Contacts of the helix formed by residues 7 - 20 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LYS* 4.2 7.6 - - - -
39E SER* 4.3 1.6 - - - -
53J GLU* 3.3 13.2 - - - -
5P TRP* 3.5 21.5 - - - -
6P SER* 1.3 76.5 - - - +
8P TYR* 1.3 61.1 + - - -
9P LEU 3.4 2.0 - - - -
10P ASP* 3.0 12.6 + - - +
11P ASP* 2.9 28.6 + - - -
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Residues in contact with TYR 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LYS* 4.0 11.9 - - + +
39E SER* 3.1 37.5 + - - +
40E ASP* 3.5 33.0 - - + +
41E PRO* 3.4 16.7 - - + +
54K TYR* 4.6 4.2 + - - -
58K ARG* 5.9 0.2 + - - -
7P GLY* 1.3 71.9 - - - -
9P LEU* 1.3 63.5 + - + +
11P ASP* 2.9 16.4 + - + +
12P VAL* 2.8 51.1 + - + +
15P LYS* 5.9 6.3 - - - -
68P PHE* 3.4 34.2 - + + -
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Residues in contact with LEU 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E SER* 3.2 24.9 + - - +
49J SER* 4.0 6.2 + - - +
52J SER* 3.5 24.7 - - - +
53J GLU* 3.5 15.3 - - + +
56J LEU* 5.8 0.4 - - + -
8P TYR* 1.3 79.2 - - + +
10P ASP* 1.3 64.9 + - - +
12P VAL* 3.3 7.2 + - + +
13P SER* 3.0 22.2 + - - -
65P VAL* 3.4 37.7 - - + +
68P PHE* 3.5 25.8 - - + +
69P LYS* 3.6 26.7 - - + +
72P ASP* 4.2 2.9 - - - +
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Residues in contact with ASP 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J SER* 3.6 14.7 + - - -
50J LYS* 3.8 28.8 + - - +
53J GLU* 2.9 34.0 + - - +
5P TRP* 3.4 9.2 - - - -
6P SER* 3.1 24.0 - - - +
7P GLY 3.0 16.1 + - - +
9P LEU* 1.3 76.3 - - - +
11P ASP* 1.3 54.8 + - - +
13P SER* 3.3 6.0 + - - -
14P ALA* 3.0 26.6 + - - +
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Residues in contact with ASP 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LYS* 2.8 31.5 + - - -
6P SER* 2.9 23.7 + - - -
7P GLY 2.9 15.3 + - - +
8P TYR* 2.9 17.4 + - + +
10P ASP* 1.3 73.4 - - - +
12P VAL* 1.3 54.0 + - - +
14P ALA* 3.2 8.2 + - - +
15P LYS* 2.7 54.2 + - - +
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Residues in contact with VAL 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 5.1 6.0 - - + +
8P TYR* 2.8 48.6 + - + +
9P LEU* 3.4 11.2 - - + +
10P ASP 3.2 0.2 - - - -
11P ASP* 1.3 76.5 - - - +
13P SER* 1.3 62.4 + - - +
15P LYS* 3.2 15.1 + - + +
16P PHE* 3.1 22.3 + - - +
64P THR* 4.1 11.2 - - - +
65P VAL* 3.9 17.5 - - + -
68P PHE* 3.6 35.4 - - + -
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Residues in contact with SER 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J SER* 4.2 16.6 + - - -
9P LEU 3.0 12.3 + - - -
10P ASP* 3.5 9.4 - - - -
12P VAL* 1.3 77.9 - - - +
14P ALA* 1.3 57.3 + - - +
16P PHE* 3.4 4.6 + - - +
17P ASP* 3.0 34.1 + - - +
61P GLN* 2.8 29.5 + - - +
64P THR* 6.1 0.2 - - - -
65P VAL* 4.1 12.5 - - - +
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Residues in contact with ALA 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P ASP 3.0 13.6 + - - +
11P ASP* 3.5 12.3 - - - +
13P SER* 1.3 73.4 - - - +
15P LYS* 1.3 57.1 + - + +
17P ASP* 3.3 6.9 + - - +
18P THR* 2.6 40.5 + - - +
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Residues in contact with LYS 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 5.0 20.9 - - + -
32K ASP* 5.3 11.3 + - - +
35K ALA* 3.4 15.8 - - - +
8P TYR* 5.9 6.5 - - - -
11P ASP* 2.7 40.6 + - - +
12P VAL* 3.2 13.4 + - + +
14P ALA* 1.3 73.6 - - + +
16P PHE* 1.3 60.9 + - - +
18P THR* 3.4 17.8 - - - -
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Residues in contact with PHE 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K LEU* 5.3 10.4 - - + +
34K LEU* 4.9 6.5 - - + -
35K ALA* 3.6 22.0 - - + +
38K PRO* 3.6 34.8 - - + -
12P VAL 3.1 12.1 + - - +
13P SER* 3.7 7.2 - - - +
15P LYS* 1.3 75.7 - - - +
17P ASP* 1.3 74.9 + - - +
18P THR 3.2 0.7 + - - -
19P GLY 3.2 10.0 + - - -
20P VAL* 3.3 25.2 - - + +
56P LEU 3.6 18.8 - - - -
57P TYR* 3.6 21.8 - - - -
60P ALA* 4.0 13.9 - - + -
61P GLN* 3.6 26.9 - - + -
64P THR* 4.8 17.0 - - + +
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Residues in contact with ASP 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P SER* 3.0 22.6 + - - +
14P ALA* 3.8 6.7 - - - +
16P PHE* 1.3 80.4 - - - +
18P THR* 1.3 58.0 + - - +
20P VAL* 2.9 6.8 + - - -
21P ASP* 2.5 43.4 + - - +
57P TYR* 3.8 24.2 + - - +
61P GLN* 3.1 34.7 + - - +
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Residues in contact with THR 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ALA* 2.6 26.7 + - - +
15P LYS* 3.4 12.9 + - - -
16P PHE 3.1 0.2 - - - -
17P ASP* 1.3 78.1 - - - +
19P GLY* 1.3 62.0 + - - +
20P VAL 3.5 0.2 + - - -
21P ASP* 3.8 13.1 + - - +
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Residues in contact with GLY 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ALA* 3.2 26.2 - - - +
36K ALA* 3.5 9.4 - - - +
15P LYS 4.0 1.8 + - - -
16P PHE 3.2 4.8 + - - -
17P ASP 3.1 0.6 - - - -
18P THR* 1.3 82.0 - - - +
20P VAL* 1.3 50.9 + - - +
21P ASP 3.7 0.4 - - - -
5V TRP* 2.6 39.5 + - - -
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Residues in contact with VAL 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ALA 3.3 15.7 - - - +
38K PRO* 3.5 25.6 - - + -
16P PHE* 3.3 29.4 - - + +
17P ASP* 3.1 5.6 - - - +
19P GLY* 1.3 81.1 - - - +
21P ASP* 1.3 62.8 + - - +
22P ASN 3.1 3.4 - - - +
23P LEU* 3.1 28.0 + - + +
57P TYR* 3.2 39.4 - - + -
5V 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