
69O LYS* 3.6 26.7 - - + +
72O ASP* 4.2 3.6 - - - +
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Residues in contact with ASP 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I SER* 3.6 15.9 + - - +
50I LYS* 3.8 29.4 + - - +
53I GLU* 2.9 33.6 + - - +
5O TRP* 3.4 8.7 - - - -
6O SER* 3.1 23.7 - - - +
7O GLY 3.0 15.5 + - - +
9O LEU* 1.3 76.7 - - - +
11O ASP* 1.3 55.6 + - - +
13O SER* 3.3 5.9 + - - -
14O ALA* 3.0 26.6 + - - +
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Residues in contact with ASP 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D LYS* 2.8 30.9 + - - -
6O SER* 2.9 23.7 + - - -
7O GLY 2.9 15.0 + - - +
8O TYR* 2.9 17.5 + - + +
10O ASP* 1.3 72.0 - - - +
12O VAL* 1.3 54.4 + - + +
14O ALA* 3.2 8.1 + - - +
15O LYS* 2.7 53.0 + - - +
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Residues in contact with VAL 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 5.1 6.0 - - + +
8O TYR* 2.8 47.7 + - + +
9O LEU* 3.4 11.7 - - + +
10O ASP 3.2 0.2 - - - -
11O ASP* 1.3 76.7 - - - +
13O SER* 1.3 61.7 + - - +
15O LYS* 3.2 14.8 + - + +
16O PHE* 3.1 23.2 + - - +
64O THR* 4.1 10.8 - - - +
65O VAL* 3.9 17.7 - - + -
68O PHE* 3.6 35.9 - - + -
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Residues in contact with SER 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I SER* 4.2 16.3 + - - -
9O LEU 3.0 12.5 + - - -
10O ASP* 3.5 10.3 - - - -
12O VAL* 1.3 77.5 - - - +
14O ALA* 1.3 58.2 + - - +
16O PHE* 3.4 4.9 + - - +
17O ASP* 3.0 33.7 + - - +
61O GLN* 2.8 29.3 + - - +
65O VAL* 4.1 12.3 - - - +
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Residues in contact with ALA 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O ASP 3.0 13.2 + - - +
11O ASP* 3.2 12.5 + - - +
13O SER* 1.3 74.4 - - - +
15O LYS* 1.3 57.3 + - + +
17O ASP* 3.7 6.1 - - - +
18O THR* 2.6 40.3 + - - +
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Residues in contact with LYS 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J LEU* 5.0 19.5 - - + -
32J ASP* 5.3 12.0 + - - +
35J ALA* 3.4 15.7 - - - +
8O TYR* 5.9 6.7 - - - -
11O ASP* 2.7 39.9 + - - +
12O VAL* 3.2 13.9 + - + +
14O ALA* 1.3 74.6 - - + +
16O PHE* 1.3 61.7 + - - +
18O THR* 3.4 18.3 - - - -
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Residues in contact with PHE 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 5.3 10.4 - - + +
34J LEU* 4.9 6.7 - - + -
35J ALA* 3.6 21.3 - - - +
38J PRO* 3.6 35.2 - - + -
12O VAL 3.1 12.9 + - - +
13O SER* 3.7 7.2 - - - +
15O LYS* 1.3 75.6 - - - +
17O ASP* 1.3 74.3 + - - +
18O THR 3.2 0.5 + - - -
19O GLY 3.2 9.7 + - - -
20O VAL* 3.3 25.8 - - + +
56O LEU 3.6 18.2 - - - -
57O TYR* 3.6 22.4 - - - -
60O ALA* 4.0 14.4 - - + -
61O GLN* 3.6 26.7 - - + -
64O THR* 4.8 15.9 - - + +
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Residues in contact with ASP 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O SER* 3.0 21.3 + - - +
14O ALA* 3.8 6.5 + - - +
16O PHE* 1.3 80.5 - - - +
18O THR* 1.3 57.9 + - - +
20O VAL* 2.9 6.4 + - - -
21O ASP* 2.5 42.9 + - - +
57O TYR* 3.8 23.5 + - - +
61O GLN* 3.1 35.6 + - - +
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Residues in contact with THR 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ALA* 2.6 28.4 + - - +
15O LYS* 3.4 13.1 + - - -
16O PHE 3.1 0.4 - - - -
17O ASP* 1.3 78.3 - - - +
19O GLY* 1.3 60.2 - - - +
21O ASP* 3.8 13.6 + - - +
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Residues in contact with GLY 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35J ALA* 3.2 26.4 - - - +
36J ALA* 3.5 9.0 - - - +
15O LYS 4.0 2.2 + - - -
16O PHE 3.2 5.3 + - - -
17O ASP 3.1 0.8 - - - -
18O THR* 1.3 79.6 - - - +
20O VAL* 1.3 51.8 + - - +
21O ASP 3.7 0.4 - - - -
5U TRP* 2.6 39.2 + - - -
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Residues in contact with VAL 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J ALA 3.3 16.4 - - - +
38J PRO* 3.5 25.1 - - + -
16O PHE* 3.3 28.5 - - + +
17O ASP* 3.1 5.6 - - - +
19O GLY* 1.3 81.3 - - - +
21O ASP* 1.3 62.9 + - - +
22O ASN 3.1 3.4 - - - +
23O LEU* 3.1 27.9 + - + +
57O TYR* 3.2 38.9 - - + -
5U TRP* 3.6 15.5 - - + +
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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