Contacts of the helix formed by residues 20 - 37 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ALA 3.3 15.9 - - - +
38C PRO* 3.5 25.6 - - + -
16H PHE* 3.3 29.2 - - + +
17H ASP* 3.1 5.8 - - - +
19H GLY* 1.3 81.1 - - - +
21H ASP* 1.3 63.4 + - - +
22H ASN 3.1 3.4 - - - +
23H LEU* 3.1 28.2 + - + +
57H TYR* 3.2 38.4 - - + -
5N TRP* 3.6 15.0 - - + +
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Residues in contact with ASP 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASP* 2.5 23.3 + - - +
18H THR* 3.8 10.9 + - - +
19H GLY 3.7 1.8 - - - -
20H VAL* 1.3 73.9 - - - +
22H ASN* 1.3 68.6 + - - +
24H GLN* 3.9 11.6 + - - +
25H THR* 4.0 10.6 + - - -
57H TYR* 5.0 6.0 + - - -
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Residues in contact with ASN 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H VAL* 3.1 0.8 - - - +
21H ASP* 1.3 86.1 - - - +
23H LEU* 1.3 66.3 + - - +
24H GLN 3.2 0.9 - - - -
25H THR* 3.0 10.4 + - - -
26H GLN* 2.8 34.1 + - + +
3N THR 5.5 1.0 + - - -
4N PRO* 5.3 2.4 - - - +
5N TRP* 3.8 34.8 - - + +
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PRO* 5.8 1.6 - - + -
20H VAL* 3.1 29.9 + - + +
22H ASN* 1.3 77.8 - - - +
24H GLN* 1.3 64.9 + - - +
26H GLN* 3.2 5.3 + - - +
27H VAL* 3.0 22.1 + - + +
50H LYS* 3.5 31.2 - - + +
53H GLU* 3.7 31.6 - - + +
54H TYR* 4.2 5.4 - - + +
57H TYR* 3.8 24.0 - - + -
5N TRP* 3.7 36.4 - - + -
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Residues in contact with GLN 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 5.4 4.8 - - - +
20H VAL 3.7 2.6 + - - -
21H ASP* 4.2 7.9 - - - +
23H LEU* 1.3 78.3 - - - +
25H THR* 1.3 56.3 + - - +
27H VAL* 3.3 8.1 - - - +
28H THR* 2.7 44.1 + - - +
54H TYR* 4.0 16.5 + - + +
57H TYR* 2.8 33.1 + - + +
58H ARG* 3.6 22.0 - - - +
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Residues in contact with THR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ASP 4.0 8.5 + - - -
22H ASN* 3.0 15.0 + - - -
24H GLN* 1.3 80.0 - - - +
26H GLN* 1.3 60.4 + - + +
28H THR* 3.4 5.8 + - - -
29H GLU* 3.0 51.7 + - + +
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Residues in contact with GLN 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H ASN* 2.8 25.5 + - + +
23H LEU* 3.6 4.3 - - - +
25H THR* 1.3 78.9 - - + +
27H VAL* 1.3 58.0 + - - +
29H GLU* 3.4 8.9 + - - +
30H ALA* 2.9 28.9 + - - +
50H LYS* 2.9 39.6 + - + +
4N PRO* 4.4 8.7 - - - +
5N TRP* 3.0 57.9 + - - +
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Residues in contact with VAL 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H LEU 3.0 15.2 + - - +
24H GLN 3.3 11.7 - - - +
26H GLN* 1.3 74.5 - - - +
28H THR* 1.3 67.3 + - - +
29H GLU 3.4 0.2 - - - -
30H ALA* 4.0 4.5 - - - -
31H LEU* 3.0 21.8 + - - +
47H TYR* 3.4 30.0 - - + +
50H LYS* 3.8 13.9 - - + +
51H LEU* 3.7 36.3 - - + +
54H TYR* 3.8 28.9 - - + -
68M PHE* 6.1 3.5 - - + -
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Residues in contact with THR 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLN* 2.7 33.5 + - - +
25H THR* 3.7 6.5 - - - -
27H VAL* 1.3 77.4 - - - +
29H GLU* 1.3 62.7 + - + +
31H LEU* 3.2 11.4 + - + +
