Contacts of the helix formed by residues 18 - 29 (chain I) in PDB entry 1CEW
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 ASP 18 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 3.5 24.1 - - + +
15I ASP* 3.0 19.7 + - + +
16I GLU 3.1 0.2 - - - -
17I ASN* 1.3 80.2 - - - +
19I GLU* 1.3 63.3 + - - +
20I GLY* 2.8 23.2 + - - -
21I LEU* 3.1 12.2 + - + +
22I GLN* 2.9 29.6 + - - +
52I ARG* 3.7 17.7 + - - -
60I TYR* 4.6 1.0 + - - -
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ASN 3.9 1.3 + - - +
18I ASP* 1.3 79.0 + - - +
20I GLY* 1.3 67.9 + - - +
22I GLN* 3.9 13.3 - - + +
23I ARG* 3.4 19.6 + - - +
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Residues in contact with GLY 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ASP* 2.8 9.8 + - - -
19I GLU* 1.3 83.7 - - - +
21I LEU* 1.3 59.8 + - - +
23I ARG* 3.2 13.5 + - - +
24I ALA* 3.0 27.4 + - - +
60I TYR* 3.5 22.6 - - - -
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 4.2 12.6 - - + -
15I ASP 3.9 3.8 - - - +
16I GLU* 3.2 49.1 - - - +
18I ASP* 3.1 21.3 + - + +
20I GLY* 1.3 72.2 - - - +
22I GLN* 1.3 54.4 + - - +
24I ALA* 2.7 26.0 + - - +
25I LEU* 2.8 19.7 + - + +
47I VAL* 5.2 0.7 - - + -
50I ALA* 3.5 25.6 - - + -
60I TYR* 3.8 19.4 - - + -
62I LEU* 3.3 32.5 - - + -
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLU* 3.9 22.0 - - - +
17I ASN* 3.2 16.0 - - - +
18I ASP 2.9 24.7 + - - +
19I GLU* 4.0 10.3 - - - +
20I GLY 3.2 0.4 - - - -
21I LEU* 1.3 80.4 - - + +
23I ARG* 1.3 54.9 + - - +
25I LEU* 4.0 7.5 - - - +
26I GLN* 3.3 33.5 + - - +
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Residues in contact with ARG 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I GLU 3.4 13.3 + - - +
20I GLY* 3.2 15.4 + - - +
21I LEU 3.1 0.6 - - - -
22I GLN* 1.3 73.9 - - - +
24I ALA* 1.3 66.8 + - - +
25I LEU 3.2 2.0 - - - -
26I GLN* 3.7 9.4 + - - +
27I PHE* 3.2 21.3 + - - +
60I TYR* 6.0 2.0 - - - -
101I SER* 3.1 24.7 + - - -
106I ASN 4.8 12.1 + - - -
107I GLN 5.1 1.0 + - - -
108I ILE* 3.9 36.2 - - + +
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I GLY 3.0 12.8 + - - +
21I LEU* 3.1 10.5 - - - +
23I ARG* 1.3 82.2 - - - +
25I LEU* 1.3 59.4 - - - +
27I PHE* 3.3 3.1 + - - +
28I ALA* 3.1 21.0 + - - +
60I TYR* 4.0 30.1 - - + -
62I LEU* 4.3 11.2 - - + -
99I VAL* 3.7 16.9 - - + +
108I ILE* 4.2 12.8 - - + -
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I GLU* 4.4 8.3 - - - +
21I LEU* 2.8 16.0 + - + +
22I GLN* 4.2 7.6 - - - +
24I ALA* 1.3 77.4 - - - +
26I GLN* 1.3 65.4 + - - +
27I PHE 2.9 2.2 + - - -
28I ALA* 3.7 7.7 + - + +
29I MET* 3.4 21.9 + - + +
44I VAL* 4.1 21.3 - - + -
47I VAL* 3.7 25.1 - - + -
62I LEU* 3.7 25.1 - - + -
64I VAL* 3.6 27.6 - - + -
97I PHE* 5.1 2.0 - - + -
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Residues in contact with GLN 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN* 3.3 20.7 + - - +
23I ARG* 3.9 8.1 - - - +
24I ALA 3.2 0.2 - - - -
25I LEU* 1.3 82.4 - - - +
27I PHE* 1.3 63.1 + - - +
29I MET* 3.9 7.2 - - - +
30I ALA* 3.9 16.6 + - - +
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Residues in contact with PHE 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I ARG* 3.2 17.2 + - + +
24I ALA 3.5 3.8 - - - +
25I LEU 2.9 0.4 - - - -
26I GLN* 1.3 81.0 - - - +
28I ALA* 1.3 68.6 + - - +
29I MET 3.1 0.5 + - - -
30I ALA* 3.3 4.4 + - + +
31I GLU* 3.3 47.6 + - - +
34I ARG* 5.9 1.3 - - - -
99I VAL* 3.5 14.8 - - + -
108I ILE* 3.5 52.9 - - + -
109I LYS* 4.4 0.9 - - - -
110I LEU* 3.6 31.0 - - + -
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Residues in contact with ALA 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I ALA 3.1 12.8 + - - +
25I LEU* 3.8 10.1 - - + +
27I PHE* 1.3 81.3 - - - +
29I MET* 1.3 58.5 + - - +
31I GLU* 3.6 4.7 - - - +
32I TYR* 2.9 25.6 + - - +
62I LEU* 4.6 1.1 - - + -
97I PHE* 3.5 45.6 - - + -
99I VAL* 4.6 1.1 - - + -
110I LEU* 4.1 17.8 - - + +
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Residues in contact with MET 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU* 3.4 15.7 + - + +
26I GLN* 3.9 4.9 - - - -
27I PHE 3.1 0.8 - - - -
28I ALA* 1.3 81.4 - - + +
30I ALA* 1.3 59.9 - - - +
31I GLU 3.2 0.2 - - - -
32I TYR* 3.2 19.9 - - + +
33I ASN* 2.8 41.4 + - - +
42I SER 5.0 0.2 - - - +
43I ARG* 4.3 5.8 - - - -
44I VAL* 3.6 35.7 - - + +
64I VAL* 4.8 0.9 - - + -
66I ILE* 3.5 32.3 - - + -
97I PHE* 3.2 36.1 - - + -
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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