Contacts of the helix formed by residues 21 - 38 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO 3.5 11.4 - - - +
20A ILE* 1.3 79.6 - - - +
22A ASN* 1.3 64.2 + - - +
23A MET* 3.1 13.0 + - - +
24A HIS* 2.9 29.1 + - + +
25A LEU* 3.4 13.0 + - - +
221A ILE* 3.2 24.5 + - - +
223A SER* 4.3 5.8 - - - +
226A ILE* 3.8 29.4 - - + -
239A LEU 3.7 8.5 - - - -
240A VAL* 3.9 10.1 - - + -
241A PRO* 4.5 6.1 - - - -
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 1.3 74.7 - - - +
23A MET* 1.3 62.2 + - + +
25A LEU* 3.1 11.5 + - - +
26A ARG* 2.8 30.5 + - + +
221A ILE* 4.3 9.5 - - + +
238A TYR* 3.1 28.5 + - - +
239A LEU* 3.0 21.2 + - - +
240A VAL 3.4 1.8 + - - +
241A PRO* 3.4 27.9 - - - +
22B ASN* 4.0 14.6 - - - +
219B ASN* 5.9 0.6 - - - +
238B TYR* 4.1 21.1 + - + +
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Residues in contact with MET 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.1 10.7 + - - +
22A ASN* 1.3 81.4 - - + +
24A HIS* 1.3 63.8 + - + +
26A ARG* 3.0 22.2 + - + +
27A LEU* 2.8 33.6 + - + +
215A GLU* 3.3 20.4 - - - +
219A ASN* 2.7 56.3 - - + +
221A ILE* 3.9 23.6 - - + +
809A TAD 3.7 35.0 - - + +
219B ASN* 4.2 2.2 - - - +
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 3.5 28.9 - + + -
19A PRO 3.8 1.2 + - - -
20A ILE* 3.5 20.6 - - + -
21A THR* 2.9 44.3 + - - +
23A MET* 1.3 77.2 - - + +
25A LEU* 1.3 63.6 + - - +
27A LEU* 3.3 24.5 - - - +
28A PHE* 3.3 14.9 - - + -
48A ILE* 5.4 1.3 - - + -
221A ILE 5.3 1.2 + - - -
223A SER* 3.4 21.3 + - - -
809A TAD 3.8 55.2 + + - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.5 3.6 - - + -
21A THR 3.4 10.3 + - - +
22A ASN* 3.1 9.1 + - - +
23A MET 3.1 0.8 - - - -
24A HIS* 1.3 75.8 - - - +
26A ARG* 1.3 63.6 + - - +
28A PHE* 3.1 18.6 + - + +
29A GLU* 3.4 13.2 + - - +
48A ILE* 4.4 12.6 - - + -
73A ALA* 3.9 15.5 - - + +
74A THR* 3.8 28.7 - - + -
77A SER* 6.2 0.2 - - - -
80A VAL* 5.3 5.4 - - + -
241A PRO* 3.5 33.7 - - + -
238B TYR* 3.7 44.7 - - + +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN 2.8 17.2 + - - +
23A MET* 3.4 34.8 - - + +
25A LEU* 1.3 72.9 - - - +
27A LEU* 1.3 68.6 + - - +
29A GLU* 2.9 20.6 + - - +
30A LEU* 2.9 65.1 + - + +
215A GLU* 5.6 0.2 + - - -
217A ILE* 4.5 10.5 - - - +
219A ASN* 4.2 3.8 + - - +
235B SER* 3.2 26.7 + - - -
237B ARG 3.2 28.3 + - - -
238B TYR* 4.1 9.4 - - + +
239B LEU* 3.5 34.7 - - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET* 2.8 20.9 + - - +
24A HIS* 3.3 25.1 - - - +
25A LEU 3.2 0.2 - - - -
26A ARG* 1.3 76.7 - - - +
28A PHE* 1.3 57.9 + - + +
30A LEU* 3.9 5.2 - - + +
31A ALA* 3.1 31.2 + - - +
154A LEU* 3.9 21.4 - - + +
155A CYS* 5.0 5.6 - - - +
186A VAL* 3.8 24.3 - - + +
809A TAD 3.5 64.2 - - + +
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Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.8 12.3 - - + -
13A ALA* 3.5 27.6 - - + -
17A PHE* 5.7 1.1 - + - -
24A HIS* 3.3 20.9 - - + -
25A LEU* 3.1 12.8 + - + +
26A ARG 3.1 0.4 - - - -
27A LEU* 1.3 76.4 - - + +
29A GLU* 1.3 67.9 - - - +
31A ALA* 3.9 1.4 - - - +
32A LYS* 2.9 26.7 + - - +
46A GLY* 3.8 8.1 - - - -
47A ILE 3.6 30.7 - - - -
48A ILE* 3.6 27.1 - - + -
79A TRP* 3.4 29.7 - + + -
80A VAL* 4.0 14.1 - - + -
154A LEU* 3.6 20.9 - - + -
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU 3.7 12.2 - - - +
26A ARG* 2.9 26.8 + - - +
28A PHE* 1.3 78.3 - - - +
30A LEU* 1.3 63.0 + - - +
32A LYS* 3.6 5.9 - - - +
33A ASP* 3.0 29.9 + - - +
78A LYS* 4.0 9.6 + - - -
79A TRP* 3.5 26.7 + - - -
