Contacts of the helix formed by residues 7 - 24 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B GLN* 3.3 35.6 + - + +
46B LEU* 5.1 0.4 - - - -
47B PRO* 5.6 4.3 - - + -
6C LEU* 1.3 72.6 - - - +
8C GLU* 1.3 62.8 + - + +
9C LEU* 3.8 8.3 - - + +
10C GLU* 2.8 36.3 + - + +
11C GLU* 2.8 35.4 + - - +
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Residues in contact with GLU 8 (chain C).
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* 4.3 15.2 - - + +
19B THR* 2.8 29.7 + - - +
45B GLN* 2.9 31.0 + - + +
7C THR* 1.3 78.9 + - - +
9C LEU* 1.3 59.1 + - + +
11C GLU* 3.2 4.1 + - - +
12C SER* 2.6 44.5 + - - +
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Residues in contact with LEU 9 (chain C).
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* 4.7 17.7 - - + +
19B THR* 4.2 25.4 - - + +
41B LEU* 3.7 32.3 - - + -
45B GLN* 3.7 35.2 - - + +
46B LEU* 4.3 17.9 - - + -
76B TYR* 5.4 4.7 - - - +
83B LEU* 5.9 5.2 - - + -
7C THR* 3.4 3.8 - - + +
8C GLU* 1.3 81.0 - - + +
10C GLU* 1.3 63.4 + - - +
12C SER* 3.1 15.8 + - - +
13C ILE* 3.2 21.3 + - + +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 4.0 16.8 - - + -
48B HIS* 2.6 38.2 + - - +
49B LEU* 3.1 28.6 + - + +
87B ILE* 4.9 3.8 - - + +
6C LEU* 3.2 28.9 - - + +
7C THR* 2.8 41.2 + - + +
9C LEU* 1.3 75.6 - - - +
11C GLU* 1.3 57.6 + - - +
13C ILE* 3.1 28.2 - - - +
14C GLU* 3.1 14.0 + - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PRO* 4.8 6.1 - - - +
6C LEU* 3.6 39.1 + - + +
7C THR 2.8 25.1 + - - +
8C GLU* 3.8 3.8 - - - +
10C GLU* 1.3 70.4 - - - +
12C SER* 1.3 59.4 + - - +
13C ILE 3.1 0.4 - - - -
14C GLU* 3.7 17.0 - - - +
15C THR* 3.0 31.0 + - - -
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Residues in contact with SER 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 4.4 12.8 - - - +
15B THR* 3.9 21.0 - - - +
16B VAL* 3.7 25.5 - - - +
8C GLU* 2.6 28.9 + - - +
9C LEU* 3.1 7.7 + - - -
11C GLU* 1.3 77.8 - - - +
13C ILE* 1.3 58.3 + - - +
15C THR* 3.2 21.8 - - - +
16C VAL* 4.3 5.9 - - - +
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Residues in contact with ILE 13 (chain C).
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* 5.0 6.7 - - + -
49B LEU* 4.0 21.5 - - + -
80B ILE* 3.8 27.1 - - + +
83B LEU* 4.2 7.0 - - + +
84B ALA* 3.9 35.9 - - + +
87B ILE* 5.3 8.5 - - + -
9C LEU* 3.2 13.2 + - + +
10C GLU* 3.1 18.8 - - + +
12C SER* 1.3 81.2 - - - +
14C GLU* 1.3 60.3 + - + +
15C THR 3.4 0.4 - - - -
16C VAL* 3.1 25.8 - - - +
17C VAL* 3.5 8.8 - - - +
77C TRP* 4.4 7.1 - - + -
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.9 11.2 - - + -
3C ALA* 5.1 11.1 + - + +
6C LEU* 4.4 16.8 - - + -
10C GLU 3.1 17.8 + - - +
11C GLU* 3.2 18.9 + - - +
13C ILE* 1.3 77.5 - - - +
15C THR* 1.3 60.9 + - - +
16C VAL 3.1 2.2 - - - -
17C VAL* 2.8 35.6 + - + +
18C THR* 2.9 25.9 + - - +
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Residues in contact with THR 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.6 13.8 + - + +
12B SER* 3.5 25.9 + - - +
11C GLU 3.0 12.4 + - - +
12C SER* 3.2 24.5 - - - +
14C GLU* 1.3 80.8 + - - +
16C VAL* 1.3 59.7 + - + +
18C THR* 3.1 19.2 + - - -
19C THR* 2.9 16.1 + - - -
