Contacts of the helix formed by residues 7 - 24 (chain B) in PDB entry 2K8M
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 THR 7 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 1.3 79.4 - - - +
8B GLU* 1.3 72.1 + - + +
9B LEU* 3.3 4.7 - - + +
10B GLU* 2.6 34.1 + - - -
11B GLU* 2.9 20.3 + - - +
44C GLN 5.9 1.1 - - - +
45C GLN* 4.3 29.8 - - + +
47C PRO* 6.4 0.2 - - + -
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Residues in contact with GLU 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU 3.8 1.4 + - - -
7B THR* 1.3 72.4 - - + +
9B LEU* 1.3 68.3 + - + +
11B GLU* 3.1 11.3 + - - +
12B SER* 2.8 30.3 + - - +
15C THR* 3.6 17.1 + - + +
18C THR* 5.5 1.0 - - - -
19C THR* 2.8 36.0 + - - +
45C GLN* 2.7 31.9 + - - +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 3.3 3.7 - - + -
8B GLU* 1.3 89.8 - - + +
10B GLU* 1.3 58.3 + - + +
12B SER* 3.2 9.0 + - - -
13B ILE* 3.0 39.3 + - + +
16C VAL* 4.9 19.1 - - + -
19C THR* 4.9 7.0 - - + +
41C LEU* 6.1 0.2 - - + -
45C GLN* 3.6 32.1 - - + +
46C LEU* 3.9 36.3 - - + -
49C LEU* 5.2 5.6 - - + -
80C ILE* 5.3 7.2 - - + -
83C LEU* 4.4 20.6 - - + -
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Residues in contact with GLU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 3.3 30.5 - - + +
7B THR* 2.6 47.2 + - - +
9B LEU* 1.3 78.3 - - + +
11B GLU* 1.3 59.5 + - - +
13B ILE* 3.1 30.5 - - + +
14B GLU* 3.2 16.9 + - - +
48C HIS* 4.1 20.9 + - - +
49C LEU* 5.9 9.0 - - + -
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B GLU 4.8 0.3 - - - +
5B PRO* 3.5 14.0 - - - +
6B LEU* 2.7 41.2 + - - +
7B THR 2.9 18.3 + - - +
8B GLU* 3.1 8.9 + - - +
10B GLU* 1.3 76.0 - - - +
12B SER* 1.3 62.8 + - - +
14B GLU* 3.2 7.8 + - - +
15B THR* 2.9 29.1 + - - -
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Residues in contact with SER 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.8 21.0 + - - +
9B LEU* 3.2 11.0 + - - -
11B GLU* 1.3 77.7 - - - +
13B ILE* 1.3 63.4 + - - +
15B THR* 3.4 16.2 + - - -
16B VAL* 3.4 17.5 + - - +
12C SER* 4.4 10.5 - - - +
15C THR* 3.5 30.0 + - - +
16C VAL* 4.6 9.5 - - - +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.0 20.3 + - + +
10B GLU* 3.1 29.6 - - + +
12B SER* 1.3 74.4 - - - +
14B GLU* 1.3 68.0 + - + +
16B VAL* 3.1 9.6 - - + +
17B VAL* 3.0 33.9 + - + +
77B TRP* 4.8 18.6 - - + -
49C LEU* 5.0 20.4 - - + -
83C LEU* 5.8 5.8 - - + -
84C ALA* 6.0 4.0 - - + -
87C ILE* 4.1 26.5 - - + -
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 5.1 12.6 - - + -
10B GLU 3.2 20.2 + - - +
11B GLU* 3.5 9.2 - - - +
13B ILE* 1.3 81.8 - - + +
15B THR* 1.3 56.2 + - - +
17B VAL* 3.4 15.3 + - - +
18B THR* 2.7 38.7 + - - -
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 2.9 16.5 + - - -
12B SER* 3.6 8.9 + - - -
13B ILE 3.3 0.2 - - - -
14B GLU* 1.3 76.5 - - - +
16B VAL* 1.3 62.3 - - - +
18B THR* 3.1 16.9 + - - -
19B THR* 3.2 16.4 + - - -
8C GLU* 4.3 21.1 - - + +
12C SER* 3.9 20.2 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER 3.4 10.1 + - - +
