Contacts of the helix formed by residues 7 - 20 (chain R) 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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LYS* 4.2 8.5 - - - -
39G SER* 4.3 2.0 - - - -
53L GLU* 3.3 12.6 - - - -
5R TRP* 3.5 21.7 - - - -
6R SER* 1.3 75.7 - - - +
8R TYR* 1.3 60.4 + - - -
9R LEU 3.4 2.2 - - - -
10R ASP* 3.0 12.3 + - - -
11R ASP* 2.9 29.3 + - - -
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Residues in contact with TYR 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LYS* 4.0 11.1 - - + +
39G SER* 3.1 37.7 + - - +
40G ASP* 3.5 33.9 - - + +
41G PRO* 3.4 17.8 - - + +
54M TYR* 4.7 4.7 + - - -
58M ARG* 5.9 0.3 + - - -
7R GLY* 1.3 71.6 - - - -
9R LEU* 1.3 64.8 + - + +
11R ASP* 2.9 16.4 + - + +
12R VAL* 2.8 50.9 + - + +
15R LYS* 5.9 7.0 - - - -
68R PHE* 3.4 34.3 - + + -
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Residues in contact with LEU 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G SER* 3.2 25.2 + - - +
49L SER* 4.0 6.3 + - - +
52L SER* 3.5 24.9 - - - +
53L GLU* 3.3 15.0 + - + +
56L LEU* 5.8 0.4 - - + -
8R TYR* 1.3 79.0 - - + +
10R ASP* 1.3 66.1 + - - +
12R VAL* 3.3 6.0 + - + +
13R SER* 3.0 22.9 + - - -
65R VAL* 3.4 36.1 - - + +
68R PHE* 3.5 25.1 - - + +
69R LYS* 3.6 27.6 - - + +
72R ASP* 4.2 3.4 - - - +
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Residues in contact with ASP 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L SER* 3.6 15.3 + - - +
50L LYS* 3.8 28.8 + - - +
53L GLU* 2.9 33.0 + - - +
5R TRP* 3.4 8.7 - - - -
6R SER* 3.1 24.6 - - - +
7R GLY 3.0 15.9 + - - +
9R LEU* 1.3 76.3 - - - +
11R ASP* 1.3 55.3 + - - +
13R SER* 3.3 6.0 + - - -
14R ALA* 3.0 26.4 + - - +
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Residues in contact with ASP 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LYS* 2.8 31.3 + - - -
6R SER* 2.9 23.4 + - - -
7R GLY 2.9 14.4 + - - +
8R TYR* 2.9 17.9 + - + +
10R ASP* 1.3 72.6 - - - +
12R VAL* 1.3 55.0 + - + +
14R ALA* 3.2 8.3 + - - +
15R LYS* 2.7 53.3 + - + +
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Residues in contact with VAL 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU* 5.1 5.5 - - + +
8R TYR* 2.8 48.8 + - + +
9R LEU* 3.4 11.7 - - + +
10R ASP 3.2 0.2 - - - -
11R ASP* 1.3 76.3 - - + +
13R SER* 1.3 62.7 + - - +
15R LYS* 3.2 14.3 + - + +
16R PHE* 3.1 22.7 + - - +
64R THR* 4.1 10.3 - - - +
65R VAL* 3.9 17.9 - - + -
68R PHE* 3.6 35.2 - - + -
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Residues in contact with SER 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L SER* 4.2 16.1 + - - -
9R LEU 3.0 12.9 + - - -
10R ASP* 3.5 9.4 - - - -
12R VAL* 1.3 76.8 - - - +
14R ALA* 1.3 58.4 + - - +
16R PHE* 3.4 5.1 + - - +
17R ASP* 3.0 33.9 + - - +
61R GLN* 2.8 30.1 + - - +
65R VAL* 4.1 12.8 - - - +
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Residues in contact with ALA 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10R ASP 3.0 14.2 + - - +
11R ASP* 3.5 11.9 - - - +
13R SER* 1.3 73.0 - - - +
15R LYS* 1.3 57.5 + - + +
17R ASP* 3.3 6.9 + - - +
18R THR* 2.6 41.6 + - - +
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Residues in contact with LYS 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M THR* 6.4 0.2 - - - +
31M LEU* 5.0 19.3 - - + -
32M ASP* 5.3 11.5 + - - +
35M ALA* 3.4 15.8 - - - +
8R TYR* 5.9 6.5 - - - -
11R ASP* 2.7 41.5 + - + +
12R VAL* 3.2 13.7 + - + +
14R ALA* 1.3 75.0 - - + +
16R PHE* 1.3 61.7 + - - +
18R THR* 3.4 18.0 - - - -
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Residues in contact with PHE 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M LEU* 5.3 10.0 - - + +
34M LEU* 4.9 6.1 - - + -
35M ALA* 3.6 22.0 - - - +
38M PRO* 3.6 35.0 - - + -
12R VAL* 3.1 13.1 + - + +
13R SER* 3.7 7.2 - - - +
15R LYS* 1.3 74.7 - - - +
17R ASP* 1.3 73.3 + - - +
18R THR 3.2 0.7 + - - -
19R GLY 3.2 10.0 + - - -
20R VAL* 3.3 26.3 - - + +
56R LEU 3.6 17.7 - - - -
57R TYR* 3.6 23.1 - - - -
60R ALA* 4.0 14.6 - - + -
61R GLN* 3.6 26.9 - - + -
64R THR* 4.8 16.2 - - + +
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Residues in contact with ASP 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R SER* 3.0 21.5 + - - +
14R ALA* 3.8 6.5 - - - +
16R PHE* 1.3 80.5 - - - +
18R THR* 1.3 58.3 + - - +
20R VAL* 2.9 6.8 + - - -
21R ASP* 2.5 43.0 + - - +
57R TYR* 3.8 23.9 + - - +
61R GLN* 3.1 35.5 + - - +
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Residues in contact with THR 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14R ALA* 2.6 27.6 + - - +
15R LYS* 3.4 13.0 + - - -
16R PHE 3.1 0.2 - - - -
17R ASP* 1.3 78.3 - - - +
19R GLY* 1.3 60.7 + - - +
20R VAL 3.5 0.2 + - - -
21R ASP* 3.8 13.1 + - - +
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Residues in contact with GLY 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ALA* 3.2 26.4 - - - +
36M ALA* 3.5 9.4 - - - +
15R LYS 4.0 2.2 + - - -
16R PHE 3.2 4.8 + - - -
17R ASP 3.1 0.8 - - - -
18R THR* 1.3 80.2 - - - +
20R VAL* 1.3 51.6 + - - +
21R ASP 3.7 0.7 - - - -
5X TRP* 2.6 39.7 + - - -
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Residues in contact with VAL 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M ALA 3.3 16.4 - - - +
38M PRO* 3.5 24.9 - - + -
16R PHE* 3.3 28.9 - - + +
17R ASP* 3.1 6.1 - - - +
19R GLY* 1.3 81.7 - - - +
21R ASP* 1.3 62.9 + - - +
22R ASN 3.1 3.4 - - - +
23R LEU* 3.1 28.3 + - + +
57R TYR* 3.2 39.3 - - + -
5X TRP* 3.6 15.7 - - + +
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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
------------------------------------------------------------
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