Contacts of the helix formed by residues 15 - 27 (chain B) in PDB entry 3KCN
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 ASP 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP* 2.7 17.8 + - - +
14B ASP* 1.3 73.8 - - + +
16B TYR* 1.3 60.4 + - - +
17B SER* 2.7 27.7 + - - -
18B LEU* 3.0 23.4 + - - +
19B LEU* 3.1 22.3 + - - +
108B LYS* 5.9 0.7 + - - +
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Residues in contact with TYR 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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14B ASP 3.7 8.5 + - - -
15B ASP* 1.3 69.6 + - - +
17B SER* 1.3 61.0 + - - +
19B LEU* 4.1 16.6 - - + -
20B ASN* 2.9 51.4 + - - +
34B THR* 5.6 4.7 - - - -
35B CYS 5.9 0.4 - - - -
36B GLU* 2.4 51.2 + - + +
40B GLU* 4.3 6.6 + - - -
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Residues in contact with SER 17 (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 ASP* 2.7 19.6 + - - -
16B TYR* 1.3 74.3 - - - +
18B LEU* 1.3 55.7 + - - -
20B ASN* 3.7 7.3 + - - +
21B THR* 3.2 26.7 + - - -
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Residues in contact with LEU 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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13B ASP* 3.7 23.6 - - + +
15B ASP* 3.0 27.8 + - + +
17B SER* 1.3 74.1 - - - +
19B LEU* 1.3 66.2 + - - +
21B THR* 4.5 10.5 - - + +
22B LEU* 3.1 45.9 + - + +
84B LEU* 4.2 14.4 - - + -
108B LYS* 3.7 18.4 - - + +
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Residues in contact with LEU 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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11B LEU* 4.1 28.7 - - + +
13B ASP* 3.2 42.8 - - + +
15B ASP 3.1 15.8 + - - +
16B TYR* 3.6 25.4 - - + +
18B LEU* 1.3 78.6 - - + +
20B ASN* 1.3 60.6 + - - +
22B LEU* 3.9 6.6 - - + +
23B LYS* 2.8 32.8 + - - +
34B THR* 4.0 25.0 - - + +
35B CYS 3.4 19.5 - - - +
36B GLU* 4.4 2.5 - - - +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 2.9 39.9 + - - +
17B SER* 3.9 6.8 - - - +
19B LEU* 1.3 77.3 - - - +
21B THR* 1.3 62.2 + - - +
23B LYS* 4.0 6.9 - - - +
24B ARG* 3.1 41.6 + - - +
34B THR* 5.8 1.4 + - - -
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Residues in contact with THR 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 SER* 3.2 17.4 + - - -
18B LEU* 3.9 14.3 - - + -
19B LEU 3.3 0.6 - - - -
20B ASN* 1.3 79.5 - - - +
22B LEU* 1.3 61.3 + - - +
24B ARG* 3.4 18.1 + - - +
25B ASN* 2.6 44.1 + - - +
112B MSE 4.7 9.2 - - + -
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Residues in contact with LEU 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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11B LEU* 4.0 24.2 - - + -
13B ASP* 6.4 0.9 - - + -
18B LEU* 3.1 43.3 + - + +
19B LEU* 3.9 7.0 - - + +
21B THR* 1.3 76.2 - - + +
23B LYS* 1.3 59.5 + - - +
26B LEU* 2.9 40.3 + - + +
55B MSE 4.9 16.6 - - - -
84B LEU* 5.0 7.2 - - + -
112B MSE 3.5 29.4 - - + -
115B ILE* 3.8 24.2 - - + -
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Residues in contact with LYS 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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11B LEU* 4.4 0.8 - - - +
19B LEU 2.8 22.8 + - - +
20B ASN* 4.2 6.5 - - - +
22B LEU* 1.3 73.6 - - - +
24B ARG* 1.3 61.7 + - - +
26B LEU 4.6 0.2 - - - +
27B SER* 2.7 42.9 + - - +
32B VAL* 3.1 44.2 + - + -
33B THR* 4.4 5.9 - - - +
34B THR* 4.1 23.7 + - + +
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Residues in contact with ARG 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 ASN* 3.1 34.0 + - - +
21B THR* 3.6 24.7 + - - +
23B LYS* 1.3 78.4 - - - +
25B ASN* 1.3 69.5 - - - +
27B SER* 4.0 7.5 + - - -
28B PHE* 4.4 4.3 + - - +
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Residues in contact with ASN 25 (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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21B THR* 2.6 40.8 + - - +
22B LEU 3.3 0.4 + - - +
24B ARG* 1.3 90.5 - - - +
26B LEU* 1.3 63.7 + - - +
27B SER 3.4 0.7 + - - -
28B PHE* 3.5 17.0 + - - +
29B ASP* 4.6 5.4 + - - +
112B MSE 4.0 33.4 - - + +
116B LYS* 4.9 8.8 + - - +
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Residues in contact with LEU 26 (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 ILE* 4.2 3.8 - - + -
11B LEU* 4.1 23.1 - - + -
22B LEU* 2.9 26.6 + - + +
25B ASN* 1.3 74.4 - - - +
27B SER* 1.3 53.0 + - - +
28B PHE 3.1 2.9 - - - -
29B ASP* 3.0 7.0 + - - +
30B PHE* 2.7 50.6 + - + -
32B VAL* 3.8 15.3 - - + -
112B MSE 3.9 16.8 - - - -
115B ILE* 4.2 9.9 - - + -
116B LYS* 3.9 28.7 - - + -
119B ILE* 3.6 27.1 - - + -
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 2.7 41.2 + - - +
24B ARG* 4.3 5.4 - - - -
25B ASN 3.3 0.6 - - - -
26B LEU* 1.3 74.1 - - - +
28B PHE* 1.3 64.2 + - - +
29B ASP 3.2 0.4 - - - -
30B PHE 3.4 17.7 + - - +
32B VAL* 3.8 9.5 + - - +
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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