Contacts of the helix formed by residues 21 - 39 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F PRO* 3.2 18.6 - - + +
20F ILE* 1.3 74.0 - - - +
22F ASN* 1.3 65.3 + - - +
23F MET* 2.8 26.3 + - - +
24F HIS* 3.0 25.8 + - + +
25F LEU* 3.4 13.2 + - - +
221F ILE* 3.3 24.5 + - + +
223F SER* 4.3 6.3 - - - +
226F ILE* 4.2 10.8 - - + -
239F LEU 3.6 9.6 - - - -
240F VAL* 3.6 14.4 - - + -
241F PRO* 4.6 4.5 - - - -
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Residues in contact with ASN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ASN* 3.3 20.8 - - - +
238E TYR* 3.8 24.9 + - + +
21F THR* 1.3 69.3 - - - +
23F MET* 1.3 57.3 + - - +
25F LEU* 4.0 8.5 - - - +
26F ARG* 2.9 29.0 + - - +
219F ASN* 4.4 2.2 + - - +
221F ILE* 4.2 9.6 - - + +
238F TYR* 3.2 28.1 + - - +
239F LEU 2.8 20.5 + - - +
240F VAL* 3.2 21.1 + - - +
241F PRO* 3.3 12.7 - - - +
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Residues in contact with MET 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F THR* 2.8 11.9 + - - +
22F ASN* 1.3 77.8 - - - +
24F HIS* 1.3 72.9 + - + +
26F ARG* 3.1 3.5 + - - +
27F LEU* 2.9 27.1 + - - +
219F ASN* 3.0 33.3 - - + +
220F ASP 5.3 0.2 - - - -
221F ILE* 3.2 34.2 - - + +
222F SER* 4.3 6.1 - - - -
223F SER 5.2 0.7 - - - +
756F XE 3.7 10.3 - - - -
782F NAD 3.0 63.3 - - + +
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Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F PHE* 3.6 24.0 - + + -
19F PRO 3.7 1.8 + - - -
20F ILE* 3.4 25.7 - - + -
21F THR* 3.0 34.6 + - - +
23F MET* 1.3 92.9 - - + +
25F LEU* 1.3 63.2 + - - +
27F LEU* 3.1 23.5 - - + +
28F PHE* 3.4 14.8 - - + -
223F SER* 3.6 19.9 + - - -
782F NAD 3.3 51.0 + + - -
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E TYR* 3.4 44.8 - - + +
20F ILE* 3.5 26.9 - - + -
21F THR 3.4 12.0 + - - +
22F ASN* 4.0 5.6 - - - +
23F MET 3.2 0.2 - - - -
24F HIS* 1.3 73.4 - - - +
26F ARG* 1.3 66.9 + - - +
28F PHE* 3.2 18.8 + - + +
29F GLU* 3.2 15.1 + - - +
48F ILE* 4.2 5.4 - - + -
73F ALA* 3.8 12.8 - - + +
74F THR* 4.1 21.1 - - + -
80F VAL* 5.7 2.0 - - + -
241F PRO* 3.6 27.1 - - + -
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Residues in contact with ARG 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E ALA* 6.0 2.0 - - - +
234E GLN* 6.2 0.6 - - - +
235E SER* 3.0 37.4 + - - -
236E ILE* 3.8 3.4 - - - +
237E ARG 3.2 24.1 + - - -
238E TYR* 4.4 3.3 - - - -
239E LEU* 3.5 41.5 - - + +
22F ASN 2.9 21.3 + - - +
23F MET* 3.2 11.4 - - - +
25F LEU* 1.3 75.5 - - - +
27F LEU* 1.3 63.6 + - - -
29F GLU* 3.1 15.4 + - - +
30F LEU* 2.9 52.1 + - + +
217F ILE* 4.9 6.7 - - - +
219F ASN* 4.3 10.5 - - - +
756F XE 4.2 10.5 - - - -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ALA* 5.9 4.0 - - + -
17F PHE* 6.5 0.2 - - + -
23F MET* 2.9 9.7 + - - +
24F HIS* 3.1 20.2 - - - +
25F LEU 3.1 0.2 - - - -
26F ARG* 1.3 76.2 - - - +
28F PHE* 1.3 64.0 + - + +
30F LEU* 3.1 5.1 + - - +
31F ALA* 3.0 23.6 + - - +
154F LEU* 3.7 28.5 - - + +
155F CYS* 4.4 4.7 - - - -
186F VAL* 3.5 22.5 - - + +
756F XE 3.7 9.2 - - - -
782F NAD 3.3 66.4 - - + +
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Residues in contact with PHE 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 3.8 7.4 - - + -
13F ALA* 3.3 31.6 - - + -
17F PHE* 5.3 4.0 - + - -
24F HIS 3.4 17.7 - - - -
25F LEU* 3.2 11.3 + - + +
27F LEU* 1.3 78.0 - - + +
29F GLU* 1.3 68.3 + - - +
31F ALA* 4.0 0.3 - - - +
32F LYS 3.1 17.7 + - - -
46F GLY* 3.7 8.3 - - - -
47F ILE 3.4 30.3 - - - -
48F ILE* 3.6 26.7 - - + -
79F TRP* 3.2 37.7 - + + -
80F VAL* 4.1 13.0 - - + -
154F LEU* 3.5 23.3 - - + +
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E SER* 2.6 40.7 + - - +
237E ARG* 3.7 11.6 - - - +
238E TYR* 3.9 22.4 - - + -
25F LEU 3.2 12.1 + - - +
26F ARG* 3.1 21.5 + - - +
28F PHE* 1.3 78.3 - - - +
30F LEU* 1.3 62.7 + - - +
32F LYS* 3.8 2.7 - - - +
33F ASP* 3.1 29.4 + - - +
