Contacts of the helix formed by residues 20 - 37 (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 VAL 20 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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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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Residues in contact with ASP 21 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17S ASP* 2.5 22.8 + - - +
18S THR* 3.8 11.2 + - - +
19S GLY 3.7 1.8 - - - -
20S VAL* 1.3 73.7 - - - +
22S ASN* 1.3 69.4 + - - +
24S GLN* 3.9 11.4 + - - +
25S THR* 4.0 10.9 + - - -
57S TYR* 5.0 6.3 + - - -
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Residues in contact with ASN 22 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20S VAL* 3.1 0.8 - - - +
21S ASP* 1.3 86.2 - - - +
23S LEU* 1.3 67.6 + - - +
24S GLN 3.2 0.7 - - - -
25S THR* 3.0 11.1 + - - -
26S GLN* 2.8 33.7 + - + +
3Y THR 5.5 1.2 + - - -
4Y PRO* 5.3 2.0 - - - +
5Y TRP* 3.8 35.6 - - + +
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Residues in contact with LEU 23 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38N PRO* 5.8 1.6 - - + -
20S VAL* 3.1 29.6 + - + +
22S ASN* 1.3 77.6 - - - +
24S GLN* 1.3 63.9 + - - +
26S GLN* 3.2 3.9 + - - +
27S VAL* 3.0 22.2 + - + +
50S LYS* 3.5 31.0 - - + +
53S GLU* 3.7 31.2 - - + +
54S TYR* 4.4 5.6 - - + -
57S TYR* 3.8 24.7 - - + +
5Y TRP* 3.7 37.4 - - + -
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Residues in contact with GLN 24 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M ALA* 5.4 4.8 - - - +
20S VAL 3.7 2.4 + - - -
21S ASP* 4.2 7.4 - - - +
22S ASN 3.2 0.4 - - - -
23S LEU* 1.3 78.3 - - - +
25S THR* 1.3 56.5 + - - +
27S VAL* 3.3 8.2 - - - +
28S THR* 2.7 44.9 + - - +
54S TYR* 4.0 16.5 + - + +
57S TYR* 2.8 33.4 + - + +
58S ARG* 3.6 22.3 + - - +
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Residues in contact with THR 25 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21S ASP 4.0 8.5 + - - -
22S ASN* 3.0 14.8 + - - -
24S GLN* 1.3 79.8 - - - +
26S GLN* 1.3 59.0 + - + +
28S THR* 3.7 5.5 - - - -
29S GLU* 3.0 51.9 + - + +
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Residues in contact with GLN 26 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ASN* 2.8 25.1 + - + +
23S LEU 3.6 3.6 - - - +
25S THR* 1.3 81.2 - - + +
27S VAL* 1.3 57.6 + - - +
29S GLU* 3.4 8.6 + - - +
30S ALA* 2.9 28.6 + - - +
50S LYS* 2.9 40.1 + - + +
4Y PRO* 4.4 8.7 - - - +
5Y TRP* 3.0 58.3 + - - +
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Residues in contact with VAL 27 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23S LEU 3.0 14.4 + - - +
24S GLN 3.3 11.9 - - - +
26S GLN* 1.3 74.5 - - - +
28S THR* 1.3 67.9 + - - +
30S ALA* 4.0 4.5 - - - -
31S LEU* 3.0 21.8 + - - +
47S TYR* 3.4 30.5 - - + +
50S LYS* 3.8 14.1 - - + +
51S LEU* 3.7 35.4 - - + +
54S TYR* 3.8 28.3 - - + -
68X PHE* 6.1 3.3 - - + -
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Residues in contact with THR 28 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24S GLN* 2.7 32.7 + - - +
25S THR* 3.7 7.1 - - - -
27S VAL* 1.3 78.8 - - - +
29S GLU* 1.3 61.8 + - + +
31S LEU* 3.2 10.9 + - + +
32S ASP* 2.9 40.4 + - - +
54S TYR* 6.0 0.5 - - - -
68X PHE* 6.5 0.4 - - - -
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Residues in contact with GLU 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S THR* 3.0 39.5 + - + +
