Contacts of the helix formed by residues 18 - 27 (chain A) in PDB entry 2L33
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 ASN 18 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MET 4.8 5.2 - - - +
12A LEU* 3.6 20.8 - - + +
13A THR* 3.8 6.1 - - - +
17A LYS* 1.3 90.3 - - - +
19A PRO* 1.4 88.8 - - - +
20A VAL* 2.9 18.7 + - - +
21A MET* 3.0 31.2 + - + +
22A GLU 2.8 13.3 + - - -
69A ALA* 4.7 4.3 - - - +
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Residues in contact with PRO 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 4.7 1.1 - - + +
12A LEU* 3.1 33.4 - - - +
13A THR* 3.5 10.2 - - + -
18A ASN* 1.4 92.6 - - - +
20A VAL* 1.3 54.5 + - - +
22A GLU* 3.8 1.3 - - + +
23A LEU* 2.9 32.9 + - - +
69A ALA* 3.5 41.1 - - + +
72A ALA* 3.6 7.3 - - + +
73A LEU* 3.7 20.4 - - + -
76A LEU* 3.9 6.5 - - + +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 2.9 18.4 + - - +
19A PRO* 1.3 78.2 - - - +
21A MET* 1.3 63.5 + - + +
24A ASN* 2.8 35.7 + - - +
32A TYR* 3.4 25.7 + - + -
65A LYS 4.5 4.5 - - - +
68A LYS* 3.9 33.0 - - + +
69A ALA* 3.8 28.3 - - - +
72A ALA* 4.2 2.0 - - - -
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 3.4 21.5 - - + +
18A ASN* 3.0 25.5 + - + +
20A VAL* 1.3 84.1 - - + +
22A GLU* 1.3 61.5 + - - +
24A ASN* 3.3 9.6 + - - +
25A GLU* 3.2 29.0 + - + +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR* 2.9 28.7 + - - +
14A LYS* 4.3 4.2 + - - +
15A HIS* 2.8 50.2 + - - +
17A LYS* 3.6 19.4 + - + +
18A ASN 2.8 17.3 + - - +
19A PRO 3.8 3.1 - - - +
21A MET* 1.3 73.6 - - - +
23A LEU* 1.3 60.2 + - - +
25A GLU* 2.8 25.0 + - - +
26A LYS* 2.9 31.7 + - + +
76A LEU* 3.3 17.7 - - + +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO 2.9 22.8 + - - +
20A VAL 3.7 3.6 - - - +
22A GLU* 1.3 72.5 - - - +
24A ASN* 1.3 56.2 + - - +
26A LYS* 4.3 1.3 - - - -
27A ARG* 2.8 29.7 + - + +
30A LEU* 3.5 10.1 - - + +
32A TYR* 3.5 16.6 - - - +
50A VAL* 3.7 10.5 - - + -
52A VAL* 3.5 42.6 - - + -
72A ALA* 3.8 21.3 - - + +
75A ALA* 4.4 5.4 - - + -
76A LEU* 3.6 28.5 - - + +
80A PHE* 4.4 10.5 - - + -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 2.8 30.6 + - - +
21A MET* 3.6 12.8 - - - +
22A GLU 3.2 0.2 - - - -
23A LEU* 1.3 73.3 - - - +
25A GLU* 1.3 57.4 + - - +
27A ARG 3.0 18.7 - - - +
28A ARG* 3.4 34.6 + - - +
30A LEU* 3.8 13.2 + - - +
32A TYR* 2.8 33.8 + - - -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LYS* 2.7 43.3 + - - +
21A MET* 3.2 16.1 + - - +
22A GLU* 2.8 8.3 + - - +
24A ASN* 1.3 79.3 - - - +
26A LYS* 1.3 68.3 + - + +
27A ARG* 3.3 3.0 + - - -
28A ARG* 5.5 2.9 - - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A HIS* 5.3 14.4 - - + +
22A GLU* 2.9 37.3 + - + +
23A LEU* 3.9 6.7 - - - +
25A GLU* 1.3 81.2 - - + +
27A ARG* 1.3 79.0 + - - +
76A LEU* 4.4 9.0 - - + -
80A PHE* 3.9 41.7 - - + -
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 2.8 13.9 + - + +
24A ASN* 3.0 23.1 - - - +
25A GLU 4.7 0.7 - - - -
26A LYS* 1.3 89.0 + - - +
28A ARG* 1.3 65.8 + - - +
30A LEU* 3.7 23.4 - - + +
52A VAL* 3.7 20.2 - - + -
53A ASP* 2.9 35.1 + - - +
79A LEU* 5.9 1.6 - - - +
80A PHE* 3.5 33.1 - - + -
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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