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 5.3 0.2 - - - -
9B LEU* 4.9 19.1 - - + -
12B SER* 4.6 12.1 - - - +
12C SER 4.3 6.3 - - - +
13C ILE* 3.1 23.8 - - - +
15C THR* 1.3 87.0 - - + +
17C VAL* 1.3 66.6 + - + +
19C THR* 3.3 15.3 + - - -
20C PHE* 3.4 13.7 + - - +
76C TYR* 5.0 2.1 + - - -
77C TRP* 3.8 24.7 - - + -
80C ILE* 4.4 24.2 - - + +
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 6.1 1.1 - - + +
87B ILE* 5.7 9.6 - - + -
13C ILE 3.5 19.3 - - - +
14C GLU* 2.8 24.1 + - + +
16C VAL* 1.3 80.0 - - + +
18C THR* 1.3 63.2 + - - +
19C THR 3.2 0.2 - - - -
20C PHE* 3.1 8.7 + - + +
21C PHE* 3.0 38.0 + - + -
73C PHE* 3.6 33.2 - - + -
77C TRP* 4.5 12.3 - - - +
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Residues in contact with THR 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 5.5 1.1 - - - -
14C GLU* 2.9 29.4 + - - +
15C THR* 3.1 17.0 + - - -
17C VAL* 1.3 76.3 - - - +
19C THR* 1.3 52.7 - - - +
21C PHE* 3.3 7.8 + - + +
22C THR* 2.7 37.4 + - + +
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 2.8 41.7 + - - +
9B LEU* 4.9 7.1 - - + +
15C THR 2.9 10.4 + - - -
16C VAL* 3.3 12.8 + - - -
17C VAL 3.2 0.2 - - - -
18C THR* 1.3 75.8 - - - +
20C PHE* 1.3 61.0 + - - +
22C THR* 3.0 17.3 + - - +
23C PHE* 3.1 36.2 + - + -
41C LEU* 5.2 4.3 - - + -
45C GLN* 4.0 15.9 - - + +
76C TYR* 5.3 2.2 - - - -
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Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL 3.4 8.3 + - - +
17C VAL* 3.1 10.7 + - - +
19C THR* 1.3 79.1 - - - +
21C PHE* 1.3 69.8 + + - +
23C PHE* 3.1 3.2 + - - +
24C ALA* 2.7 44.8 + - + +
30C LYS 3.8 15.5 - - - -
31C ASP* 3.7 27.8 - - - -
32C SER 3.9 0.9 - - - -
33C LEU* 3.5 33.0 - - + -
71C LEU 4.8 1.1 - - - -
72C LYS 5.4 0.2 - - - -
73C PHE* 3.6 39.5 - + + -
76C TYR* 3.4 48.7 + + + +
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Residues in contact with PHE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET 4.9 12.1 - - - -
17C VAL* 3.0 45.6 + - + +
18C THR* 3.3 9.6 + - + +
20C PHE* 1.3 80.7 - + - +
22C THR* 1.3 62.1 + - + +
24C ALA 3.8 2.0 - - - +
25C ARG* 3.6 22.2 - - - +
30C LYS* 3.4 54.6 - - + +
31C ASP* 5.3 3.6 - - + -
73C PHE* 3.8 21.5 - + - -
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C THR* 2.7 22.5 + - + +
19C THR* 3.0 16.1 + - - +
21C PHE* 1.3 77.1 - - + +
23C PHE* 1.3 62.9 + - - +
25C ARG* 3.3 20.0 + - - +
26C GLN* 3.2 15.8 + - - -
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Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C THR* 3.1 36.1 + - + +
20C PHE* 3.9 2.5 - - - +
22C THR* 1.3 80.8 - - - +
24C ALA* 1.3 58.2 + - - +
25C ARG 3.0 3.8 + - - -
26C GLN* 3.0 22.8 + - - +
33C LEU* 4.7 10.1 - - + -
37C GLU* 3.2 35.2 - - - +
40C GLU* 3.8 21.3 - - + -
41C LEU* 3.6 46.9 - - + -
44C GLN* 4.2 15.5 - - - -
45C GLN* 4.2 21.3 - - + -
76C TYR* 5.9 0.2 - - - +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 2.7 34.9 + - + +
21C PHE 3.8 3.3 - - - +
23C PHE* 1.3 68.7 - - - +
25C ARG* 1.3 60.8 + - - +
29C ARG 3.9 3.8 - - - -
30C LYS* 2.9 26.1 - - - +
32C SER 3.5 19.3 - - - +
33C LEU* 3.5 21.5 - - + -
37C GLU* 3.7 11.4 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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