Contacts of the helix formed by residues 7 - 20 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5F TRP* 3.5 26.2 - - - -
6F SER* 1.3 75.1 - - - +
8F TYR* 1.3 60.6 + - - -
9F LEU 3.4 2.5 - - - -
10F ASP* 3.0 16.8 + - - -
11F ASP* 2.9 29.2 + - - -
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Residues in contact with TYR 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR* 4.6 6.2 + - - -
7F GLY* 1.3 70.6 - - - -
9F LEU* 1.3 69.0 + - + +
11F ASP* 2.9 16.3 + - + +
12F VAL* 2.8 50.0 + - + +
15F LYS* 5.9 6.3 - - - -
68F PHE* 3.4 39.7 - + + -
71F ILE* 5.8 0.9 - - + -
72F ASP* 5.1 8.1 - - - +
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Residues in contact with LEU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLY* 3.4 0.4 - - - -
8F TYR* 1.3 80.2 - - + +
10F ASP* 1.3 68.1 + - - +
12F VAL* 3.3 5.9 + - + +
13F SER* 3.0 22.3 + - - -
65F VAL* 3.4 43.5 - - + +
68F PHE* 3.5 26.7 - - + +
69F LYS* 3.6 32.1 - - + +
72F ASP* 4.2 10.3 - - - +
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Residues in contact with ASP 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F TRP* 3.4 18.1 - - - +
6F SER* 3.1 24.4 - - - +
7F GLY* 3.0 22.9 + - - +
9F LEU* 1.3 79.8 - - - +
11F ASP* 1.3 55.1 + - - +
13F SER* 3.3 8.3 + - - -
14F ALA* 3.0 26.5 + - - +
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Residues in contact with ASP 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F SER* 2.9 27.1 + - - +
7F GLY 2.9 18.9 + - - +
8F TYR* 2.9 18.1 + - + +
10F ASP* 1.3 73.4 - - - +
12F VAL* 1.3 53.6 + - - +
14F ALA* 3.2 7.4 + - - +
15F LYS* 2.7 53.3 + - - +
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Residues in contact with VAL 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.1 6.9 - - + +
8F TYR* 2.8 47.7 + - + +
9F LEU* 3.4 11.4 - - - +
10F ASP 3.2 0.2 - - - -
11F ASP* 1.3 78.1 - - + +
13F SER* 1.3 62.1 + - - +
15F LYS* 3.2 14.3 + - + +
16F PHE* 3.1 22.0 + - - +
64F THR* 4.1 10.5 - - - +
65F VAL* 3.9 18.2 - - + -
68F PHE* 3.6 35.2 - - + -
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Residues in contact with SER 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LEU 3.0 12.5 + - - -
10F ASP* 3.5 11.4 - - - -
12F VAL* 1.3 76.4 - - - +
14F ALA* 1.3 57.7 + - - +
16F PHE* 3.4 5.0 + - - +
17F ASP* 3.0 33.9 + - - +
61F GLN* 2.8 29.4 + - - +
65F VAL* 4.3 15.0 - - - -
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASP 3.0 14.2 + - - +
11F ASP* 3.5 12.1 - - - +
13F SER* 1.3 73.0 - - - +
15F LYS* 1.3 55.9 + - + +
17F ASP* 3.7 7.0 - - - +
18F THR* 2.6 40.4 + - - +
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Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.0 20.2 - - + -
32A ASP* 5.3 12.3 + - - +
35A ALA* 3.4 15.9 - - - +
8F TYR* 5.9 6.3 - - - -
11F ASP* 2.7 41.7 + - + +
12F VAL* 3.2 13.4 + - + +
14F ALA* 1.3 74.3 - - + +
16F PHE* 1.3 60.2 + - - +
18F THR* 3.4 18.1 - - - -
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Residues in contact with PHE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.3 11.1 - - + +
34A LEU* 4.9 6.3 - - + -
35A ALA* 3.6 23.1 - - + +
38A PRO* 3.6 35.7 - - + -
12F VAL 3.1 12.4 + - - +
13F SER* 3.7 6.5 - - - +
15F LYS* 1.3 76.6 - - - +
17F ASP* 1.3 73.4 + - - +
18F THR 3.2 0.7 + - - -
19F GLY 3.2 9.9 + - - -
20F VAL* 3.3 25.3 - - + +
56F LEU 3.6 18.6 - - - -
57F TYR* 3.6 22.2 - - - -
60F ALA* 4.0 13.7 - - + -
61F GLN* 3.6 27.8 - - + -
64F THR* 4.8 16.8 - - + +
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Residues in contact with ASP 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F SER* 3.0 22.2 + - - +
14F ALA* 3.8 6.9 - - - +
16F PHE* 1.3 80.2 - - - +
18F THR* 1.3 59.0 + - - +
20F VAL* 2.9 6.4 + - - -
21F ASP* 2.5 43.3 + - - +
57F TYR* 3.8 23.7 + - - +
61F GLN* 3.1 35.7 + - - +
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Residues in contact with THR 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ALA* 2.6 26.5 + - - +
15F LYS* 3.4 12.6 + - - -
16F PHE 3.1 0.2 - - - -
17F ASP* 1.3 77.8 - - - +
19F GLY* 1.3 61.6 + - - +
20F VAL 3.5 0.3 + - - -
21F ASP* 3.8 13.2 + - - +
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Residues in contact with GLY 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.2 26.4 - - - +
36A ALA* 3.5 9.2 - - - +
15F LYS 4.0 1.6 + - - -
16F PHE 3.2 4.8 + - - -
17F ASP 3.1 0.8 - - - -
18F THR* 1.3 81.3 - - - +
20F VAL* 1.3 51.9 + - - +
21F ASP 3.7 0.7 - - - -
5L TRP* 2.6 39.6 + - - -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 3.3 15.7 - - - +
38A PRO* 3.5 25.8 - - + -
16F PHE* 3.3 30.5 - - + +
17F ASP* 3.1 5.8 - - - +
19F GLY* 1.3 81.9 - - - +
21F ASP* 1.3 62.6 + - - +
22F ASN 3.1 3.8 - - - +
23F LEU* 3.1 28.0 + - + +
24F GLN 3.7 0.2 + - - -
57F TYR* 3.2 38.3 - - + -
5L 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