26S GLN* 3.8 7.6 - - - +
28S THR* 1.3 75.8 - - + +
30S ALA* 1.3 60.6 + - - +
32S ASP* 3.3 13.8 + - - +
33S LYS* 3.0 45.0 + - - +
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Residues in contact with ALA 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S GLN 2.9 18.5 + - - +
27S VAL* 3.7 8.5 - - - +
28S THR 3.3 0.2 - - - -
29S GLU* 1.3 77.1 - - - +
31S LEU* 1.3 57.2 + - - +
33S LYS* 4.0 8.1 - - - +
34S LEU* 2.9 30.1 + - - +
43S LEU* 4.8 5.8 - - + +
46S ALA* 4.8 5.6 - - + -
47S TYR* 3.8 31.5 - - + +
50S LYS* 4.9 5.4 - - + -
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Residues in contact with LEU 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27S VAL 3.0 14.9 + - - +
28S THR* 3.2 14.3 + - + +
30S ALA* 1.3 73.9 - - - +
32S ASP* 1.3 63.1 + - - +
34S LEU* 3.2 6.0 + - + -
35S ALA* 2.8 34.9 + - + +
47S TYR* 3.6 30.7 - - + +
12X VAL* 5.1 7.6 - - + +
15X LYS* 5.0 21.8 - - + -
16X PHE* 5.3 12.3 - - + +
64X THR* 4.4 14.1 - - + +
68X PHE* 3.8 32.3 - - + -
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Residues in contact with ASP 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28S THR* 2.9 32.2 + - - +
29S GLU* 3.3 18.1 + - - +
31S LEU* 1.3 82.0 - - - +
33S LYS* 1.3 63.0 + - + +
35S ALA* 3.5 14.6 - - - +
36S ALA* 3.7 6.2 + - - +
15X LYS* 5.3 13.0 + - - +
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Residues in contact with LYS 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S GLU* 3.0 31.3 + - - +
30S ALA* 4.0 3.4 - - - +
32S ASP* 1.3 75.3 - - + +
34S LEU* 1.3 66.0 + - - +
36S ALA* 2.9 19.1 + - - +
37S LYS 3.2 8.1 + - - -
43S LEU* 3.5 33.1 - - + +
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Residues in contact with LEU 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ALA 2.9 20.2 + - - +
31S LEU* 3.7 7.2 - - + +
33S LYS* 1.3 76.5 - - - +
35S ALA* 1.3 58.2 + - - +
37S LYS 3.0 13.4 - - - +
38S PRO* 2.8 55.2 - - + +
43S LEU* 3.5 30.2 - - + +
44S LEU* 3.6 25.6 - - + +
47S TYR* 3.3 38.8 - - + -
16X PHE* 5.4 6.3 - - + -
60X ALA* 6.2 2.5 - - + -
64X THR* 5.4 4.7 - - + -
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Residues in contact with ALA 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S LEU* 2.8 19.2 + - + +
32S ASP* 3.5 11.0 - - - +
34S LEU* 1.3 76.5 - - - +
36S ALA* 1.3 60.0 + - - +
38S PRO* 3.6 1.2 - - - +
15X LYS 3.4 26.5 - - - +
16X PHE* 3.6 25.5 - - + +
19X GLY* 3.2 22.3 - - - +
20X VAL* 3.3 11.8 - - - +
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Residues in contact with ALA 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S ASP 3.7 4.8 + - - +
33S LYS* 2.9 13.9 + - - +
35S ALA* 1.3 81.3 - - - +
37S LYS* 1.3 71.4 + - + +
38S PRO* 3.6 4.0 - - - +
19X GLY* 3.5 24.8 - - - +
20X VAL* 4.1 2.1 - - - +
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Residues in contact with LYS 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LYS 3.2 2.6 + - - -
34S LEU* 3.0 12.2 + - - +
36S ALA* 1.3 89.1 - - + +
38S PRO* 1.3 67.0 - - - +
39S SER* 3.0 7.7 + - - +
40S ASP* 3.1 29.0 + - + +
43S LEU* 3.7 13.6 - - + +
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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
------------------------------------------------------------
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