32H ASP* 2.9 40.7 + - - +
54H TYR* 5.8 0.7 - - - -
15M LYS* 6.4 0.2 - - - +
68M PHE* 6.5 0.7 - - - -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H THR* 3.0 39.1 + - + +
26H GLN* 3.8 7.4 - - - +
28H THR* 1.3 75.1 - - + +
30H ALA* 1.3 60.7 + - - +
32H ASP* 3.3 13.4 + - - +
33H LYS* 3.0 45.5 + - - +
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLN 2.9 18.3 + - - +
27H VAL* 3.7 9.2 - - - +
28H THR 3.3 0.2 - - - -
29H GLU* 1.3 77.8 - - - +
31H LEU* 1.3 56.3 + - - +
33H LYS* 3.6 7.6 + - - +
34H LEU* 2.9 30.1 + - - +
43H LEU* 4.8 6.2 - - + +
46H ALA* 4.8 6.3 - - + -
47H TYR* 3.8 31.3 - - + +
50H LYS* 4.9 5.2 - - + -
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Residues in contact with LEU 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H VAL 3.0 14.9 + - - +
28H THR* 3.2 14.3 + - + +
30H ALA* 1.3 74.3 - - - +
32H ASP* 1.3 64.3 + - - +
34H LEU* 3.7 6.2 - - + -
35H ALA* 2.8 34.1 + - + +
47H TYR* 3.6 30.5 - - + +
12M VAL* 5.1 7.9 - - + +
15M LYS* 5.0 22.7 - - + -
16M PHE* 5.3 11.9 - - + +
64M THR* 4.4 14.8 - - + +
68M PHE* 3.8 31.0 - - + -
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Residues in contact with ASP 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H THR* 2.9 31.3 + - - +
29H GLU* 3.3 17.3 + - - +
31H LEU* 1.3 80.6 - - - +
33H LYS* 1.3 64.2 + - + +
35H ALA* 3.5 15.2 - - - +
36H ALA* 3.7 6.4 + - - +
15M LYS* 5.3 13.5 + - - +
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H GLU* 3.0 30.2 + - - +
30H ALA* 4.0 3.1 - - - +
32H ASP* 1.3 76.4 - - + +
34H LEU* 1.3 66.2 + - - +
36H ALA* 2.9 19.8 + - - +
37H LYS 3.2 7.6 + - - -
43H LEU* 3.5 32.9 - - + +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ALA 2.9 19.7 + - - +
31H LEU* 3.7 7.9 - - + +
33H LYS* 1.3 77.0 - - - +
35H ALA* 1.3 57.7 + - - +
37H LYS 3.0 13.4 - - - +
38H PRO* 2.8 55.5 - - + +
43H LEU* 3.5 29.5 - - + +
44H LEU* 3.6 26.0 - - + +
47H TYR* 3.3 38.4 - - + -
16M PHE* 5.4 6.5 - - + -
60M ALA* 6.2 2.0 - - + -
64M THR* 5.4 4.5 - - + -
79S PHE* 5.6 1.1 - - + -
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 2.8 19.0 + - + +
32H ASP* 3.5 10.1 - - - +
33H LYS 3.1 0.2 - - - -
34H LEU* 1.3 77.5 - - - +
36H ALA* 1.3 60.4 + - - +
38H PRO* 3.6 0.9 - - - +
15M LYS 3.4 26.5 - - - +
16M PHE* 3.6 25.9 - - + +
19M GLY* 3.2 22.7 - - - +
20M VAL* 3.3 12.0 - - - +
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Residues in contact with ALA 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ASP 3.7 5.5 + - - +
33H LYS* 2.9 14.1 + - - +
35H ALA* 1.3 80.1 - - - +
37H LYS* 1.3 68.3 + - + +
19M GLY* 3.5 14.0 - - - +
5S TRP* 2.7 36.5 + - + +
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Residues in contact with LYS 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LYS 3.2 2.8 + - - -
34H LEU* 3.0 12.1 + - - +
36H ALA* 1.3 89.5 - - + +
38H PRO* 1.3 67.1 - - - +
39H SER 3.0 3.7 + - - -
40H ASP* 3.1 26.4 + - + +
43H LEU* 3.7 13.9 - - + +
6S SER 3.5 23.1 - - - +
7S GLY* 4.2 1.1 - - - -
8S TYR* 4.0 25.3 - - + +
11S ASP* 2.8 21.4 + - - +
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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