Contacts of the helix formed by residues 21 - 38 (chain D) in PDB entry 1KR2
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PRO* 3.6 11.2 - - + +
20D ILE* 1.3 81.9 - - - +
22D ASN* 1.3 66.2 + - - +
23D MET* 2.9 15.5 + - - +
24D HIS* 2.9 28.1 + - + +
25D LEU* 3.5 12.1 + - - +
221D ILE* 3.0 29.7 + - - +
223D SER* 4.3 3.6 - - - +
226D ILE* 3.7 25.8 - - + -
239D LEU 3.6 12.1 - - - -
240D VAL* 4.0 6.3 - - + +
241D PRO* 4.5 5.2 - - - -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ASN* 3.9 14.3 - - - +
238C TYR* 3.9 28.1 - - + +
21D THR* 1.3 71.4 - - - +
23D MET* 1.3 57.9 + - - +
25D LEU* 3.3 9.2 + - - +
26D ARG* 2.9 29.8 + - - +
219D ASN* 5.9 0.6 - - - +
221D ILE* 4.4 8.6 - - + +
238D TYR* 3.2 27.7 + - - +
239D LEU* 3.0 24.3 + - - +
240D VAL* 3.6 3.6 + - - +
241D PRO* 3.2 28.4 - - - +
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Residues in contact with MET 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D THR* 2.9 9.7 + - - +
22D ASN* 1.3 78.8 - - - +
24D HIS* 1.3 79.8 + - - +
26D ARG* 3.3 7.7 + - + +
27D LEU* 3.0 24.1 + - + +
219D ASN 3.6 25.4 - - - +
220D ASP* 4.5 0.4 - - - +
221D ILE* 3.3 35.9 - - + +
222D SER* 4.2 5.8 - - - -
223D SER 5.3 0.2 - - - +
812D TAD 2.7 70.9 - - + +
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Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PHE* 3.8 28.0 - + + -
19D PRO 3.5 9.6 - - - -
20D ILE* 3.4 17.4 - - + -
21D THR* 2.9 36.9 + - + +
23D MET* 1.3 93.6 - - + +
25D LEU* 1.3 58.7 + - - +
27D LEU* 3.1 25.4 - - + +
28D PHE* 3.4 16.0 - - - -
48D ILE* 5.8 0.4 - - + -
223D SER* 3.3 24.8 + - - -
812D TAD 3.4 44.3 + - - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 3.5 46.4 - - + +
20D ILE* 3.8 22.9 - - + -
21D THR 3.9 10.3 - - - +
22D ASN* 3.3 5.7 + - - +
23D MET 3.2 0.4 - - - -
24D HIS* 1.3 73.9 - - - +
26D ARG* 1.3 65.7 + - - +
27D LEU 3.1 1.6 - - - -
28D PHE* 3.1 17.0 + - - +
29D GLU* 3.2 14.0 + - - +
48D ILE* 4.2 6.7 - - + -
73D ALA* 3.8 12.1 - - + +
74D THR* 4.2 21.1 - - + -
77D SER* 6.4 0.2 - - - -
80D VAL* 5.2 5.4 - - + -
241D PRO* 3.7 28.5 - - + -
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C GLN* 5.6 3.8 + - - +
235C SER* 2.7 34.8 + - - -
236C ILE* 4.1 1.4 - - - +
237C ARG 3.9 10.3 + - - -
238C TYR* 4.0 11.6 - - + +
239C LEU* 3.4 41.6 - - + +
22D ASN 2.9 17.9 + - - +
23D MET* 3.7 9.4 - - + +
25D LEU* 1.3 75.6 - - - +
27D LEU* 1.3 64.3 + - - +
29D GLU* 2.9 11.1 + - - +
30D LEU* 2.8 46.5 + - + +
33D ASP* 5.4 1.2 + - - -
215D GLU* 3.1 38.7 + - - +
217D ILE* 4.1 11.1 - - - +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ALA* 5.7 4.0 - - + -
17D PHE* 6.6 0.2 - - + -
23D MET* 3.0 14.3 + - + +
24D HIS* 3.1 22.2 - - + +
26D ARG* 1.3 77.7 - - - +
28D PHE* 1.3 62.5 + - + +
30D LEU* 3.5 4.9 + - - +
31D ALA* 3.1 24.4 + - - +
154D LEU* 4.2 19.6 - - + +
155D CYS* 4.8 8.1 - - - +
186D VAL* 3.7 28.5 - - + +
812D TAD 3.3 64.4 - - + +
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Residues in contact with PHE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 3.7 27.8 - - + -
13D ALA* 3.4 30.3 - - + -
17D PHE* 5.5 2.7 - + - -
24D HIS 3.4 23.8 - - - -
25D LEU* 3.1 11.6 + - - +
27D LEU* 1.3 77.2 - - + +
29D GLU* 1.3 67.5 + - - +
31D ALA* 3.3 2.7 + - - +
32D LYS* 2.9 26.2 + - - +
46D GLY* 4.0 13.9 - - - -
47D ILE 3.6 11.9 - - - -
48D ILE* 3.4 32.3 - - + -
79D TRP* 3.4 21.6 - + + -
80D VAL* 4.0 16.2 - - + -
154D LEU* 3.7 20.2 - - + -
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C SER* 3.1 35.6 + - - +
237C ARG* 4.3 4.4 - - + +
238C TYR* 3.8 24.0 + - + -
25D LEU 3.2 11.0 + - - +
26D ARG* 2.9 17.6 + - - +
