Contacts of the helix formed by residues 7 - 20 (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 GLY 7 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLU* 3.3 13.5 - - - -
5H TRP* 3.5 22.0 - - - -
6H SER* 1.3 75.9 - - - +
8H TYR* 1.3 61.7 + - - -
9H LEU 3.4 2.0 - - - -
10H ASP* 3.0 12.3 + - - -
11H ASP* 2.9 28.9 + - - -
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Residues in contact with TYR 8 (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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53B GLU* 3.7 0.8 + - - +
54C TYR* 4.6 5.9 + - - -
58C ARG* 5.9 0.3 + - - -
7H GLY* 1.3 71.2 - - - -
9H LEU* 1.3 70.5 + - + +
11H ASP* 2.9 16.7 + - + +
12H VAL* 2.8 50.2 + - + +
15H LYS* 5.9 6.7 - - - -
68H PHE* 3.4 39.3 - + + -
71H ILE* 5.8 1.6 - - + -
72H ASP* 5.1 8.1 - - - +
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Residues in contact with LEU 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 4.0 5.9 + - - +
52B SER* 3.5 25.6 - - - +
53B GLU* 3.3 22.9 + - + +
56B LEU* 5.8 3.1 - - + -
8H TYR* 1.3 80.9 - - + +
10H ASP* 1.3 66.9 + - - +
12H VAL* 3.4 6.5 - - + +
13H SER* 3.0 22.7 + - - -
65H VAL* 3.4 36.0 - - + +
68H PHE* 3.5 25.8 - - + +
69H LYS* 3.6 26.9 - - + +
72H ASP* 4.2 11.7 - - - +
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Residues in contact with ASP 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 3.6 15.9 + - - +
50B LYS* 3.8 30.1 + - - +
53B GLU* 2.9 33.6 + - - +
5H TRP* 3.4 8.8 - - - -
6H SER* 3.1 23.5 - - - +
7H GLY 3.0 16.2 + - - +
9H LEU* 1.3 76.5 - - - +
11H ASP* 1.3 55.1 + - - +
13H SER* 3.3 6.2 + - - -
14H ALA* 3.0 26.2 + - - +
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Residues in contact with ASP 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H SER* 2.9 26.6 + - - +
7H GLY 2.9 18.4 + - - +
8H TYR* 2.9 19.1 + - + +
10H ASP* 1.3 72.6 - - - +
12H VAL* 1.3 53.7 + - - +
14H ALA* 3.2 8.5 + - - +
15H LYS* 2.7 54.3 + - - +
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Residues in contact with VAL 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 5.1 6.0 - - + +
8H TYR* 2.8 47.3 + - + +
9H LEU* 3.4 11.7 - - + +
11H ASP* 1.3 77.0 - - + +
13H SER* 1.3 62.3 + - - +
15H LYS* 3.2 15.0 + - + +
16H PHE* 3.1 23.1 + - + +
64H THR* 4.1 10.5 - - - +
65H VAL* 3.9 17.7 - - + -
68H PHE* 3.6 36.3 - - + -
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Residues in contact with SER 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER* 4.2 16.3 + - - -
9H LEU 3.0 12.5 + - - -
10H ASP* 3.5 9.6 - - - -
12H VAL* 1.3 76.6 - - - +
14H ALA* 1.3 58.1 + - - +
16H PHE* 3.4 5.1 + - - +
17H ASP* 3.0 33.5 + - - +
61H GLN* 2.8 29.5 + - - +
65H VAL* 4.3 13.5 - - - -
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Residues in contact with ALA 14 (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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10H ASP 3.0 13.4 + - - +
11H ASP* 3.2 12.3 + - - +
13H SER* 1.3 73.6 - - - +
15H LYS* 1.3 56.7 + - + +
17H ASP* 3.3 6.3 + - - +
18H THR* 2.6 40.4 + - - +
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Residues in contact with LYS 15 (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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31C LEU* 5.0 20.0 - - + -
32C ASP* 5.3 12.2 + - - +
35C ALA* 3.4 15.5 - - - +
8H TYR* 5.9 6.7 - - - -
11H ASP* 2.7 41.3 + - + +
12H VAL* 3.2 13.2 + - + +
14H ALA* 1.3 74.6 - - + +
16H PHE* 1.3 62.0 + - - +
18H THR* 3.4 18.2 - - - -
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Residues in contact with PHE 16 (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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31C LEU* 5.3 10.2 - - + +
34C LEU* 4.9 6.5 - - + -
35C ALA* 3.6 22.0 - - - +
38C PRO* 3.6 35.4 - - + -
12H VAL* 3.1 12.9 + - + +
13H SER* 3.7 7.2 - - - +
15H LYS* 1.3 74.9 - - - +
17H ASP* 1.3 74.2 + - - +
18H THR 3.2 0.9 + - - -
19H GLY 3.2 9.9 + - - -
20H VAL* 3.3 26.0 - - + +
56H LEU 3.6 18.6 - - - -
57H TYR* 3.6 22.7 - - - -
60H ALA* 4.0 14.1 - - + -
61H GLN* 3.6 26.5 - - + -
64H THR* 4.8 15.9 - - + +
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Residues in contact with ASP 17 (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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13H SER* 3.0 20.9 + - - +
14H ALA* 3.8 6.7 + - - +
16H PHE* 1.3 80.0 - - - +
18H THR* 1.3 59.2 + - - +
20H VAL* 2.9 6.6 + - - -
21H ASP* 2.5 42.6 + - - +
57H TYR* 3.8 23.8 + - - +
61H GLN* 3.1 36.1 + - - +
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Residues in contact with THR 18 (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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14H ALA* 2.6 28.1 + - - +
15H LYS* 3.4 12.9 + - - -
16H PHE 3.1 0.2 - - - -
17H ASP* 1.3 77.8 - - - +
19H GLY* 1.3 60.6 - - - +
21H ASP* 3.8 13.1 + - - +
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Residues in contact with GLY 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ALA* 3.2 26.9 - - - +
36C ALA* 3.5 8.4 - - - +
15H LYS 4.0 2.2 + - - -
16H PHE 3.2 5.3 + - - -
17H ASP 3.1 0.6 - - - -
18H THR* 1.3 79.5 - - - +
20H VAL* 1.3 51.8 + - - +
21H ASP 3.7 0.7 - - - -
5N TRP* 2.6 39.7 + - - -
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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