Contacts of the helix formed by residues 21 - 38 (chain E) in PDB entry 1KQN
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 21 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 3.5 13.0 - - + +
20E ILE* 1.3 81.3 - - - +
22E ASN* 1.3 66.9 + - - +
23E MET* 3.0 14.7 + - - +
24E HIS* 2.9 26.4 + - + +
25E LEU* 3.4 16.8 + - - +
221E ILE* 3.0 29.7 + - - +
223E SER* 4.2 6.1 - - - +
226E ILE* 4.0 20.9 - - + -
239E LEU 3.6 11.7 - - - -
240E VAL* 4.0 7.6 - - + +
241E PRO* 4.8 1.1 - - - -
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Residues in contact with ASN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E THR* 1.3 72.1 - - - +
23E MET* 1.3 57.7 + - - +
25E LEU* 3.6 9.5 + - - +
26E ARG* 2.9 28.1 + - - +
221E ILE* 4.2 10.3 - - + +
238E TYR* 3.3 29.9 + - - +
239E LEU 2.8 19.8 + - - +
240E VAL 3.2 22.0 + - - +
241E PRO* 3.2 10.8 - - - +
22F ASN* 3.3 19.2 - - - +
238F TYR* 3.9 25.5 + - + +
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Residues in contact with MET 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E THR* 3.0 7.7 + - - +
22E ASN* 1.3 78.3 - - - +
24E HIS* 1.3 76.0 + - + +
26E ARG* 3.2 7.5 + - + +
27E LEU* 2.9 25.4 + - - +
219E ASN* 3.5 24.5 - - + +
220E ASP* 4.8 0.4 - - - -
221E ILE* 3.4 33.4 - - + +
222E SER* 4.2 8.7 - - - +
758E XE 3.7 14.3 - - - -
781E NAD 2.9 59.9 - - + +
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Residues in contact with HIS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E PHE* 3.7 22.5 - + + -
19E PRO 3.6 13.7 + - - -
20E ILE* 3.4 19.9 - - + -
21E THR* 2.9 44.4 + - - +
23E MET* 1.3 90.0 - - + +
25E LEU* 1.3 67.9 + - - +
27E LEU* 3.0 17.9 + - - +
28E PHE* 3.4 14.1 + - + -
48E ILE* 6.1 0.7 - - + -
223E SER* 3.6 10.3 + - - -
757E XE 3.7 7.1 - - - -
781E NAD 3.7 48.6 + + - -
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 4.1 15.7 - - + -
21E THR 3.4 11.1 + - - +
22E ASN* 3.7 8.7 - - - +
23E MET 3.3 0.4 - - - -
24E HIS* 1.3 76.3 - - - +
26E ARG* 1.3 63.1 + - - +
28E PHE* 3.2 18.5 + - + +
29E GLU* 3.3 14.4 + - - +
48E ILE* 4.7 3.8 - - + -
73E ALA* 3.9 9.0 - - + +
74E THR* 3.8 30.3 - - + -
80E VAL* 5.7 3.4 - - + -
241E PRO* 3.5 33.2 - - + -
238F TYR* 3.5 45.4 - - + +
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ASN 2.9 19.0 + - - +
23E MET* 3.4 10.5 - - + +
24E HIS 3.1 0.4 - - - -
25E LEU* 1.3 75.1 - - - +
27E LEU* 1.3 65.4 + - - +
29E GLU* 3.2 10.5 + - - +
30E LEU* 3.0 46.9 + - + +
215E GLU* 3.2 29.4 + - - +
217E ILE* 4.5 6.5 - - - +
758E XE 4.0 7.6 - - - -
229F ALA* 5.8 2.8 - - - +
234F GLN* 5.9 2.2 - - - +
235F SER* 3.0 35.8 + - - -
236F ILE* 3.7 5.3 - - - +
237F ARG 3.7 17.5 + - - +
238F TYR* 4.3 5.1 - - + -
239F LEU* 3.7 35.7 - - + +
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E MET* 2.9 12.2 + - - +
24E HIS* 3.0 12.1 + - - +
26E ARG* 1.3 76.7 - - - +
28E PHE* 1.3 63.6 + - - +
30E LEU* 3.4 4.9 + - - +
31E ALA* 3.0 24.9 + - - +
154E LEU* 4.3 8.7 - - + -
155E CYS* 3.7 26.2 - - - +
186E VAL* 3.4 26.0 - - + +
757E XE 3.1 21.1 - - - -
758E XE 3.5 11.0 - - - -
781E NAD 3.3 49.4 - - + +
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Residues in contact with PHE 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 3.8 9.0 - - + -
13E ALA* 3.4 32.8 - - + -
17E PHE* 5.4 1.8 - + - -
24E HIS 3.4 15.6 + - - -
25E LEU* 3.2 11.2 + - + +
27E LEU* 1.3 78.9 - - - +
29E GLU* 1.3 63.2 + - - +
31E ALA* 3.3 2.1 + - - +
32E LYS* 3.0 25.6 + - - +
46E GLY* 3.6 25.8 - - - -
47E ILE 3.6 10.1 - - - -
48E ILE* 3.5 34.1 - - + -
79E TRP* 3.6 30.0 - + + -
80E VAL* 4.0 14.6 - - + -
154E LEU* 3.9 18.4 - - + -
757E XE 4.1 6.1 - - - -
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU 3.3 11.6 + - - +
26E ARG* 3.2 16.1 + - - +
28E PHE* 1.3 76.4 - - - +
30E LEU* 1.3 62.3 + - - +