28D PHE* 1.3 79.0 - - - +
30D LEU* 1.3 61.9 + - - +
32D LYS* 3.3 6.1 + - - +
33D ASP* 3.0 29.3 + - - -
77D SER* 5.3 0.2 + - - -
78D LYS* 3.3 17.7 + - - -
79D TRP* 3.1 32.0 + - - -
80D VAL* 4.9 3.1 - - - +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLN* 6.4 1.8 - - - -
26D ARG* 2.8 39.9 + - + +
27D LEU* 3.8 4.5 - - - +
29D GLU* 1.3 77.4 - - - +
31D ALA* 1.3 62.7 + - - +
33D ASP* 3.3 8.7 + - + +
34D TYR* 3.0 23.4 + - - +
186D VAL* 3.8 19.1 - - + -
213D VAL* 4.2 10.1 - - + -
214D ASN 4.1 15.7 - - - +
215D GLU* 2.8 50.0 - - + +
216D TRP 5.7 0.2 - - - +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.7 21.8 - - + -
27D LEU 3.1 15.9 + - - +
28D PHE 3.8 0.2 - - - +
30D LEU* 1.3 79.0 - - - +
32D LYS* 1.3 57.8 + - - +
34D TYR* 3.2 5.8 + - - +
35D MET* 2.8 36.2 + - - +
154D LEU* 3.9 9.9 - - + -
184D ILE* 3.8 26.2 - - + -
186D VAL* 4.3 5.3 - - + +
213D VAL* 4.8 1.1 - - - -
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Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.2 1.5 - - - +
28D PHE 2.9 18.7 + - - +
29D GLU* 3.6 8.5 - - - +
31D ALA* 1.3 78.5 - - - +
33D ASP* 1.3 68.6 + - - +
36D ASN* 3.0 47.4 + - - +
43D VAL* 4.0 27.0 + - + -
79D TRP* 3.5 58.1 - - + +
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Residues in contact with ASP 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C GLY 4.7 4.1 - - - +
234C GLN* 3.3 22.8 - - + +
235C SER* 2.6 39.7 + - - +
26D ARG* 5.4 1.2 + - - -
29D GLU 3.0 19.1 + - - +
30D LEU* 3.7 9.3 - - + +
32D LYS* 1.3 80.8 - - - +
34D TYR* 1.3 58.6 + - - +
36D ASN* 4.2 4.0 + - - +
37D GLY* 2.8 28.2 + - - -
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Residues in contact with TYR 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.0 18.1 + - + +
31D ALA 3.6 2.7 - - - +
33D ASP* 1.3 74.7 - - - +
35D MET* 1.3 87.8 + - + +
37D GLY* 3.0 11.2 + - - -
38D THR* 3.2 34.0 + - + +
40D ARG* 5.8 0.7 + - - -
211D HIS* 3.9 35.9 + - + +
212D VAL 4.6 9.8 + - - -
213D VAL* 3.5 36.3 - - + -
214D ASN 5.8 0.2 - - - -
207F ARG* 6.5 0.7 - - - -
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Residues in contact with MET 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.5 10.5 - - + -
11D LEU* 4.7 2.9 - - + -
31D ALA 2.8 26.2 + - - +
34D TYR* 1.3 95.9 - - + +
36D ASN* 1.3 59.5 + - - +
38D THR* 2.8 26.5 + - - -
41D TYR* 3.5 58.0 + - + +
43D VAL* 3.7 22.0 - - + -
152D LYS* 4.8 4.5 - - - -
184D ILE* 4.1 37.9 - - + -
211D HIS* 4.2 13.7 - - + +
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Residues in contact with ASN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LYS* 5.3 2.8 + - - -
32D LYS* 3.0 45.8 + - - +
33D ASP* 4.2 3.5 + - - +
35D MET* 1.3 75.0 - - - +
37D GLY* 1.3 64.9 + - - +
39D GLY* 3.0 17.0 + - - -
41D TYR 3.7 8.7 - - - +
42D THR* 3.4 10.0 - - - +
43D VAL* 2.9 33.2 + - - +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ASP 2.8 20.8 + - - -
34D TYR* 3.0 4.0 + - - -
36D ASN* 1.3 78.4 - - - +
38D THR* 1.3 59.6 + - - +
39D GLY* 3.1 2.2 + - - -
207F ARG* 4.3 21.4 + - - -
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Residues in contact with THR 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D TYR* 3.2 42.1 + - + +
35D MET* 2.8 17.2 + - - +
37D GLY* 1.3 76.0 - - - +
39D GLY* 1.3 55.6 + - - +
40D ARG* 3.0 50.2 + - - +
41D TYR* 3.4 13.4 - - + -
211D HIS* 5.9 0.4 - - - +
208F SER* 5.8 4.4 - - - -
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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
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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