Contacts of the helix formed by residues 20 - 37 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H ALA 3.3 15.7 - - - +
38H PRO* 3.5 25.8 - - + -
16M PHE* 3.3 30.5 - - + +
17M ASP* 3.1 5.8 - - - +
19M GLY* 1.3 81.3 - - - +
21M ASP* 1.3 62.7 + - - +
22M ASN 3.1 3.1 - - - +
23M LEU* 3.1 27.4 + - + +
24M GLN 3.7 0.2 + - - -
57M TYR* 3.2 38.5 - - + -
5S TRP* 3.6 15.7 - - + +
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Residues in contact with ASP 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ASP* 2.5 23.2 + - - +
18M THR* 3.8 11.8 + - - +
19M GLY 3.7 1.0 - - - -
20M VAL* 1.3 75.2 - - - +
22M ASN* 1.3 68.6 + - - +
24M GLN* 3.9 11.6 + - - +
25M THR* 4.0 10.9 + - - -
57M TYR* 5.0 6.0 + - - -
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Residues in contact with ASN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M VAL* 3.1 1.2 - - - +
21M ASP* 1.3 84.5 - - - +
23M LEU* 1.3 66.1 + - - +
24M GLN 3.2 0.7 - - - -
25M THR* 3.0 10.4 + - - -
26M GLN* 2.8 35.3 + - + +
3S THR 5.5 1.0 + - - -
4S PRO* 5.3 2.4 - - - +
5S TRP* 3.8 35.9 - - + +
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PRO* 5.8 1.6 - - + -
20M VAL* 3.1 29.8 + - + +
22M ASN* 1.3 77.9 - - - +
24M GLN* 1.3 64.9 + - - +
26M GLN* 3.2 4.5 + - - +
27M VAL* 3.0 21.7 + - - +
50M LYS* 3.5 30.7 - - + +
53M GLU* 3.7 32.8 - - + +
54M TYR* 4.4 5.6 - - + -
57M TYR* 3.8 24.0 - - + -
5S TRP* 3.7 35.8 - - + -
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Residues in contact with GLN 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ALA* 5.4 4.8 - - - +
20M VAL 3.7 2.6 + - - -
21M ASP* 4.2 7.7 - - - +
22M ASN 3.2 0.2 - - - -
23M LEU* 1.3 79.1 - - - +
25M THR* 1.3 55.7 + - - +
27M VAL* 3.3 8.1 - - - +
28M THR* 2.7 44.9 + - - +
54M TYR* 4.0 17.4 + - + +
57M TYR* 2.8 33.2 + - + +
58M ARG* 3.6 22.4 + - - +
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Residues in contact with THR 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M ASP 4.0 8.1 + - - -
22M ASN* 3.0 15.4 + - - -
24M GLN* 1.3 79.5 - - - +
26M GLN* 1.3 60.3 + - + +
28M THR* 3.4 4.9 + - - -
29M GLU* 3.0 52.2 + - + +
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Residues in contact with GLN 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22M ASN* 2.8 25.3 + - + +
23M LEU* 3.2 4.4 + - - +
25M THR* 1.3 79.7 - - + +
27M VAL* 1.3 57.2 + - - +
29M GLU* 3.4 8.8 + - - +
30M ALA* 2.9 28.1 + - - +
50M LYS* 2.9 39.8 + - + +
4S PRO* 4.4 8.7 - - - +
5S TRP* 3.0 58.1 + - - +
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Residues in contact with VAL 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M LEU 3.0 15.2 + - - +
24M GLN 3.3 11.0 - - - +
26M GLN* 1.3 74.7 - - - +
28M THR* 1.3 67.4 + - - +
30M ALA* 3.7 4.3 - - - -
31M LEU* 3.0 21.8 + - - +
47M TYR* 3.4 31.2 - - + +
50M LYS* 3.8 13.7 - - + +
51M LEU* 3.7 36.3 - - + +
54M TYR* 3.8 28.9 - - + -
68R PHE* 6.1 4.0 - - + -
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Residues in contact with THR 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M GLN* 2.7 32.6 + - - +
25M THR* 3.7 6.9 - - - -
27M VAL* 1.3 78.8 - - - +
29M GLU* 1.3 61.2 + - + +
31M LEU* 3.2 11.9 + - + +
32M ASP* 2.9 40.0 + - - +
54M TYR* 5.8 0.5 - - - -
68R PHE* 6.5 0.4 - - - -
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Residues in contact with GLU 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M THR* 3.0 39.0 + - + +
