Contacts of the helix formed by residues 21 - 38 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO* 3.3 17.0 - - + +
20B ILE* 1.3 75.2 - - - +
22B ASN* 1.3 67.0 + - - +
23B MET* 3.2 14.6 + - - +
24B HIS* 2.8 27.9 + - + +
25B LEU* 3.5 12.5 + - - +
221B ILE* 3.0 29.4 + - - +
223B SER* 4.3 5.6 - - - +
226B ILE* 3.8 25.1 - - + -
239B LEU 3.8 8.7 - - - -
240B VAL* 3.9 10.1 - - + -
241B PRO* 4.6 4.0 - - - -
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN* 4.2 4.8 - - - +
238A TYR* 4.0 33.5 + - + +
21B THR* 1.3 71.3 - - - +
23B MET* 1.3 51.7 + - - +
25B LEU* 3.3 11.0 + - - +
26B ARG* 2.7 38.5 + - + +
221B ILE* 4.3 8.9 - - + +
238B TYR* 3.1 29.5 + - - +
239B LEU 2.9 20.9 + - - +
240B VAL* 3.3 19.2 + - - +
241B PRO* 3.4 12.0 - - - +
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Residues in contact with MET 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 3.0 11.3 + - - +
22B ASN* 1.3 79.3 - - - +
24B HIS* 1.3 74.7 + - + +
26B ARG* 3.2 8.2 + - - +
27B LEU* 2.8 30.0 + - - +
219B ASN* 4.8 8.5 - - + +
220B ASP 3.7 15.5 - - - +
221B ILE* 3.0 42.1 - - + +
222B SER* 4.0 7.4 - - - -
223B SER 4.8 0.7 - - - +
755B XE 3.6 14.0 - - - -
778B NAD 3.0 56.3 - - + +
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Residues in contact with HIS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PHE* 3.8 24.0 - + + -
19B PRO 3.6 13.7 + - - -
20B ILE* 3.4 19.2 - - + -
21B THR* 2.8 43.7 + - - +
23B MET* 1.3 95.4 - - + +
25B LEU* 1.3 62.9 + - - +
27B LEU* 3.1 19.5 - - - +
28B PHE* 3.4 16.5 - - + -
48B ILE* 5.7 0.4 - - + -
223B SER* 3.6 9.0 + - - -
760B XE 3.7 6.9 - - - -
778B NAD 3.7 44.4 + + - -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR* 3.7 44.3 - - + +
20B ILE* 4.3 15.7 - - + -
21B THR 3.9 11.4 - - - +
22B ASN* 3.3 7.5 + - - +
24B HIS* 1.3 73.2 - - - +
26B ARG* 1.3 65.8 + - - +
28B PHE* 3.1 19.3 + - - +
29B GLU* 3.2 14.7 + - - +
48B ILE* 4.5 4.9 - - + -
73B ALA* 4.3 11.9 - - + +
74B THR* 4.0 26.7 - - + -
77B SER* 6.1 0.4 - - - -
80B VAL* 5.2 7.2 - - + -
241B PRO* 3.7 30.1 - - + -
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA* 6.2 0.4 - - - +
234A GLN* 5.9 0.4 - - - +
235A SER* 2.7 43.4 + - - +
236A ILE 3.6 0.6 - - - -
237A ARG 2.8 38.5 + - - +
238A TYR* 4.3 4.4 - - + +
239A LEU* 3.5 38.7 - - + +
22B ASN* 2.7 19.4 + - + +
23B MET* 3.3 10.5 - - - +
25B LEU* 1.3 78.1 - - - +
27B LEU* 1.3 62.5 + - - +
29B GLU* 3.1 19.7 + - - +
30B LEU* 3.0 51.0 + - + +
33B ASP* 5.1 2.0 + - - -
217B ILE* 5.2 3.6 - - - +
219B ASN* 5.9 5.4 - - + +
755B XE 4.2 9.9 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 2.8 14.7 + - - +
24B HIS 3.1 12.8 - - - +
25B LEU 3.1 0.2 - - - -
26B ARG* 1.3 77.6 - - - +
28B PHE* 1.3 56.9 + - - +
30B LEU* 3.5 5.8 + - - +
31B ALA* 3.0 29.3 + - - +
154B LEU* 3.2 40.2 - - + -
155B CYS* 4.2 13.7 - - - +
186B VAL* 3.8 16.2 - - + +
755B XE 3.9 13.2 - - - -
760B XE 3.5 12.8 - - - -
778B NAD 3.0 47.6 - - + +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 12.3 - - + +
13B ALA* 3.8 17.5 - - + -
17B PHE* 5.6 0.9 - + - -
24B HIS 3.4 20.8 + - - -
25B LEU* 3.1 11.7 + - - +
27B LEU* 1.3 79.5 - - - +
29B GLU* 1.3 56.4 + - - +
31B ALA* 3.3 3.5 + - - +
32B LYS* 2.9 30.7 + - - +
46B GLY* 3.6 8.5 - - - -
47B ILE 3.6 40.4 - - - -
48B ILE* 3.5 27.6 - - + -
79B TRP* 3.5 30.3 - + + -
80B VAL* 4.1 15.7 - - + -
154B LEU* 3.8 22.9 - - + -
760B XE 4.1 4.7 - - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER* 3.0 29.1 + - - +
237A ARG* 4.4 5.3 - - - +
238A TYR* 3.9 23.3 - - + -
25B LEU 3.2 11.6 + - - +
26B ARG* 3.1 31.2 + - - +
28B PHE* 1.3 76.9 - - - +
30B LEU* 1.3 57.5 + - - +
32B LYS* 3.3 6.5 + - - +
