Contacts of the helix formed by residues 7 - 20 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37I LYS* 4.2 7.6 - - - -
38I PRO* 5.8 0.2 - - - -
39I SER* 4.3 1.3 - - - -
53N GLU* 3.3 13.0 - - - -
5T TRP* 3.5 21.9 - - - -
6T SER* 1.3 76.3 - - - +
8T TYR* 1.3 60.2 + - - -
9T LEU 3.4 2.0 - - - -
10T ASP* 3.0 12.4 + - - +
11T ASP* 2.9 28.8 + - - -
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Residues in contact with TYR 8 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LYS* 4.0 12.2 - - + +
39I SER* 3.1 34.1 + - - +
40I ASP* 3.5 38.4 - - + +
41I PRO* 3.4 16.7 - - + +
54O TYR* 4.7 4.7 + - - -
58O ARG* 5.9 0.2 + - - -
7T GLY* 1.3 72.3 - - - -
9T LEU* 1.3 62.7 + - + +
11T ASP* 2.9 16.0 + - + +
12T VAL* 2.8 51.2 + - + +
15T LYS* 5.9 6.5 - - - -
68T PHE* 3.4 33.6 - + + -
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Residues in contact with LEU 9 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I SER* 3.2 25.3 + - - +
49N SER* 4.0 6.4 + - - +
52N SER* 3.5 24.9 - - - +
53N GLU* 3.5 15.7 - - + +
56N LEU* 5.8 0.2 - - + -
8T TYR* 1.3 78.6 - - + +
10T ASP* 1.3 64.1 + - - +
12T VAL* 3.3 6.8 + - + +
13T SER* 3.0 22.7 + - - -
65T VAL* 3.4 37.2 - - + +
68T PHE* 3.5 25.4 - - + +
69T LYS* 3.6 27.4 - - + +
72T ASP* 4.2 2.7 - - - +
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Residues in contact with ASP 10 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N SER* 3.6 15.4 + - - -
50N LYS* 3.8 29.2 + - - +
53N GLU* 2.9 33.6 + - - +
5T TRP* 3.4 8.8 - - - -
6T SER* 3.1 24.0 - - - +
7T GLY 3.0 16.5 + - - +
9T LEU* 1.3 75.7 - - - +
11T ASP* 1.3 55.3 + - - +
13T SER* 3.3 5.6 + - - -
14T ALA* 3.0 26.9 + - - +
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Residues in contact with ASP 11 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LYS* 2.8 31.3 + - - -
6T SER* 2.9 23.6 + - - +
7T GLY 2.9 15.1 + - - +
8T TYR* 2.9 18.0 + - + +
10T ASP* 1.3 73.2 - - - +
12T VAL* 1.3 54.0 + - - +
14T ALA* 3.2 7.9 + - - +
15T LYS* 2.7 54.1 + - - +
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Residues in contact with VAL 12 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31O LEU* 5.1 6.0 - - + +
8T TYR* 2.8 48.3 + - + +
9T LEU* 3.4 11.4 - - + +
10T ASP 3.2 0.2 - - - -
11T ASP* 1.3 77.2 - - + +
13T SER* 1.3 62.1 + - - +
15T LYS* 3.2 15.2 + - + +
16T PHE* 3.1 22.2 + - - +
64T THR* 4.1 10.8 - - - +
65T VAL* 3.9 17.9 - - + -
68T PHE* 3.6 35.9 - - + -
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Residues in contact with SER 13 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N SER* 4.2 16.5 + - - -
9T LEU 3.0 12.7 + - - -
10T ASP* 3.5 9.2 - - - -
12T VAL* 1.3 77.3 - - - +
14T ALA* 1.3 58.7 + - - +
16T PHE* 3.4 5.0 + - - +
17T ASP* 3.0 34.1 + - - +
61T GLN* 2.8 29.3 + - - +
65T VAL* 4.1 12.1 - - - +
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Residues in contact with ALA 14 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T ASP 3.0 12.9 + - - +
11T ASP* 3.5 12.3 - - - +
13T SER* 1.3 73.1 - - - +
15T LYS* 1.3 56.8 + - + +
17T ASP* 3.7 7.0 - - - +
18T THR* 2.6 41.0 + - - +
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Residues in contact with LYS 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O LEU* 5.0 20.2 - - + -
32O ASP* 5.3 11.7 + - - +
35O ALA* 3.4 16.5 - - - +
8T TYR* 5.9 6.3 - - - -
11T ASP* 2.7 41.2 + - - +
12T VAL* 3.2 14.3 + - + +
14T ALA* 1.3 73.8 - - + +
16T PHE* 1.3 59.4 + - - +
18T THR* 3.4 17.6 - - - -
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Residues in contact with PHE 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O LEU* 5.3 10.4 - - + +
34O LEU* 4.9 6.5 - - + -
35O ALA* 3.6 22.0 - - + +
38O PRO* 3.6 35.4 - - + -
12T VAL 3.1 11.9 + - - +
13T SER* 3.7 7.0 - - - +
15T LYS* 1.3 75.7 - - - +
17T ASP* 1.3 74.4 + - - +
18T THR 3.2 0.7 + - - -
19T GLY 3.2 10.2 + - - -
20T VAL* 3.3 25.2 - - + +
56T LEU 3.6 18.8 - - - -
57T TYR* 3.6 22.2 - - - -
60T ALA* 4.0 13.7 - - + -
61T GLN* 3.6 26.9 - - + +
64T THR* 4.8 16.6 - - + +
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Residues in contact with ASP 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13T SER* 3.0 22.5 + - - +
14T ALA* 3.8 6.5 - - - +
16T PHE* 1.3 81.7 - - - +
18T THR* 1.3 58.8 + - - +
20T VAL* 2.9 5.7 + - - -
21T ASP* 2.5 43.0 + - - +
57T TYR* 3.8 24.1 + - - +
61T GLN* 3.1 35.1 + - - +
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Residues in contact with THR 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14T ALA* 2.6 27.6 + - - +
15T LYS* 3.4 12.7 + - - -
16T PHE 3.1 0.2 - - - -
17T ASP* 1.3 77.4 - - - +
19T GLY* 1.3 61.5 + - - +
20T VAL 3.5 0.2 + - - -
21T ASP* 3.8 12.6 + - - +
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Residues in contact with GLY 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ALA* 3.2 26.4 - - - +
36O ALA* 3.5 9.7 - - - +
15T LYS 4.0 1.8 + - - -
16T PHE 3.2 4.8 + - - -
17T ASP 3.1 0.6 - - - -
18T THR* 1.3 81.3 - - - +
20T VAL* 1.3 51.7 + - - +
21T ASP 3.7 0.4 - - - -
5Z TRP* 2.6 39.7 + - - -
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Residues in contact with VAL 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ALA 3.3 15.9 - - - +
38O PRO* 3.5 25.6 - - + -
16T PHE* 3.3 29.8 - - + +
17T ASP* 3.1 5.8 - - - +
19T GLY* 1.3 81.3 - - - +
21T ASP* 1.3 63.0 + - - +
22T ASN 3.1 3.6 - - - +
23T LEU* 3.1 27.9 + - + +
24T GLN 3.7 0.2 + - - -
57T TYR* 3.2 39.9 - - + -
5Z TRP* 3.6 15.0 - - + +
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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