26M GLN* 3.8 8.2 - - - +
28M THR* 1.3 75.6 - - + +
30M ALA* 1.3 60.5 + - - +
32M ASP* 3.5 12.8 - - - +
33M LYS* 3.0 45.5 + - - +
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Residues in contact with ALA 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M GLN 2.9 18.6 + - - +
27M VAL* 3.7 8.1 - - - +
29M GLU* 1.3 78.0 - - - +
31M LEU* 1.3 56.9 + - - +
33M LYS* 4.0 7.0 - - - +
34M LEU* 2.9 30.7 + - - +
43M LEU* 4.8 5.1 - - + +
46M ALA* 4.8 7.0 - - + -
47M TYR* 3.8 32.8 - - + +
50M LYS* 4.9 4.9 - - + -
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Residues in contact with LEU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M VAL 3.0 14.7 + - - +
28M THR* 3.2 13.9 + - + +
30M ALA* 1.3 75.9 - - - +
32M ASP* 1.3 63.7 + - - +
34M LEU* 4.3 6.1 - - + -
35M ALA* 2.8 34.6 + - + +
47M TYR* 3.6 29.5 - - + +
12R VAL* 5.1 7.2 - - + +
15R LYS* 5.0 23.1 - - + -
16R PHE* 5.3 13.0 - - + +
64R THR* 4.4 14.6 - - + +
68R PHE* 3.8 31.2 - - + -
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Residues in contact with ASP 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M THR* 2.9 31.7 + - - +
29M GLU* 3.3 17.4 + - - +
31M LEU* 1.3 80.6 - - - +
33M LYS* 1.3 62.9 + - + +
35M ALA* 3.5 16.0 - - - +
36M ALA* 3.7 6.4 + - - +
15R LYS* 5.3 12.8 + - - +
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Residues in contact with LYS 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M GLU* 3.0 29.7 + - - +
30M ALA* 4.0 3.6 - - - +
32M ASP* 1.3 75.3 - - + +
34M LEU* 1.3 66.2 + - - +
36M ALA* 2.9 18.8 + - - +
37M LYS 3.2 8.1 + - - -
43M LEU* 3.5 32.9 - - + +
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Residues in contact with LEU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M ALA 2.9 19.3 + - - +
31M LEU* 3.7 8.3 - - + +
33M LYS* 1.3 76.6 - - - +
35M ALA* 1.3 58.9 + - - +
37M LYS 3.6 13.0 - - - +
38M PRO* 2.8 54.9 - - + +
43M LEU* 3.5 29.8 - - + +
44M LEU* 3.6 24.9 - - + +
47M TYR* 3.3 39.3 - - + -
16R PHE* 5.4 6.1 - - + -
60R ALA* 6.2 2.2 - - + -
64R THR* 5.4 4.7 - - + -
79X PHE* 5.6 1.3 - - + -
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Residues in contact with ALA 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M LEU* 2.8 19.2 + - + +
32M ASP* 3.5 10.5 - - - +
33M LYS 3.1 0.2 - - - -
34M LEU* 1.3 77.5 - - - +
36M ALA* 1.3 59.9 + - - +
38M PRO* 3.6 1.0 - - - +
15R LYS 3.4 26.0 - - - +
16R PHE* 3.6 27.1 - - + +
19R GLY* 3.2 22.5 - - - +
20R VAL* 3.3 11.4 - - - +
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Residues in contact with ALA 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ASP 3.7 4.9 + - - +
33M LYS* 2.9 14.7 + - - +
35M ALA* 1.3 80.5 - - - +
37M LYS* 1.3 67.1 + - + +
38M PRO* 3.6 0.4 - - - -
19R GLY* 3.5 14.7 - - - +
5X TRP* 2.7 36.5 + - + +
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Residues in contact with LYS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33M LYS 3.2 3.0 + - - -
34M LEU* 3.0 12.0 + - - +
36M ALA* 1.3 89.9 - - + +
38M PRO* 1.3 66.6 - - - +
39M SER 3.0 4.4 + - - +
40M ASP* 3.1 27.1 + - + +
43M LEU* 3.7 12.8 - - + +
6X SER 3.5 22.2 - - - +
7X GLY* 4.2 1.6 - - - -
8X TYR* 4.0 25.8 - - + +
11X ASP* 2.8 21.9 + - - +
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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