Contacts of the helix formed by residues 7 - 20 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37J LYS* 4.2 9.0 - - - -
38J PRO* 5.8 0.2 - - - -
39J SER* 4.3 1.3 - - - -
53O GLU* 3.3 12.3 - - - -
5U TRP* 3.5 21.3 - - - -
6U SER* 1.3 76.7 - - - +
8U TYR* 1.3 59.9 - - - -
9U LEU 3.4 2.0 - - - -
10U ASP* 3.0 12.7 + - - -
11U ASP* 2.9 28.9 + - - -
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Residues in contact with TYR 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LYS* 4.0 11.6 - - + +
39J SER* 3.1 38.0 + - - +
40J ASP* 3.5 34.1 - - + +
41J PRO* 3.4 18.0 - - + +
54P TYR* 4.6 4.5 + - - -
58P ARG* 5.9 0.3 + - - -
7U GLY* 1.3 71.4 - - - -
9U LEU* 1.3 63.8 + - + +
11U ASP* 2.9 15.9 + - + +
12U VAL* 2.8 51.1 + - + +
15U LYS* 5.9 7.0 - - - -
68U PHE* 3.4 33.5 - + + -
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Residues in contact with LEU 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39J SER* 3.2 24.5 + - - +
49O SER* 4.0 6.5 + - - +
52O SER* 3.5 24.7 - - - +
53O GLU* 3.3 15.7 + - + +
56O LEU* 5.8 0.7 - - + -
8U TYR* 1.3 78.6 - - + +
10U ASP* 1.3 66.1 + - - +
12U VAL* 3.3 5.2 + - + +
13U SER* 3.0 23.0 + - - -
65U VAL* 3.4 36.9 - - + +
68U PHE* 3.5 25.6 - - + +
69U LYS* 3.6 26.7 - - + +
72U ASP* 4.2 2.9 - - - +
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Residues in contact with ASP 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O SER* 3.6 15.8 + - - +
50O LYS* 3.8 29.8 + - - +
53O GLU* 2.9 33.8 + - - +
5U TRP* 3.4 8.7 - - - -
6U SER* 3.1 24.4 - - - +
7U GLY 3.0 15.9 + - - +
9U LEU* 1.3 75.7 - - - +
11U ASP* 1.3 55.3 + - - +
13U SER* 3.3 6.6 + - - -
14U ALA* 3.0 26.6 + - - +
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Residues in contact with ASP 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LYS* 2.8 30.9 + - - -
6U SER* 2.9 23.8 + - - +
7U GLY 2.9 14.9 + - - +
8U TYR* 2.9 18.0 + - + +
10U ASP* 1.3 71.9 - - - +
12U VAL* 1.3 54.6 + - + +
14U ALA* 3.2 8.8 + - - +
15U LYS* 2.7 53.5 + - + +
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Residues in contact with VAL 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LEU* 5.1 6.5 - - + +
8U TYR* 2.8 49.0 + - + +
9U LEU* 3.4 12.1 - - + +
10U ASP 3.2 0.2 - - - -
11U ASP* 1.3 75.9 - - + +
13U SER* 1.3 62.3 + - - +
15U LYS* 3.2 14.3 + - + +
16U PHE* 3.1 22.3 + - - +
64U THR* 4.1 10.3 - - - +
65U VAL* 3.9 18.2 - - + -
68U PHE* 3.6 35.0 - - + -
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Residues in contact with SER 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O SER* 4.2 16.3 + - - -
9U LEU 3.0 13.1 + - - -
10U ASP* 3.5 9.4 - - - -
12U VAL* 1.3 77.4 - - - +
14U ALA* 1.3 57.7 + - - +
16U PHE* 3.4 5.1 + - - +
17U ASP* 3.0 33.7 + - - +
61U GLN* 2.8 29.9 + - - +
65U VAL* 4.1 12.3 - - - +
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Residues in contact with ALA 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U ASP 3.0 13.8 + - - +
11U ASP* 3.5 11.7 - - - +
13U SER* 1.3 72.9 - - - +
15U LYS* 1.3 56.9 - - + +
17U ASP* 3.7 6.7 - - - +
18U THR* 2.6 41.2 + - - +
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Residues in contact with LYS 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31P LEU* 5.0 19.5 - - + -
32P ASP* 5.3 11.5 + - - +
35P ALA* 3.4 15.8 - - - +
8U TYR* 5.9 6.3 - - - -
11U ASP* 2.7 42.1 + - + +
12U VAL* 3.2 14.6 + - + +
14U ALA* 1.3 74.0 - - + +
16U PHE* 1.3 61.2 + - - +
18U THR* 3.4 18.2 - - - -
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Residues in contact with PHE 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LEU* 5.3 10.2 - - + +
34P LEU* 4.9 6.1 - - + -
35P ALA* 3.6 21.9 - - - +
38P PRO* 3.6 35.0 - - + -
12U VAL 3.1 12.1 + - - +
13U SER* 3.7 6.7 - - - +
15U LYS* 1.3 75.7 - - - +
17U ASP* 1.3 72.4 + - - +
18U THR 3.2 0.9 + - - -
19U GLY 3.2 9.9 + - - -
20U VAL* 3.3 25.7 - - + +
56U LEU 3.6 17.5 - - - -
57U TYR* 3.6 23.6 - - - -
60U ALA* 4.0 14.6 - - + -
61U GLN* 3.6 26.9 - - + -
64U THR* 4.8 16.6 - - + +
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Residues in contact with ASP 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U SER* 3.0 22.6 + - - +
14U ALA* 3.3 6.9 + - - +
16U PHE* 1.3 79.8 - - - +
18U THR* 1.3 58.7 + - - +
20U VAL* 2.9 6.4 + - - -
21U ASP* 2.5 43.0 + - - +
57U TYR* 3.8 25.0 + - - +
61U GLN* 3.1 36.4 + - - +
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Residues in contact with THR 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14U ALA* 2.6 27.0 + - - +
15U LYS* 3.4 13.1 + - - -
16U PHE 3.1 0.2 - - - -
17U ASP* 1.3 78.0 - - - +
19U GLY* 1.3 60.3 + - - +
20U VAL 3.5 0.2 + - - -
21U ASP* 3.8 13.3 + - - +
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Residues in contact with GLY 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P ALA* 3.2 26.7 - - - +
36P ALA* 3.5 9.2 - - - +
15U LYS 4.0 2.0 + - - -
16U PHE 3.2 4.8 + - - -
17U ASP 3.1 1.0 - - - -
18U THR* 1.3 80.4 - - - +
20U VAL* 1.3 51.2 + - - +
21U ASP 3.7 0.7 - - - -
5a TRP* 2.6 39.4 + - - -
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Residues in contact with VAL 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ALA 3.3 15.9 - - - +
38P PRO* 3.5 25.6 - - + -
16U PHE* 3.3 29.4 - - + +
17U ASP* 3.1 5.6 - - - +
19U GLY* 1.3 81.3 - - - +
21U ASP* 1.3 62.9 + - - +
22U ASN 3.1 3.4 - - - +
23U LEU* 3.1 28.8 + - + +
24U GLN 3.7 0.2 + - - -
57U TYR* 3.2 39.8 - - + -
5a 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