Contacts of the helix formed by residues 7 - 20 (chain V) 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 V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K LYS* 4.2 7.9 - - - -
39K SER* 4.3 1.3 - - - -
53P GLU* 3.3 12.3 - - - -
5V TRP* 3.5 21.7 - - - -
6V SER* 1.3 76.3 - - - +
8V TYR* 1.3 62.2 + - - -
9V LEU 3.4 2.2 - - - -
10V ASP* 3.0 12.9 + - - -
11V ASP* 2.9 29.0 + - - -
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Residues in contact with TYR 8 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LYS* 4.0 12.2 - - + +
39K SER* 3.1 33.5 + - - +
40K ASP* 3.5 37.2 - - + +
41K PRO* 3.4 17.2 - - + +
54Q TYR* 4.7 4.5 + - - -
58Q ARG* 5.9 0.3 + - - -
7V GLY* 1.3 71.0 - - - -
9V LEU* 1.3 64.3 + - + +
11V ASP* 2.9 16.3 + - + +
12V VAL* 2.8 50.6 + - + +
15V LYS* 5.9 7.0 - - - -
68V PHE* 3.4 33.1 - + + -
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Residues in contact with LEU 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K SER* 3.2 24.5 + - - +
49P SER* 4.0 6.1 + - - +
52P SER* 3.5 25.4 - - - +
53P GLU* 3.5 15.3 - - + +
56P LEU* 5.8 0.2 - - + -
8V TYR* 1.3 79.0 - - + +
10V ASP* 1.3 65.6 + - - +
12V VAL* 3.4 6.2 - - + +
13V SER* 3.0 23.4 + - - -
65V VAL* 3.4 36.1 - - + +
68V PHE* 3.5 25.6 - - + +
69V LYS* 3.6 26.7 - - + +
72V ASP* 4.2 3.6 - - - +
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Residues in contact with ASP 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P SER* 3.6 15.7 + - - +
50P LYS* 3.8 29.0 + - - +
53P GLU* 2.9 33.7 + - - +
5V TRP* 3.4 8.8 - - - -
6V SER* 3.1 24.0 - - - +
7V GLY 3.0 15.7 + - - +
9V LEU* 1.3 76.5 - - - +
11V ASP* 1.3 55.0 + - - +
13V SER* 3.3 5.8 + - - -
14V ALA* 3.0 26.4 + - - +
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Residues in contact with ASP 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K LYS* 2.8 30.9 + - - -
6V SER* 2.9 23.3 + - - -
7V GLY 2.9 15.0 + - - +
8V TYR* 2.9 17.9 + - + +
10V ASP* 1.3 72.0 - - - +
12V VAL* 1.3 54.5 + - + +
14V ALA* 3.2 8.3 + - - +
15V LYS* 2.7 53.2 + - + +
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Residues in contact with VAL 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q LEU* 5.1 5.9 - - + +
8V TYR* 2.8 48.1 + - + +
9V LEU* 3.4 11.2 - - + +
10V ASP 3.2 0.2 - - - -
11V ASP* 1.3 76.3 - - + +
13V SER* 1.3 62.1 + - - +
15V LYS* 3.2 14.3 + - + +
16V PHE* 3.1 22.7 + - - +
64V THR* 4.1 10.8 - - - +
65V VAL* 3.9 17.9 - - + -
68V PHE* 3.6 36.1 - - + -
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Residues in contact with SER 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P SER* 4.2 16.5 + - - -
9V LEU 3.0 13.1 + - - -
10V ASP* 3.3 10.3 + - - -
12V VAL* 1.3 76.7 - - - +
14V ALA* 1.3 58.3 + - - +
16V PHE* 3.4 4.7 + - - +
17V ASP* 3.0 33.5 + - - +
61V GLN* 2.8 29.7 + - - +
65V VAL* 4.1 12.5 - - - +
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Residues in contact with ALA 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V ASP 3.0 13.4 + - - +
11V ASP* 3.2 12.1 + - - +
13V SER* 1.3 74.0 - - - +
15V LYS* 1.3 57.4 + - + +
17V ASP* 3.7 6.1 - - - +
18V THR* 2.6 40.2 + - - +
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Residues in contact with LYS 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q LEU* 5.0 19.7 - - + -
32Q ASP* 5.3 12.2 + - - +
35Q ALA* 3.4 15.6 - - - +
8V TYR* 5.9 6.5 - - - -
11V ASP* 2.7 41.0 + - - +
12V VAL* 3.2 14.3 + - + +
14V ALA* 1.3 74.4 - - + +
16V PHE* 1.3 62.3 + - - +
18V THR* 3.4 17.7 - - - -
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Residues in contact with PHE 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Q LEU* 5.3 10.2 - - + +
34Q LEU* 4.9 7.0 - - + -
35Q ALA* 3.6 21.0 - - - +
38Q PRO* 3.6 34.8 - - + -
12V VAL 3.1 12.7 + - - +
13V SER* 3.7 6.7 - - - +
15V LYS* 1.3 75.4 - - - +
17V ASP* 1.3 74.4 + - - +
18V THR 3.2 0.7 + - - -
19V GLY 3.2 10.0 + - - -
20V VAL* 3.3 26.6 - - + +
56V LEU 3.6 18.8 - - - -
57V TYR* 3.6 21.5 - - - -
60V ALA* 4.0 13.9 - - + -
61V GLN* 3.6 27.6 - - + -
64V THR* 4.8 15.7 - - + +
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Residues in contact with ASP 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13V SER* 3.0 21.4 + - - +
14V ALA* 3.8 6.5 + - - +
16V PHE* 1.3 80.2 - - - +
18V THR* 1.3 57.7 + - - +
20V VAL* 2.9 6.9 + - - -
21V ASP* 2.5 43.1 + - - +
57V TYR* 3.8 23.5 + - - +
61V GLN* 3.1 36.0 + - - +
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Residues in contact with THR 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V ALA* 2.6 27.7 + - - +
15V LYS* 3.4 13.1 + - - -
16V PHE 3.1 0.2 - - - -
17V ASP* 1.3 78.1 - - - +
19V GLY* 1.3 61.0 + - - +
20V VAL 3.5 0.2 + - - -
21V ASP* 3.8 13.3 + - - +
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Residues in contact with GLY 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q ALA* 3.2 26.0 - - - +
36Q ALA* 3.5 8.9 - - - +
15V LYS 4.0 2.4 + - - -
16V PHE 3.2 4.8 + - - -
17V ASP 3.1 0.8 - - - -
18V THR* 1.3 80.2 - - - +
20V VAL* 1.3 51.9 + - - +
21V ASP 3.7 0.4 - - - -
5b TRP* 2.6 39.5 + - - -
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Residues in contact with VAL 20 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Q ALA 3.3 15.9 - - - +
38Q PRO* 3.5 25.1 - - + -
16V PHE* 3.3 28.9 - - + +
17V ASP* 2.9 6.0 + - - +
19V GLY* 1.3 81.1 - - - +
21V ASP* 1.3 62.2 + - - +
22V ASN 3.1 3.4 - - - +
23V LEU* 3.1 27.6 + - + +
57V TYR* 3.2 39.9 - - + -
5b TRP* 3.6 15.5 - - + +
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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
------------------------------------------------------------
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