Contacts of the helix formed by residues 7 - 20 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H LYS* 4.2 7.4 - - - -
39H SER* 4.3 1.6 - - - -
53M GLU* 3.3 13.2 - - - -
5S TRP* 3.5 21.6 - - - -
6S SER* 1.3 76.7 - - - +
8S TYR* 1.3 61.8 + - - -
9S LEU 3.4 2.0 - - - -
10S ASP* 3.0 13.0 + - - +
11S ASP* 2.9 28.5 + - - -
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Residues in contact with TYR 8 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LYS* 4.0 12.4 - - + +
39H SER* 3.1 33.9 + - - +
40H ASP* 3.5 37.9 - - + +
41H PRO* 3.4 16.1 - - + +
54N TYR* 4.6 4.9 + - - -
58N ARG* 5.9 0.3 + - - -
7S GLY* 1.3 71.7 - - - -
9S LEU* 1.3 64.4 + - + +
11S ASP* 2.9 16.1 + - + +
12S VAL* 2.8 50.1 + - + +
15S LYS* 5.9 7.2 - - - -
68S PHE* 3.4 33.7 - + + -
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Residues in contact with LEU 9 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H SER* 3.2 24.9 + - - +
49M SER* 4.0 6.1 + - - +
52M SER* 3.5 24.9 - - - +
53M GLU* 3.5 15.0 - - + +
56M LEU* 5.8 0.4 - - + -
8S TYR* 1.3 79.6 - - + +
10S ASP* 1.3 65.9 + - - +
12S VAL* 3.3 6.7 + - + +
13S SER* 3.0 22.5 + - - -
65S VAL* 3.4 36.7 - - + +
68S PHE* 3.5 25.8 - - + +
69S LYS* 3.6 26.7 - - + +
72S ASP* 4.2 3.4 - - - +
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Residues in contact with ASP 10 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M SER* 3.6 15.3 + - - -
50M LYS* 3.8 29.2 + - - +
53M GLU* 2.9 35.4 + - - +
5S TRP* 3.4 9.0 - - - -
6S SER* 3.1 24.2 - - - +
7S GLY 3.0 15.4 + - - +
9S LEU* 1.3 76.9 - - - +
11S ASP* 1.3 55.4 + - - +
13S SER* 3.3 5.7 + - - -
14S ALA* 3.0 26.4 + - - +
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Residues in contact with ASP 11 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H LYS* 2.8 31.5 + - - -
6S SER* 2.9 23.8 + - - -
7S GLY 2.9 15.5 + - - +
8S TYR* 2.9 17.6 + - + +
10S ASP* 1.3 73.0 - - - +
12S VAL* 1.3 54.2 + - + +
14S ALA* 3.2 8.6 + - - +
15S LYS* 2.7 53.6 + - - +
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Residues in contact with VAL 12 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N LEU* 5.1 6.1 - - + +
8S TYR* 2.8 48.6 + - + +
9S LEU* 3.4 11.7 - - + +
10S ASP 3.2 0.2 - - - -
11S ASP* 1.3 75.5 - - - +
13S SER* 1.3 62.2 + - - +
15S LYS* 3.2 14.5 + - + +
16S PHE* 3.1 23.3 + - + +
64S THR* 4.1 10.8 - - - +
65S VAL* 3.9 18.4 - - + -
68S PHE* 3.6 35.2 - - + -
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Residues in contact with SER 13 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M SER* 4.2 16.2 + - - -
9S LEU 3.0 12.1 + - - -
10S ASP* 3.5 9.6 - - - -
12S VAL* 1.3 78.1 - - - +
14S ALA* 1.3 58.0 + - - +
16S PHE* 3.4 4.7 + - - +
17S ASP* 3.0 33.9 + - - +
61S GLN* 2.8 29.9 + - - +
65S VAL* 4.1 12.5 - - - +
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Residues in contact with ALA 14 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ASP 3.0 13.0 + - - +
11S ASP* 3.2 12.8 + - - +
13S SER* 1.3 74.3 + - - +
15S LYS* 1.3 57.5 + - + +
17S ASP* 3.7 6.4 - - - +
18S THR* 2.6 41.0 + - - +
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Residues in contact with LYS 15 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N LEU* 5.0 20.0 - - + -
32N ASP* 5.3 11.7 + - - +
35N ALA* 3.4 15.6 - - - +
8S TYR* 5.9 6.5 - - - -
11S ASP* 2.7 41.2 + - - +
12S VAL* 3.2 13.7 + - + +
14S ALA* 1.3 73.4 - - + +
16S PHE* 1.3 62.4 + - - +
18S THR* 3.4 18.1 - - - -
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Residues in contact with PHE 16 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N LEU* 5.3 10.7 - - + +
34N LEU* 4.9 6.5 - - + -
35N ALA* 3.6 21.3 - - + +
38N PRO* 3.6 35.4 - - + -
12S VAL 3.1 12.3 + - - +
13S SER* 3.7 7.4 - - - +
15S LYS* 1.3 75.3 - - - +
17S ASP* 1.3 74.1 + - - +
18S THR 3.2 0.7 + - - -
19S GLY 3.2 9.9 + - - -
20S VAL* 3.3 26.2 - - + +
56S LEU 3.6 18.4 - - - -
57S TYR* 3.6 22.7 - - - -
60S ALA* 4.0 13.9 - - + -
61S GLN* 3.6 27.4 - - + -
64S THR* 4.8 16.4 - - + +
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Residues in contact with ASP 17 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13S SER* 3.0 21.7 + - - +
14S ALA* 3.8 6.5 + - - +
16S PHE* 1.3 80.5 - - - +
18S THR* 1.3 57.6 + - - +
20S VAL* 2.9 6.6 + - - -
21S ASP* 2.5 43.3 + - - +
57S TYR* 3.8 24.5 + - - +
61S GLN* 3.1 35.4 + - - +
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Residues in contact with THR 18 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S ALA* 2.6 27.0 + - - +
15S LYS* 3.4 13.0 + - - -
16S PHE 3.1 0.4 - - - -
17S ASP* 1.3 78.1 - - - +
19S GLY* 1.3 60.8 + - - +
21S ASP* 3.8 13.9 + - - +
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Residues in contact with GLY 19 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ALA* 3.2 25.5 - - - +
36N ALA* 3.5 9.4 - - - +
15S LYS 4.0 2.0 + - - -
16S PHE 3.2 4.9 + - - -
17S ASP 3.1 0.4 - - - -
18S THR* 1.3 80.9 - - - +
20S VAL* 1.3 51.1 + - - +
21S ASP 3.7 0.4 - - - -
5Y TRP* 2.6 39.3 + - - -
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Residues in contact with VAL 20 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ALA 3.3 16.2 - - - +
38N PRO* 3.5 25.8 - - + -
16S PHE* 3.3 29.2 - - + +
17S ASP* 3.1 5.6 - - - +
19S GLY* 1.3 80.7 - - - +
21S ASP* 1.3 62.2 + - - +
22S ASN 3.1 3.4 - - - +
23S LEU* 3.1 28.6 + - + +
57S TYR* 3.2 40.1 - - + -
5Y TRP* 3.6 15.3 - - + +
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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