Contacts of the helix formed by residues 17 - 32 (chain N) 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 GLU 17 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14N ARG* 2.9 48.8 + - + +
16N LYS* 1.3 94.7 - - + +
18N GLY* 1.3 73.1 + - - +
20N ILE* 3.3 10.7 - - - +
21N ALA* 3.2 11.2 + - - +
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Residues in contact with GLY 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N GLU* 1.3 82.8 - - - +
19N GLN* 1.3 59.0 + - - -
21N ALA* 2.8 22.4 + - - +
22N GLU* 3.5 4.0 + - - +
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Residues in contact with GLN 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 3.2 35.4 + - + +
3H TYR* 3.4 16.3 - - - +
61H MET* 3.2 48.9 + - + +
64H PRO* 6.1 1.6 - - - +
18N GLY* 1.3 68.4 - - - -
20N ILE* 1.3 65.5 + - - +
22N GLU* 3.0 20.1 + - - +
23N LEU* 3.0 16.0 + - - +
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Residues in contact with ILE 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H GLU* 4.0 12.1 - - - +
61H MET* 4.3 12.1 - - + +
11N ALA* 3.7 23.6 - - + +
12N TRP* 3.1 57.2 - - + +
14N ARG 4.0 1.1 - - - +
15N PRO* 3.7 20.6 - - + -
17N GLU 3.3 13.2 - - - +
19N GLN* 1.3 78.5 - - - +
21N ALA* 1.3 59.7 + - - +
23N LEU* 4.1 12.1 - - + -
24N MET* 2.9 37.7 + - + +
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Residues in contact with ALA 21 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N PRO 3.5 11.2 - - - -
16N LYS* 3.6 17.5 - - - +
17N GLU 3.2 16.2 - - - +
18N GLY 2.8 17.4 + - - +
20N ILE* 1.3 82.2 - - - +
22N GLU* 1.3 60.2 + - - +
24N MET* 3.6 3.4 + - - +
25N TRP* 3.2 21.0 + - - +
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Residues in contact with GLU 22 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 4.2 20.6 - - + +
18N GLY 3.5 3.0 + - - +
19N GLN* 3.0 12.8 + - - +
21N ALA* 1.3 80.3 - - - +
23N LEU* 1.3 64.2 + - - +
25N TRP* 3.5 7.9 + - + +
26N HIS* 3.1 45.6 + - + +
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Residues in contact with LEU 23 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 3.5 29.2 - - + -
57H GLU* 3.6 28.7 - - + +
58H GLU* 3.9 25.6 - - - +
61H MET* 3.6 26.7 - - - -
19N GLN 3.0 16.0 + - - +
20N ILE* 3.1 9.6 + - - +
22N GLU* 1.3 74.5 - - - +
24N MET* 1.3 57.8 + - - +
26N HIS* 2.8 10.8 + - + +
27N ARG* 2.7 58.7 + - + +
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Residues in contact with MET 24 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N TRP* 3.9 14.8 - - + -
15N PRO* 4.3 13.0 - - + +
20N ILE* 2.9 29.7 + - + +
21N ALA* 3.7 5.8 - - - +
23N LEU* 1.3 76.9 - - - +
25N TRP* 1.3 63.4 - - - +
26N HIS 3.0 0.5 + - - -
27N ARG* 3.8 27.4 - - - -
28N MET* 2.9 66.8 + - + +
31N TRP* 4.1 7.9 - - + -
120N VAL 3.2 26.9 - - - +
121N GLY* 3.8 7.6 - - - -
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Residues in contact with TRP 25 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2133A U 4.2 26.8 + - - +
2134A G 5.8 1.8 + - - -
2243A C 3.7 43.0 + + - -
2244A A 3.3 46.9 + - - +
2258A A 5.6 1.0 + - - -
21N ALA 3.2 11.9 + - - +
22N GLU* 3.6 12.8 - - + +
24N MET* 1.3 78.1 - - - +
