Contacts of the helix formed by residues 18 - 29 (chain A) in PDB entry 1EIK
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
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Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.3 2.8 + - - +
17A LEU* 1.3 75.1 - - - +
19A GLU* 1.3 57.9 + - - +
20A SER* 2.7 18.6 + - - +
21A GLU* 2.6 33.7 + - - +
22A ALA* 2.6 33.9 + - - +
55A ASP* 4.8 3.7 + - - -
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Residues in contact with GLU 19 (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 LEU 3.8 2.0 + - - -
18A ASN* 1.3 71.7 - - - +
20A SER* 1.3 55.4 + - - +
22A ALA* 4.0 0.5 - - - +
23A LYS* 2.7 74.0 + - + +
54A GLY* 4.2 16.7 + - - +
56A ILE* 3.9 19.3 - - + +
74A LEU* 6.4 2.2 - - + -
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Residues in contact with SER 20 (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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18A ASN* 2.7 14.9 + - - +
19A GLU* 1.3 74.9 + - - +
21A GLU* 1.3 66.8 + - - +
23A LYS* 3.1 21.5 + - - +
24A ARG* 3.2 11.4 + - - +
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Residues in contact with GLU 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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16A ILE 5.6 0.3 - - - +
17A LEU* 3.6 21.5 - - + +
18A ASN* 2.6 42.4 + - + +
20A SER* 1.3 78.2 + - - +
22A ALA* 1.3 52.4 + - - +
24A ARG* 3.0 47.2 + - - +
25A VAL* 2.7 31.4 - - + +
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Residues in contact with ALA 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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17A LEU* 3.4 18.8 - - + +
18A ASN 2.6 16.4 + - - +
21A GLU* 1.3 71.3 - - - +
23A LYS* 1.3 57.3 + - - +
25A VAL* 3.9 0.2 - - - +
26A LEU* 2.9 35.9 + - - +
56A ILE* 3.2 52.3 - - + -
72A TYR* 4.1 5.0 - - + -
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Residues in contact with LYS 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 GLU* 2.7 61.2 + - + +
20A SER* 3.1 10.9 + - - +
22A ALA* 1.3 78.7 - - - +
24A ARG* 1.3 63.0 + - - +
26A LEU* 3.8 5.0 - - - +
27A LYS* 3.1 28.9 + - - +
32A HIS* 4.2 20.5 - - + +
33A PRO* 5.2 12.6 - - + -
56A ILE* 5.0 1.1 - - + +
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Residues in contact with ARG 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 SER 3.2 5.1 + - - +
21A GLU* 3.0 51.5 + - - +
23A LYS* 1.3 79.1 - - - +
25A VAL* 1.3 69.3 + - + +
27A LYS* 3.4 4.1 + - - +
28A GLU* 2.5 53.2 + - + +
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Residues in contact with VAL 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 LEU* 3.8 8.7 - - + -
21A GLU* 2.7 30.0 + - + +
22A ALA 3.9 0.2 - - - +
24A ARG* 1.3 86.1 - - + +
26A LEU* 1.3 51.1 + - - +
28A GLU* 3.0 7.4 + - + +
29A LEU* 2.6 60.1 + - + +
58A LYS* 5.1 1.3 - - - -
70A VAL* 5.6 0.2 - - + -
72A TYR* 2.8 43.3 - - + +
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Residues in contact with LEU 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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22A ALA 2.9 20.2 + - - +
23A LYS 3.8 4.0 - - - +
25A VAL* 1.3 75.9 - - - +
27A LYS* 1.3 57.8 + - - +
29A LEU* 3.1 17.4 + - - +
30A ASP 3.2 1.0 + - - -
31A ALA* 2.6 33.4 + - + +
32A HIS* 2.9 37.5 - - - +
33A PRO* 3.3 37.5 - - + -
36A LEU* 3.1 33.9 - - + -
56A ILE* 4.6 9.0 - - + -
72A TYR* 4.2 15.8 - - + -
74A LEU* 5.9 0.7 - - + +
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Residues in contact with LYS 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 LYS 3.1 11.4 + - - +
24A ARG* 3.9 3.6 - - - +
26A LEU* 1.3 73.2 - - - +
28A GLU* 1.3 61.5 + - - +
29A LEU 3.1 0.4 - - - -
30A ASP* 2.8 22.2 + - - +
31A ALA* 2.7 41.5 + - - +
32A HIS* 2.9 61.0 - - + +
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Residues in contact with GLU 28 (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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24A ARG* 2.5 43.4 + - + +
25A VAL* 3.2 10.2 - - - +
27A LYS* 1.3 73.3 - - - +
29A LEU* 1.3 64.0 + - + +
30A ASP* 3.3 1.6 + - - +
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Residues in contact with LEU 29 (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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25A VAL* 2.6 50.1 + - + +
26A LEU* 3.2 14.1 - - + +
27A LYS 3.1 0.2 - - - -
28A GLU* 1.3 78.7 - - + +
30A ASP* 1.3 68.5 + - - +
31A ALA* 5.0 2.8 - - + +
36A LEU* 5.8 3.4 - - + -
70A VAL* 4.0 40.2 - - + +
71A THR* 5.3 1.3 - - - -
72A TYR* 4.7 8.7 - - + +
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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