Contacts of the helix formed by residues 9 - 27 (chain H) 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 9 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H ASP* 3.2 15.0 - - - +
8H VAL* 1.3 87.7 - - + +
10H ALA* 1.3 67.7 + - - +
11H ASP* 3.2 6.5 - - + +
12H LEU* 3.0 27.4 + - + +
13H GLU* 3.1 8.5 + - - +
118H LEU* 3.8 22.0 - - + -
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Residues in contact with ALA 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL 3.4 3.0 + - - -
9H PRO* 1.3 70.6 - - - +
11H ASP* 1.3 63.6 + - - +
13H GLU* 3.2 13.4 + - - +
14H ASP* 2.8 33.5 + - - +
78H GLU* 6.4 0.2 - - - -
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Residues in contact with ASP 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H PRO* 3.2 5.5 - - + +
10H ALA* 1.3 77.3 + - - +
12H LEU* 1.3 66.0 + - - +
14H ASP* 3.2 21.5 + - - +
15H ASP* 3.2 20.9 + - - +
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Residues in contact with LEU 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 3.8 8.7 - - + -
9H PRO* 3.0 21.1 + - + +
11H ASP* 1.3 78.6 - - - +
13H GLU* 1.3 63.1 + - - +
15H ASP* 3.2 11.1 + - + +
16H ALA* 3.0 17.0 + - - +
75H ILE* 3.8 9.4 - - + -
111H ILE* 3.7 29.4 - - + -
114H LYS* 4.3 30.5 - - + -
115H VAL* 4.3 12.1 - - + -
118H LEU* 4.0 28.7 - - + -
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Residues in contact with GLU 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H VAL* 3.9 14.9 - - + +
9H PRO 3.1 6.9 + - - +
10H ALA* 3.3 14.1 - - - +
12H LEU* 1.3 79.7 - - - +
14H ASP* 1.3 57.7 + - - +
16H ALA* 3.2 8.9 - - - +
17H LEU* 2.9 43.7 + - + +
75H ILE* 4.8 1.3 - - - -
76H PHE 4.4 1.4 - - - +
77H VAL* 3.2 22.0 - - + +
78H GLU* 3.0 57.1 + - - +
79H GLN* 4.2 2.3 + - - +
82H ASP* 5.1 3.8 - - - +
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Residues in contact with ASP 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ALA* 2.8 26.3 + - - +
11H ASP* 3.4 14.9 - - - +
12H LEU 3.2 0.4 - - - -
13H GLU* 1.3 77.9 - - - +
15H ASP* 1.3 53.6 + - - +
17H LEU* 3.2 11.1 + - - +
18H GLU* 2.8 51.7 + - + +
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Residues in contact with ASP 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H ASP* 3.2 16.3 + - - +
12H LEU* 3.2 11.6 + - + +
14H ASP* 1.3 77.8 - - - +
16H ALA* 1.3 57.3 + - - +
18H GLU* 3.6 18.3 + - - +
19H ALA* 3.0 30.0 + - - +
107H VAL* 4.8 10.8 - - + +
111H ILE* 3.6 15.5 - - + +
114H LYS* 3.9 19.8 + - - +
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Residues in contact with ALA 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H LEU 3.0 7.9 + - - +
13H GLU* 3.2 11.0 - - + +
15H ASP* 1.3 75.0 - - - +
17H LEU* 1.3 67.2 + - + +
19H ALA* 3.1 6.8 + - - +
20H LEU 2.9 17.5 + - - -
49H PHE* 3.6 25.5 - - + -
75H ILE* 3.5 32.5 - - + -
77H VAL* 5.8 1.3 - - + -
111H ILE* 3.7 15.4 - - + +
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Residues in contact with LEU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H GLU* 2.9 39.5 + - + +
14H ASP* 3.8 9.4 - - - +
16H ALA* 1.3 72.4 - - + +
18H GLU* 1.3 66.0 + - + +
20H LEU* 2.9 22.6 + - + +
21H GLU* 3.0 20.6 + - + +
49H PHE* 4.5 2.0 - - + -
77H VAL* 4.3 17.0 - - + -
82H ASP* 4.3 20.9 - - + +
83H LEU* 4.2 17.0 - - + -
86H ALA* 3.6 25.5 - - + +
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ASP* 2.8 38.1 + - - +
15H ASP* 3.7 17.6 - - - +
17H LEU* 1.3 71.5 - - + +
19H ALA* 1.3 62.5 + - - +
