Contacts of the helix formed by residues 7 - 20 (chain c) 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 c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37R LYS* 4.2 8.5 - - - -
39R SER* 4.3 1.6 - - - -
53W GLU* 3.3 12.3 - - - -
5c TRP* 3.5 20.9 - - - -
6c SER* 1.3 76.9 - - - +
8c TYR* 1.3 61.6 + - - -
9c LEU 3.4 2.0 - - - -
10c ASP* 3.0 13.3 + - - -
11c ASP* 2.9 28.9 + - - -
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Residues in contact with TYR 8 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R LYS* 4.0 11.8 - - + +
39R SER* 3.1 37.8 + - - +
40R ASP* 3.5 33.4 - - + +
41R PRO* 3.4 17.2 - - + +
54X TYR* 4.6 4.5 + - - -
7c GLY* 1.3 71.6 - - - -
9c LEU* 1.3 64.5 + - + +
11c ASP* 2.9 16.1 + - + +
12c VAL* 2.8 51.2 + - + +
15c LYS* 5.9 7.2 - - - -
68c PHE* 3.4 32.9 - + + -
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Residues in contact with LEU 9 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R SER* 3.2 24.3 + - - +
49W SER* 4.0 5.8 + - - +
52W SER* 3.5 25.8 - - - +
53W GLU* 3.5 14.8 - - + +
56W LEU* 5.8 0.2 - - + -
8c TYR* 1.3 78.1 - - + +
10c ASP* 1.3 66.5 + - - +
12c VAL* 3.4 6.6 - - + +
13c SER* 3.0 22.5 + - - -
65c VAL* 3.4 37.3 - - + +
68c PHE* 3.5 25.1 - - + +
69c LYS* 3.6 26.9 - - + +
72c ASP* 4.2 3.6 - - - +
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Residues in contact with ASP 10 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W SER* 3.6 15.8 + - - -
50W LYS* 3.8 28.9 + - - +
53W GLU* 2.9 35.0 + - - +
5c TRP* 3.4 8.5 - - - -
6c SER* 3.1 23.9 - - - +
7c GLY 3.0 15.5 + - - +
9c LEU* 1.3 76.1 - - - +
11c ASP* 1.3 55.0 + - - +
13c SER* 3.3 5.7 + - - -
14c ALA* 3.0 26.6 + - - +
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Residues in contact with ASP 11 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37R LYS* 2.8 31.1 + - - -
6c SER* 2.9 23.4 + - - -
7c GLY 2.9 15.2 + - - +
8c TYR* 2.9 17.8 + - + +
10c ASP* 1.3 71.9 - - - +
12c VAL* 1.3 55.0 + - + +
14c ALA* 3.2 8.2 + - - +
15c LYS* 2.7 53.4 + - + +
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Residues in contact with VAL 12 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31X LEU* 5.1 6.3 - - + +
8c TYR* 2.8 48.3 + - + +
9c LEU* 3.4 11.2 - - + +
10c ASP 3.2 0.2 - - - -
11c ASP* 1.3 75.9 - - + +
13c SER* 1.3 62.2 + - - +
15c LYS* 3.2 14.7 + - + +
16c PHE* 3.1 22.7 + - - +
64c THR* 4.1 10.8 - - - +
65c VAL* 3.9 18.2 - - + -
68c PHE* 3.6 34.8 - - + -
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Residues in contact with SER 13 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W SER* 4.2 16.5 + - - -
9c LEU 3.0 13.3 + - - -
10c ASP* 3.3 9.8 + - - -
12c VAL* 1.3 76.5 - - - +
14c ALA* 1.3 58.0 + - - +
16c PHE* 3.4 4.5 + - - +
17c ASP* 3.0 33.5 + - - +
61c GLN* 2.8 29.6 + - - +
65c VAL* 4.1 12.5 - - - +
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Residues in contact with ALA 14 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10c ASP 3.0 14.2 + - - +
11c ASP* 3.2 12.1 + - - +
13c SER* 1.3 74.2 - - - +
15c LYS* 1.3 57.0 + - + +
17c ASP* 3.7 6.5 - - - +
18c THR* 2.6 40.6 + - - +
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Residues in contact with LYS 15 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31X LEU* 5.0 19.5 - - + -
32X ASP* 5.3 12.4 + - - +
35X ALA* 3.4 16.0 - - - +
8c TYR* 5.9 7.0 - - - -
11c ASP* 2.7 41.4 + - - +
12c VAL* 3.2 14.6 + - + +
14c ALA* 1.3 73.8 - - + +
16c PHE* 1.3 62.3 + - - +
18c THR* 3.4 17.5 - - - -
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Residues in contact with PHE 16 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31X LEU* 5.3 10.0 - - + +
34X LEU* 4.9 7.0 - - + -
35X ALA* 3.6 22.0 - - - +
38X PRO* 3.6 35.2 - - + -
12c VAL 3.1 12.3 + - - +
13c SER* 3.7 7.2 - - - +
15c LYS* 1.3 75.3 - - - +
17c ASP* 1.3 73.6 + - - +
18c THR 3.2 0.7 + - - -
19c GLY 3.2 9.9 + - - -
20c VAL* 3.3 26.2 - - + +
56c LEU 3.6 18.8 - - - -
57c TYR* 3.6 22.4 - - - -
60c ALA* 4.0 14.1 - - + -
61c GLN* 3.6 26.2 - - + -
64c THR* 4.8 15.9 - - + +
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Residues in contact with ASP 17 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13c SER* 3.0 22.0 + - - +
14c ALA* 3.8 6.4 + - - +
16c PHE* 1.3 80.6 - - - +
18c THR* 1.3 57.7 + - - +
20c VAL* 2.9 6.9 + - - -
21c ASP* 2.5 42.8 + - - +
57c TYR* 3.8 24.1 + - - +
61c GLN* 3.1 35.0 + - - +
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Residues in contact with THR 18 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14c ALA* 2.6 28.3 + - - +
15c LYS* 3.4 12.7 + - - -
16c PHE 3.1 0.4 - - - -
17c ASP* 1.3 77.7 - - - +
19c GLY* 1.3 61.0 + - - +
20c VAL 3.5 0.2 + - - -
21c ASP* 3.8 12.7 + - - +
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Residues in contact with GLY 19 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X ALA* 3.2 25.3 - - - +
36X ALA* 3.5 23.9 - - - +
15c LYS 4.0 2.2 + - - -
16c PHE 3.2 4.6 + - - -
17c ASP 3.1 0.8 - - - -
18c THR* 1.3 81.1 - - - +
20c VAL* 1.3 57.1 + - - +
21c ASP 3.7 0.4 - - - -
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Residues in contact with VAL 20 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35X ALA 3.3 15.9 - - - +
36X ALA 4.1 2.7 - - - +
38X PRO* 3.5 25.1 - - + -
16c PHE* 3.3 28.7 - - + +
17c ASP* 2.9 6.0 + - - +
19c GLY* 1.3 81.5 - - - +
21c ASP* 1.3 62.4 + - - +
22c ASN 3.1 3.6 - - - +
23c LEU* 3.1 33.6 + - + +
24c GLN 3.7 0.2 + - - -
57c TYR* 3.2 39.3 - - + -
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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