80A VAL* 5.2 1.0 - - - +
235B SER* 2.5 34.2 + - - +
237B ARG* 3.6 13.1 - - - +
238B TYR* 4.0 21.3 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.9 56.3 + - + +
27A LEU* 3.9 3.1 - - + +
29A GLU* 1.3 73.9 - - - +
31A ALA* 1.3 57.6 + - - +
33A ASP* 3.4 6.3 + - + +
34A TYR* 2.9 30.6 + - - +
186A VAL* 3.9 24.0 - - + -
213A VAL* 4.1 8.7 - - + +
214A ASN 4.6 13.2 - - - +
215A GLU* 3.3 34.3 - - + +
216A TRP 5.8 0.7 - - - +
217A ILE* 6.0 2.2 - - + -
234B GLN* 6.1 2.9 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 16.6 - - + -
27A LEU 3.1 17.4 + - - +
28A PHE 3.9 2.9 - - - +
30A LEU* 1.3 76.5 - - - +
32A LYS* 1.3 60.8 + - - +
34A TYR* 3.7 5.6 - - - +
35A MET* 2.8 35.4 + - - +
154A LEU* 4.0 9.9 - - + -
184A ILE* 3.8 26.7 - - + -
186A VAL* 4.6 2.2 - - + +
213A VAL* 4.8 3.4 - - - -
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.3 0.9 - - - +
28A PHE 2.9 17.5 + - - +
29A GLU* 3.6 5.4 - - - +
31A ALA* 1.3 75.4 - - - +
33A ASP* 1.3 72.4 - - - +
35A MET* 4.1 0.2 - - - +
36A ASN* 2.9 49.7 + - - +
43A VAL* 4.1 25.7 + - + -
79A TRP* 3.5 63.3 - - + +
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 3.0 18.5 + - - +
30A LEU* 3.7 6.8 - - + +
32A LYS* 1.3 79.5 - - - +
34A TYR* 1.3 58.6 + - - +
36A ASN* 3.8 3.6 + - - +
37A GLY* 2.8 29.3 + - - -
233B GLY 4.7 3.2 - - - +
234B GLN* 3.3 28.1 + - + +
235B SER* 2.7 39.1 + - - +
207C ARG* 5.3 1.2 + - - -
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Residues in contact with TYR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.9 18.5 + - - +
31A ALA 3.7 3.1 - - - +
32A LYS 3.1 0.2 - - - -
33A ASP* 1.3 76.9 - - - +
35A MET* 1.3 81.3 + - + +
37A GLY* 3.1 11.9 + - - -
38A THR* 3.2 34.2 + - + +
40A ARG* 5.5 2.6 + - - -
211A HIS* 3.9 30.3 + - + +
212A VAL 4.2 17.3 + - - -
213A VAL* 3.6 33.7 - - + -
214A ASN 5.7 0.7 - - - -
204C TRP* 6.2 3.8 - + - -
207C ARG* 6.1 4.3 - - - +
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Residues in contact with MET 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 4.4 9.4 - - + -
11A LEU* 4.8 0.4 - - + -
31A ALA 2.8 25.3 + - - +
34A TYR* 1.3 93.3 - - + +
36A ASN* 1.3 60.3 + - - +
38A THR* 2.8 27.0 + - - -
41A TYR* 3.5 56.9 + - + +
43A VAL* 3.6 22.7 - - + -
152A LYS* 5.0 3.4 - - - -
184A ILE* 3.8 35.4 - - + -
211A HIS* 4.0 20.6 - - + +
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Residues in contact with ASN 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS* 5.3 3.5 + - - -
32A LYS* 2.9 48.1 + - - +
33A ASP* 4.1 4.0 + - - +
35A MET* 1.3 73.2 - - - +
37A GLY* 1.3 62.7 + - - +
39A GLY* 3.2 14.0 + - - -
41A TYR 3.7 8.3 - - - +
42A THR* 3.4 11.0 - - - +
43A VAL* 2.9 32.4 + - - +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP 2.8 23.0 + - - -
34A TYR 3.1 3.1 + - - -
36A ASN* 1.3 72.4 - - - +
38A THR* 1.3 61.5 + - - +
39A GLY* 3.1 2.3 + - - -
207C ARG* 3.9 26.3 + - - -
208C SER* 5.9 2.8 - - - -
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Residues in contact with THR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A TYR* 3.2 41.0 + - + +
35A MET* 2.8 16.9 + - - +
37A GLY* 1.3 76.8 - - - +
39A GLY* 1.3 56.4 + - - +
40A ARG* 2.9 54.0 + - - +
41A TYR* 3.5 14.1 - - + -
211A HIS* 6.0 0.2 - - - +
208C SER* 5.7 7.2 - - - -
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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
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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