33B ASP* 2.9 35.4 + - - +
78B LYS* 3.9 10.5 + - - -
79B TRP* 3.1 33.7 + - - -
80B VAL* 5.0 2.6 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 6.2 2.7 - - - +
26B ARG* 3.0 41.7 + - + +
27B LEU 3.7 6.5 - - - +
29B GLU* 1.3 75.5 - - - +
31B ALA* 1.3 66.7 + - - +
33B ASP* 3.3 8.7 + - + +
34B TYR* 2.9 25.3 + - - +
186B VAL* 4.2 15.0 - - + -
213B VAL* 4.1 14.2 - - + +
214B ASN 4.6 13.2 - - - +
215B GLU* 4.1 28.7 - - + -
216B TRP 6.0 0.2 - - - +
755B XE 4.2 7.6 - - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.7 20.4 - - + -
27B LEU 3.0 18.1 + - - +
28B PHE 3.8 0.9 - - - +
30B LEU* 1.3 76.3 - - - +
32B LYS* 1.3 57.1 + - - +
34B TYR* 3.7 4.2 - - - +
35B MET* 2.8 36.4 + - - +
154B LEU* 3.8 11.2 - - + -
184B ILE* 3.7 28.7 - - + -
186B VAL* 4.3 4.5 - - + +
213B VAL* 4.8 0.7 - - - -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.1 1.3 - - - +
28B PHE 2.9 17.2 + - - +
29B GLU* 3.6 9.8 + - - +
31B ALA* 1.3 78.5 - - - +
33B ASP* 1.3 57.6 + - - +
35B MET* 3.8 0.2 - - - -
36B ASN* 2.8 60.8 + - - +
43B VAL* 3.8 30.3 - - + -
78B LYS* 5.9 0.2 - - - +
79B TRP* 3.4 56.5 - - + +
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Residues in contact with ASP 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY 4.8 2.9 - - - +
234A GLN* 3.3 28.5 - - + +
235A SER* 2.5 42.3 + - - +
26B ARG* 5.1 2.1 + - - -
29B GLU 2.9 18.6 + - - +
30B LEU* 3.8 9.4 - - + +
32B LYS* 1.3 78.4 - - - +
34B TYR* 1.3 54.1 + - - +
36B ASN* 3.7 3.7 + - - +
37B GLY* 2.7 33.8 + - - -
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Residues in contact with TYR 34 (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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30B LEU 2.9 17.9 + - - +
31B ALA 3.7 2.2 - - - +
33B ASP* 1.3 77.0 - - - +
35B MET* 1.3 81.8 + - + +
37B GLY* 3.2 2.1 + - - -
38B THR* 3.2 44.3 + - + +
40B ARG* 5.4 2.3 + - - -
184B ILE* 5.2 0.4 - - + -
211B HIS* 3.5 43.2 + - + +
212B VAL 4.6 11.4 + - - -
213B VAL* 3.6 31.4 - - + -
204E TRP* 6.4 2.0 - + - -
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Residues in contact with MET 35 (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 VAL* 4.8 11.0 - - + -
11B LEU* 4.8 1.3 - - + -
31B ALA 2.8 25.8 + - - +
34B TYR* 1.3 95.2 - - + +
36B ASN* 1.3 60.1 + - - +
38B THR* 2.9 25.2 + - - -
41B TYR* 3.5 57.4 + - + +
43B VAL* 3.7 20.6 - - + -
152B LYS* 4.9 4.9 - - - -
184B ILE* 3.6 38.1 - - + -
211B HIS* 4.4 11.4 - - + +
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Residues in contact with ASN 36 (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 LYS* 5.3 3.8 + - - -
32B LYS* 2.8 49.5 + - - +
33B ASP* 4.2 3.5 + - - +
35B MET* 1.3 72.4 - - - +
37B GLY* 1.3 62.3 + - - +
39B GLY* 3.3 13.2 + - - -
41B TYR 3.9 7.6 - - - +
42B THR* 3.4 10.9 - - - +
43B VAL* 2.9 32.1 + - - +
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Residues in contact with GLY 37 (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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33B ASP 2.7 19.3 + - - -
34B TYR* 3.6 2.7 - - - -
35B MET 3.2 0.4 - - - -
36B ASN* 1.3 74.1 - - - +
38B THR* 1.3 56.1 + - - +
39B GLY* 2.9 12.5 + - - -
207E ARG* 4.2 21.9 + - - -
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Residues in contact with THR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.2 44.5 + - + +
35B MET* 2.9 17.0 + - - +
37B GLY* 1.3 74.7 - - - +
39B GLY* 1.3 58.4 + - - +
40B ARG* 3.1 48.3 + - - +
41B TYR* 3.4 16.8 - - + -
211B HIS* 5.7 0.2 - - - +
207E ARG* 5.7 0.7 - - - +
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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