32E LYS* 3.9 6.9 + - - +
33E ASP* 3.2 29.3 + - - +
78E LYS* 3.5 16.4 + - - -
79E TRP* 3.3 31.2 + - - -
80E VAL* 5.0 3.6 - - - +
235F SER* 2.8 37.3 + - - +
237F ARG* 4.3 5.1 - - - +
238F TYR* 3.9 28.5 + - + -
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Residues in contact with LEU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ARG* 3.0 34.9 + - - +
27E LEU 3.6 4.3 - - - +
29E GLU* 1.3 75.9 - - - +
31E ALA* 1.3 65.9 + - - +
33E ASP* 3.3 9.6 + - + +
34E TYR* 3.0 22.9 + - - +
186E VAL* 3.8 19.7 - - + -
213E VAL* 4.3 7.7 - - + +
214E ASN 4.4 11.0 - - - +
215E GLU* 3.1 53.4 - - + +
758E XE 4.5 2.9 - - - -
234F GLN* 6.0 5.2 - - + +
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 3.9 18.8 - - + -
27E LEU 3.0 17.0 + - - +
28E PHE 3.9 1.1 - - - +
30E LEU* 1.3 77.6 - - - +
32E LYS* 1.3 57.2 + - - +
34E TYR* 3.4 6.8 + - - +
35E MET* 3.0 35.5 + - - +
154E LEU* 3.9 21.8 - - + -
184E ILE* 3.9 15.5 - - + -
186E VAL* 4.3 6.7 - - + +
213E VAL* 4.8 1.1 - - - -
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Residues in contact with LYS 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.1 2.1 - - - +
28E PHE 3.0 16.0 + - - +
29E GLU* 3.9 9.2 + - - +
30E LEU 3.3 0.2 - - - -
31E ALA* 1.3 74.6 - - - +
33E ASP* 1.3 71.4 + - - +
35E MET 3.4 0.2 + - - -
36E ASN* 2.9 46.8 + - - +
43E VAL* 3.8 25.5 - - + +
78E LYS* 5.3 2.8 - - - +
79E TRP* 3.1 63.3 - - + +
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Residues in contact with ASP 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ARG* 5.8 0.3 + - - -
29E GLU 3.2 18.9 + - - +
30E LEU* 3.3 10.8 + - + +
32E LYS* 1.3 80.6 - - - +
34E TYR* 1.3 57.3 + - - +
36E ASN* 4.3 3.6 + - - +
37E GLY* 2.8 27.9 + - - -
233F GLY 4.8 2.7 - - - +
234F GLN* 3.1 25.8 - - + +
235F SER* 2.7 37.0 + - - +
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Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LEU 3.0 13.6 + - - +
31E ALA 3.6 7.0 - - - +
32E LYS 3.2 0.2 - - - -
33E ASP* 1.3 77.5 - - - +
35E MET* 1.3 80.9 + - + +
37E GLY* 3.2 2.3 + - - -
38E THR* 3.1 46.8 + - + +
40E ARG* 5.8 1.4 + - - -
184E ILE* 5.1 0.2 - - + -
211E HIS* 3.7 38.5 + + + +
212E VAL 4.3 14.2 + - - -
213E VAL* 3.7 35.2 - - + -
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Residues in contact with MET 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL* 4.3 14.6 - - + -
11E LEU* 4.8 1.6 - - + -
31E ALA 3.0 19.5 + - - +
34E TYR* 1.3 93.5 - - + +
36E ASN* 1.3 64.1 + - - +
38E THR* 2.6 28.2 + - - -
41E TYR* 3.8 49.5 + - + +
43E VAL* 3.5 21.1 - - + -
152E LYS* 4.8 5.2 - - - -
184E ILE* 3.4 36.3 - - + -
211E HIS* 4.2 12.8 - - + -
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Residues in contact with ASN 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LYS* 5.1 4.2 + - - -
32E LYS* 2.9 45.0 + - - +
33E ASP* 4.3 2.6 + - - +
35E MET* 1.3 72.9 - - - +
37E GLY* 1.3 64.1 + - - +
38E THR 3.1 0.9 + - - -
39E GLY* 3.2 14.2 + - - -
41E TYR 3.8 11.0 - - - +
42E THR* 3.4 8.8 - - - +
43E VAL* 2.7 35.7 + - - +
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Residues in contact with GLY 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ARG* 4.0 23.4 + - - -
33E ASP 2.8 21.4 + - - -
34E TYR* 3.6 2.5 - - - -
35E MET 3.1 0.2 - - - -
36E ASN* 1.3 78.8 - - - +
38E THR* 1.3 60.6 + - - +
39E GLY* 3.1 1.7 + - - -
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Residues in contact with THR 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B SER* 5.7 4.9 - - - -
34E TYR* 3.1 43.2 + - + +
35E MET* 2.6 19.2 + - - +
37E GLY* 1.3 75.8 - - - +
39E GLY* 1.3 59.8 + - - +
40E ARG* 3.2 39.3 + - - +
41E TYR* 3.4 15.4 - - + -
211E HIS* 5.9 0.9 - - + +
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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