77F SER* 5.4 0.2 + - - -
78F LYS* 4.0 10.3 + - - -
79F TRP* 3.1 32.1 + - - -
80F VAL* 5.0 2.3 - - - +
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Residues in contact with LEU 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234E GLN* 5.8 6.1 - - - +
26F ARG* 2.9 40.0 + - + +
27F LEU 3.4 9.2 - - - +
29F GLU* 1.3 76.2 - - - +
31F ALA* 1.3 64.6 + - - +
33F ASP* 3.4 7.5 + - + +
34F TYR* 3.0 22.5 + - - +
186F VAL* 4.1 17.3 - - + -
213F VAL* 4.2 10.4 - - + +
214F ASN 4.6 10.3 - - - +
215F GLU* 3.9 31.0 - - + -
756F XE 4.4 8.3 - - - -
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Residues in contact with ALA 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 3.8 20.0 - - + -
27F LEU 3.0 15.1 + - - +
28F PHE 4.0 1.3 - - - +
30F LEU* 1.3 73.8 - - - +
32F LYS* 1.3 58.4 + - - +
34F TYR* 3.1 7.6 + - - +
35F MET* 2.8 34.5 + - - +
154F LEU* 4.1 12.6 - - + -
184F ILE* 3.8 28.3 - - + -
186F VAL* 4.6 2.6 - - + +
213F VAL* 4.7 3.4 - - - -
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 4.2 0.8 - - - +
28F PHE 3.1 15.7 + - - +
29F GLU* 3.8 4.5 - - - +
31F ALA* 1.3 78.5 - - - +
33F ASP* 1.3 70.3 + - - +
36F ASN* 2.9 49.4 + - - +
43F VAL* 3.8 28.7 + - + -
79F TRP* 3.5 61.8 - - + +
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Residues in contact with ASP 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ARG* 5.3 1.6 + - - -
233E GLY 5.0 2.5 - - - -
234E GLN* 2.9 29.2 - - + +
235E SER* 2.9 37.8 + - - -
29F GLU* 3.1 17.9 + - - +
30F LEU* 3.8 8.1 - - + +
32F LYS* 1.3 81.3 - - - +
34F TYR* 1.3 53.0 + - - +
36F ASN* 3.8 4.2 - - - +
37F GLY* 2.7 32.2 + - - -
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Residues in contact with TYR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D TRP* 6.4 1.8 - + - -
207D ARG* 5.6 2.2 + - - +
30F LEU 3.0 14.1 + - - +
31F ALA 3.3 7.0 - - - +
33F ASP* 1.3 74.6 - - - +
35F MET* 1.3 90.0 + - + +
37F GLY* 3.1 2.2 + - - -
38F THR* 3.1 38.9 + - + +
211F HIS* 3.9 30.5 + + + +
212F VAL 4.4 13.6 + - - -
213F VAL* 3.6 34.5 - - + -
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Residues in contact with MET 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.6 12.8 - - + -
11F LEU* 4.9 1.8 - - + -
31F ALA 2.8 23.8 + - - +
34F TYR* 1.3 95.1 - - + +
36F ASN* 1.3 60.4 + - - +
38F THR* 2.7 26.0 + - - -
39F GLY 4.0 0.3 + - - -
41F TYR* 3.6 52.1 + - + +
43F VAL* 3.6 19.5 - - + -
152F LYS* 4.8 4.7 - - + -
184F ILE* 3.3 40.2 - - + -
211F HIS* 4.1 12.1 - - + +
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Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS* 5.5 2.6 + - - -
32F LYS* 2.9 45.4 + - - +
33F ASP* 4.0 4.0 - - - +
35F MET* 1.3 77.1 - - - +
37F GLY* 1.3 62.7 + - - +
39F GLY* 3.1 15.9 + - - -
41F TYR 3.9 9.6 - - - +
42F THR* 3.5 8.4 - - - +
43F VAL* 2.9 35.2 + - - +
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Residues in contact with GLY 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ARG* 4.0 25.4 + - - -
208D SER* 6.2 0.3 - - - -
33F ASP 2.7 21.0 + - - -
34F TYR 3.1 3.1 + - - -
36F ASN* 1.3 77.5 - - - +
38F THR* 1.3 62.3 + - - +
39F GLY* 3.1 1.6 + - - -
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Residues in contact with THR 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D SER* 5.5 7.3 - - - -
34F TYR* 3.1 39.0 + - + +
35F MET* 2.7 20.0 + - - +
37F GLY* 1.3 75.2 - - - +
39F GLY* 1.3 59.1 + - - +
40F ARG* 3.1 48.5 + - - +
41F TYR* 3.2 15.7 - - + -
211F HIS* 6.0 1.1 - - - +
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Residues in contact with GLY 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F LYS* 3.1 32.8 - - - +
35F MET 4.0 0.2 + - - -
36F ASN 3.1 15.0 + - - -
37F GLY 3.1 2.2 - - - -
38F THR* 1.3 80.1 + - - +
40F ARG* 1.3 59.1 + - - +
41F TYR 3.3 2.2 - - - -
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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