Contacts of the helix formed by residues 13 - 29 (chain I) in PDB entry 1KD1
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 PRO 13 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1148A C 3.4 28.9 - - - +
1149A U 5.0 3.6 - - - +
1150A A 4.7 8.0 - - + +
12I ILE* 1.3 92.9 - - - +
14I GLU* 1.3 63.6 + - - +
15I TRP* 3.8 24.5 - - + +
16I LYS* 3.5 30.0 + - + +
17I GLN* 3.5 16.8 + - - +
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Residues in contact with GLU 14 (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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12I ILE* 3.1 7.4 + - + +
13I PRO* 1.3 68.5 - - - +
15I TRP* 1.3 63.0 + - - +
16I LYS 3.0 2.0 - - - -
17I GLN* 2.8 33.2 + - + +
18I GLU* 2.9 27.2 + - + +
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Residues in contact with TRP 15 (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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1210A G 4.6 5.8 - - - -
13I PRO* 3.8 19.0 - - + +
14I GLU* 1.3 78.7 - - - +
16I LYS* 1.3 85.4 + - + +
18I GLU* 3.6 12.9 + - - +
19I GLU* 3.1 31.6 + - + +
63I ARG* 3.3 41.7 - - - -
66I LEU* 4.4 14.4 - - + -
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Residues in contact with LYS 16 (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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1148A C 4.8 5.6 + - - -
1149A U 3.9 4.6 + - - -
1150A A 2.7 47.7 + - + +
1151A G 2.3 40.7 + - - -
13I PRO* 3.5 27.0 + - + +
14I GLU 3.0 0.4 - - - -
15I TRP* 1.3 112.4 - - + +
17I GLN* 1.3 62.9 + - - +
19I GLU* 3.5 4.5 + - - +
20I VAL* 3.0 30.7 + - - +
63I ARG* 3.6 13.4 - - - +
66I LEU* 4.4 9.3 - - + +
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Residues in contact with GLN 17 (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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1150A A 3.7 27.8 - - + +
12I ILE* 2.9 48.8 + - - +
13I PRO 3.5 7.1 + - - +
14I GLU* 2.8 21.6 + - - +
16I LYS* 1.3 73.6 - - - +
18I GLU* 1.3 62.5 + - + +
20I VAL* 3.4 5.5 + - - +
21I ASP* 2.9 27.5 + - - +
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Residues in contact with GLU 18 (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 GLU* 2.9 32.1 + - + +
15I TRP* 3.8 9.2 - - - +
17I GLN* 1.3 76.3 - - + +
19I GLU* 1.3 66.0 + - - +
21I ASP* 3.0 12.6 + - - +
22I ALA* 2.9 23.0 + - - +
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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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1188A A 4.3 23.1 + - - +
15I TRP* 3.1 24.4 + - + +
16I LYS 3.8 1.3 - - - +
17I GLN 3.3 0.2 - - - -
18I GLU* 1.3 77.9 - - - +
20I VAL* 1.3 57.2 + - - +
21I ASP 2.8 0.5 + - - -
22I ALA* 3.1 14.8 + - - +
23I ILE* 2.8 52.2 + - + +
26I MET* 5.9 1.6 - - - +
63I ARG 5.2 5.0 + - - -
66I LEU* 3.4 31.7 - - + +
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Residues in contact with VAL 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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1150A A 3.5 22.9 - - + +
16I LYS 3.0 18.7 + - - +
17I GLN* 3.7 8.3 - - - +
18I GLU 3.2 0.4 - - - -
19I GLU* 1.3 74.6 - - - +
21I ASP* 1.3 57.7 + - - +
23I ILE* 4.0 8.5 - - - +
24I VAL* 3.0 34.8 + - + +
66I LEU* 4.1 13.9 - - + +
69I ARG* 3.5 34.5 - - + +
70I ALA 4.1 3.6 - - - +
73I ASP* 3.8 16.8 - - - +
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Residues in contact with ASP 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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17I GLN* 2.9 20.1 + - - +
18I GLU* 3.0 12.1 + - - +
19I GLU 2.8 1.0 + - - -
20I VAL* 1.3 75.7 - - - +
22I ALA* 1.3 54.8 + - - +
23I ILE 3.0 1.1 - - - -
24I VAL* 2.8 9.4 + - - +
25I GLU* 2.7 41.1 + - - +
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Residues in contact with ALA 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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18I GLU 2.9 13.9 + - - +
19I GLU* 3.7 16.4 - - - +
21I ASP* 1.3 75.3 - - - +
23I ILE* 1.3 62.2 + - - +
25I GLU* 3.2 13.9 + - - +
26I MET* 3.1 39.7 + - + +
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Residues in contact with ILE 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* 2.8 44.2 + - + +
20I VAL* 4.0 1.3 - - - +
22I ALA* 1.3 69.9 - - + +
24I VAL* 1.3 66.0 + - - +
26I MET* 3.3 11.9 + - + +
27I ILE* 2.9 37.5 + - + +
63I ARG 5.6 0.9 - - - +
66I LEU* 3.4 33.4 - - + +
67I LEU* 3.4 36.6 - - + -
70I ALA* 3.2 23.6 - - + -
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Residues in contact with VAL 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 VAL* 3.0 21.9 + - + +
21I ASP* 2.8 11.5 + - - +
23I ILE* 1.3 74.5 - - - +
25I GLU* 1.3 57.6 + - - +
27I ILE* 3.1 11.0 + - + +
28I GLU* 2.8 46.5 + - + +
70I ALA* 3.3 31.2 - - + +
73I ASP* 3.6 24.2 - - + +
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Residues in contact with GLU 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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21I ASP* 2.7 21.1 + - - +
22I ALA* 3.3 16.4 - - - +
23I ILE 3.1 0.2 - - - -
24I VAL* 1.3 73.0 - - - +
26I MET* 1.3 60.0 + - + +
28I GLU* 2.8 28.8 + - + +
29I SER* 3.0 15.7 + - - -
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Residues in contact with MET 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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1188A A 4.8 18.6 - - - +
19I GLU* 5.9 1.6 - - - +
22I ALA* 3.1 28.3 + - + +
23I ILE* 4.0 9.2 - - + +
25I GLU* 1.3 81.5 - - + +
27I ILE* 1.3 61.1 + - + +
28I GLU 3.4 0.2 + - - -
29I SER* 3.6 24.1 + - - +
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Residues in contact with ILE 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 ILE* 2.9 29.5 + - + +
24I VAL* 3.4 7.9 - - + +
25I GLU 3.0 0.2 - - - -
26I MET* 1.3 79.2 - - + +
28I GLU* 1.3 62.6 + - + +
29I SER 3.8 2.4 + - - +
67I LEU* 4.7 0.9 - - + +
70I ALA* 3.4 36.1 - - + +
71I LEU* 3.7 32.8 - - + +
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Residues in contact with GLU 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 VAL* 2.8 29.9 + - + +
25I GLU* 2.8 18.4 + - + +
27I ILE* 1.3 80.3 - - + +
29I SER* 1.3 57.9 + - - +
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Residues in contact with SER 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 GLU 3.0 13.3 + - - -
26I MET* 3.8 20.7 - - - +
27I ILE 3.5 2.2 - - - +
28I GLU* 1.3 80.6 - - - +
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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