13B ILE* 3.1 22.9 - - - +
15B THR* 1.3 77.2 - - - +
17B VAL* 1.3 57.1 + - - +
19B THR* 3.3 7.7 + - - -
20B PHE* 2.8 30.4 + - - +
76B TYR* 5.5 0.7 + - - -
77B TRP* 3.8 24.2 - - + -
80B ILE* 5.0 15.3 - - + -
9C LEU* 4.7 16.0 - - + +
12C SER* 3.7 29.2 - - - +
13C ILE* 5.0 10.5 - - + -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ILE* 3.0 28.7 + - + +
14B GLU* 3.8 17.0 - - - +
16B VAL* 1.3 76.5 - - - +
18B THR* 1.3 59.3 + - - +
20B PHE* 3.4 16.3 - - + -
21B PHE* 2.8 35.1 + - + +
73B PHE* 4.6 13.5 - - + -
77B TRP* 4.4 20.2 - - + -
87C ILE* 6.3 3.4 - - + -
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Residues in contact with THR 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 2.7 26.0 + - - -
15B THR* 3.1 10.4 + - - -
17B VAL* 1.3 79.1 - - - +
19B THR* 1.3 52.7 + - - +
21B PHE* 3.4 5.3 + - - +
22B THR* 2.7 39.8 + - + +
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B THR* 3.2 13.4 + - - +
16B VAL* 3.3 6.0 + - - -
18B THR* 1.3 75.6 - - - +
20B PHE* 1.3 64.4 + - - +
22B THR* 2.9 16.4 + - - +
23B PHE* 3.1 36.8 - - + +
41B LEU* 4.3 6.5 - - + +
45B GLN* 3.7 16.4 - - - +
76B TYR* 5.4 1.6 - - - +
8C GLU* 2.8 32.6 + - - +
9C LEU* 4.2 17.3 - - + +
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B VAL 2.8 18.0 + - - +
17B VAL* 3.4 21.3 - - + -
19B THR* 1.3 77.9 - - - +
21B PHE* 1.3 83.1 + + + +
23B PHE* 3.4 4.6 + - - +
24B ALA* 3.0 31.5 + - + +
31B ASP* 3.6 30.1 - - - -
33B LEU* 3.5 29.7 - - + +
73B PHE* 3.6 39.3 - + - -
76B TYR* 3.6 40.3 + + + +
77B TRP* 6.1 2.5 - + + -
88C ARG* 5.6 1.1 - - - -
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Residues in contact with PHE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 2.8 26.5 + - + +
18B THR* 3.8 5.6 - - - +
20B PHE* 1.3 88.3 - + + +
22B THR* 1.3 63.5 + - + +
24B ALA* 3.3 10.2 + - + -
25B ARG* 3.0 29.8 + - + +
30B LYS* 3.9 51.8 - - + +
31B ASP* 5.6 0.7 - - - -
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B THR* 2.7 25.2 + - + +
19B THR* 2.9 17.0 + - - +
21B PHE* 1.3 76.7 - - + +
23B PHE* 1.3 65.8 + - - +
25B ARG* 3.3 40.0 + - - +
26B GLN* 3.7 11.1 + - - -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 3.1 27.8 - - + +
20B PHE* 3.4 3.9 + - - +
21B PHE 3.2 0.2 - - - -
22B THR* 1.3 82.9 - - - +
24B ALA* 1.3 57.3 + - - +
25B ARG 3.1 6.0 + - - -
26B GLN* 3.7 10.4 + - - +
33B LEU* 3.7 14.8 - - + -
37B GLU* 3.2 34.9 - - - +
40B GLU* 3.5 29.2 - - - -
41B LEU* 3.6 36.6 - - + -
44B GLN* 3.4 34.3 - - + -
45B GLN* 3.5 25.8 - - - -
76B TYR* 6.0 0.4 - - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.0 23.3 + - + +
21B PHE* 3.3 10.4 + - - +
23B PHE* 1.3 76.5 - - - +
25B ARG* 1.3 57.1 + - - +
28B GLY 4.0 1.0 - - - +
29B ARG 3.5 5.7 - - - +
30B LYS* 3.0 24.2 + - - -
31B ASP* 3.9 13.9 - - - +
32B SER 3.6 19.9 - - - +
33B LEU* 3.8 13.5 - - + -
37B GLU* 3.4 9.1 - - - +
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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