21H GLU* 3.1 26.9 + - - +
22H VAL* 3.3 18.7 + - + +
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Residues in contact with ALA 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ASP 3.0 15.6 + - - +
16H ALA 3.1 9.4 + - - +
18H GLU* 1.3 76.3 - - - +
20H LEU* 1.3 57.7 + - - +
22H VAL* 2.7 30.2 - - - +
23H ALA* 3.0 13.3 + - - +
49H PHE* 5.5 2.5 - - + -
98H VAL* 5.8 0.7 - - - -
104H ALA* 4.2 12.2 - - + +
107H VAL* 4.9 7.6 - - + -
108H LEU* 5.0 9.6 - - + +
111H ILE* 3.8 17.0 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ALA 2.9 11.5 + - - +
17H LEU* 2.9 12.0 + - + +
19H ALA* 1.3 76.5 - - - +
21H GLU* 1.3 57.0 + - - +
23H ALA* 3.0 24.5 + - - +
24H ARG* 3.0 9.9 + - - +
29H VAL* 4.0 15.9 - - + -
49H PHE* 4.1 17.4 - - + -
83H LEU* 3.5 31.9 - - + -
86H ALA* 3.8 24.9 - - + +
87H ALA* 4.1 11.9 - - + +
96H ALA* 4.6 7.0 - - + -
98H VAL* 3.4 30.1 - - + +
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Residues in contact with GLU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 3.2 14.8 - - - +
18H GLU* 3.1 19.3 + - - +
20H LEU* 1.3 77.7 - - - +
22H VAL* 1.3 56.6 + - + +
24H ARG* 2.7 45.2 + - - +
25H ASP* 2.6 26.9 - - - +
85H HIS* 4.5 11.8 + - - -
86H ALA* 3.7 25.3 - - - +
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Residues in contact with VAL 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H GLU* 3.3 10.3 + - + +
19H ALA* 2.7 31.0 - - - +
21H GLU* 1.3 77.1 - - + +
23H ALA* 1.3 53.2 + - - +
25H ASP* 4.2 6.3 - - - -
26H THR* 2.7 44.9 + - - +
102H GLY 3.9 3.8 - - - +
103H ALA* 4.5 5.6 - - + +
104H ALA* 3.3 27.8 - - + -
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Residues in contact with ALA 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ALA 3.0 14.5 + - - +
20H LEU* 3.0 17.7 + - - +
22H VAL* 1.3 76.8 - - - +
24H ARG* 1.3 59.0 + - - +
27H GLY 2.7 39.4 + - - +
28H ALA 4.9 0.2 - - - +
29H VAL* 3.5 17.5 - - + -
98H VAL* 3.8 22.0 - - + -
101H ALA* 4.8 4.3 - - + -
102H GLY 4.4 7.9 - - - +
104H ALA* 5.7 0.4 - - + -
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Residues in contact with ARG 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H LEU 3.0 8.7 + - - +
21H GLU* 2.7 58.1 + - - +
23H ALA* 1.3 76.7 - - - +
25H ASP* 1.3 75.0 + - - +
27H GLY 3.6 8.3 - - - +
29H VAL* 3.7 28.2 - - + +
31H LYS* 6.1 0.4 - - - -
85H HIS* 4.2 9.3 + - - -
86H ALA 3.1 20.0 + - - +
87H ALA 3.9 12.8 - - - +
88H GLY* 3.6 18.1 - - - -
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Residues in contact with ASP 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H GLU* 2.6 23.6 - - - +
22H VAL* 3.4 6.3 + - - +
23H ALA 3.2 0.4 - - - -
24H ARG* 1.3 99.2 + - - +
26H THR* 1.3 63.3 + - - +
27H GLY 4.6 0.9 - - - +
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Residues in contact with THR 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H VAL* 2.7 20.5 + - - +
25H ASP* 1.3 75.6 - - - +
27H GLY* 1.3 57.9 + - - +
102H GLY* 3.1 37.0 + - - -
103H ALA* 3.2 18.6 - - + +
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Residues in contact with GLY 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H ALA 2.7 21.1 + - - +
24H ARG 3.6 10.9 - - - +
25H ASP 4.6 0.7 - - - +
26H THR* 1.3 78.5 - - - +
28H ALA* 1.3 60.6 + - - +
100H ASP 3.4 0.7 - - - -
101H ALA 3.2 22.9 - - - -
102H GLY* 3.4 2.0 - - - -
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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