26N HIS* 1.3 89.4 + + - +
28N MET* 4.6 5.5 - - - +
29N GLN* 3.0 46.3 + - - +
32N ARG* 4.9 2.7 + - - +
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Residues in contact with HIS 26 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1H PRO* 6.3 1.3 - - + -
2H VAL* 4.0 26.9 - - + +
57H GLU* 5.5 1.6 + - - -
22N GLU* 3.1 38.2 + - + +
23N LEU* 2.8 13.1 + - + +
25N TRP* 1.3 100.2 - + - +
27N ARG* 1.3 67.4 + - + +
29N GLN* 3.1 27.3 + - - +
30N GLU* 3.9 11.2 + - - +
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Residues in contact with ARG 27 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H GLN* 5.0 5.7 - - - +
56H PRO* 3.5 14.3 - - - +
57H GLU 4.2 2.0 - - - +
58H GLU* 2.4 46.0 + - - -
12N TRP* 4.0 0.6 - - - -
20N ILE* 5.0 0.4 - - - +
23N LEU* 2.7 42.5 + - + +
24N MET* 3.8 24.9 - - - +
26N HIS* 1.3 71.7 - - + +
28N MET* 1.3 56.7 - - - +
30N GLU* 2.5 38.7 + - - +
31N TRP* 2.8 40.3 + - + +
44N THR* 3.3 24.9 + - - +
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Residues in contact with MET 28 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132A C 5.9 0.7 - - - +
2133A U 5.5 4.7 - - - -
24N MET* 2.9 59.2 + - + +
25N TRP* 4.6 3.1 - - - +
27N ARG* 1.3 75.3 - - - +
29N GLN* 1.3 53.7 + - - +
31N TRP* 3.4 17.4 - - + +
32N ARG* 2.7 71.8 + - - +
121N GLY* 4.1 0.4 - - - -
122N GLU* 3.2 40.2 - - - +
123N ASP* 4.1 2.7 - - - -
128N TRP* 4.0 15.0 - - + -
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Residues in contact with GLN 29 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2244A A 3.4 44.4 + - - +
2245A C 3.7 10.7 + - - +
25N TRP* 3.0 51.0 + - - +
26N HIS* 3.1 13.6 + - - +
27N ARG 2.8 2.4 + - - -
28N MET* 1.3 77.7 - - - +
30N GLU* 1.3 63.1 + - + +
32N ARG* 3.7 13.5 + - - +
33N ASN* 3.2 22.5 + - - -
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Residues in contact with GLU 30 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N HIS* 4.3 11.9 - - - +
27N ARG* 2.5 19.5 + - - +
29N GLN* 1.3 73.2 - - + +
31N TRP* 1.3 67.3 + - + +
33N ASN* 3.0 17.9 + - - +
34N GLU* 2.9 27.1 + - + +
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Residues in contact with TRP 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N MET* 4.1 19.1 - - + -
27N ARG* 2.8 39.7 + - + +
28N MET* 3.4 19.5 - - + +
30N GLU* 1.3 79.9 - - + +
32N ARG* 1.3 57.6 + - - +
34N GLU* 2.8 39.9 + - - +
35N PRO 5.0 0.9 - - - +
44N THR* 4.4 9.0 - - + -
64N ARG* 3.0 52.6 - - - +
120N VAL* 3.2 40.4 - - + -
128N TRP* 3.6 51.1 + + + +
130N GLU* 4.6 0.2 - - - -
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Residues in contact with ARG 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2132A C 5.0 2.0 + - - -
2133A U 4.9 7.5 + - - -
2244A A 3.1 22.1 + - - -
2245A C 2.8 39.1 + - - +
25N TRP* 4.9 2.8 + - - +
28N MET* 2.7 55.4 + - - +
29N GLN* 3.8 17.4 - - - +
30N GLU 3.3 0.4 - - - -
31N TRP* 1.3 71.1 - - - +
33N ASN* 1.3 61.8 + - - +
34N GLU 3.3 4.4 + - - +
123N ASP* 3.1 26.9 + - - +
126N HIS* 3.9 30.3 + - + -
128N TRP* 3.9 7.4 - - + -
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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