Contacts of the helix formed by residues 21 - 38 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 3.4 16.8 - - + +
20C ILE* 1.3 74.5 - - - +
22C ASN* 1.3 66.8 + - - +
23C MET* 3.1 14.4 + - - +
24C HIS* 3.0 33.1 + - + +
25C LEU* 3.5 13.9 + - - +
221C ILE* 3.4 34.2 + - - +
223C SER* 4.1 4.9 - - - +
226C ILE* 3.9 22.2 - - + -
239C LEU 3.9 1.8 - - - -
240C VAL* 3.8 10.5 - - + -
241C PRO* 4.6 3.6 - - - -
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Residues in contact with ASN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 1.3 75.5 - - - +
23C MET* 1.3 58.9 + - - +
25C LEU* 3.1 12.3 + - - +
26C ARG* 2.9 31.6 + - + +
221C ILE* 4.2 9.1 - - + +
238C TYR* 3.1 28.9 + - - +
239C LEU* 2.9 24.7 + - - +
240C VAL* 3.3 20.0 + - - +
241C PRO* 3.3 10.7 - - - +
22D ASN* 3.9 15.1 - - - +
219D ASN* 5.2 4.1 - - - +
238D TYR* 4.2 23.0 + - + +
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Residues in contact with MET 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR* 3.1 10.3 + - - +
22C ASN* 1.3 81.2 - - + +
24C HIS* 1.3 62.4 + - - +
26C ARG* 3.1 36.4 + - + +
27C LEU* 2.9 31.6 + - - +
30C LEU* 5.5 1.8 - - - -
215C GLU* 4.7 5.2 - - - +
217C ILE 5.2 2.9 - - - +
219C ASN* 3.2 42.0 - - + +
221C ILE* 4.2 15.0 - - + +
811C TAD 3.6 23.6 - - + +
219D ASN* 3.3 35.2 - - - +
238D TYR 5.8 0.2 - - - +
239D LEU* 4.7 7.4 - - + -
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Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PHE* 3.7 31.3 - + + -
19C PRO 3.8 7.2 - - - -
20C ILE* 3.5 18.6 - - + -
21C THR* 3.0 36.1 + - + +
23C MET* 1.3 77.0 - - - +
25C LEU* 1.3 63.4 + - - +
27C LEU* 3.2 24.2 - - + +
28C PHE* 3.5 13.9 - - - -
48C ILE* 5.6 0.4 - - + -
221C ILE 5.5 0.2 - - - -
222C SER* 6.3 0.2 - - - -
223C SER* 3.5 25.8 - - - -
811C TAD 3.3 54.8 + + - -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ILE* 3.9 17.9 - - + -
21C THR 3.8 12.8 - - - +
22C ASN* 3.1 7.7 + - - +
24C HIS* 1.3 73.9 - - - +
26C ARG* 1.3 67.0 + - - +
28C PHE* 3.2 17.6 + - - +
29C GLU* 3.4 14.6 + - - +
48C ILE* 4.1 5.4 - - + -
73C ALA* 4.0 9.6 - - + +
74C THR* 3.8 28.3 - - + -
80C VAL* 5.4 3.6 - - + -
241C PRO* 3.6 32.1 - - + -
238D TYR* 3.5 44.9 - - + +
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Residues in contact with ARG 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASN 2.9 17.6 + - - +
23C MET* 3.3 40.3 - - + +
25C LEU* 1.3 74.3 - - - +
27C LEU* 1.3 66.2 + - - +
29C GLU* 2.9 34.1 + - - +
30C LEU* 2.9 49.5 + - + +
215C GLU* 5.7 1.8 + - - -
217C ILE* 4.6 10.1 - - - +
235D SER 3.2 25.9 + - - -
237D ARG 3.2 28.3 + - - -
238D TYR* 4.0 7.0 - - + +
239D LEU* 3.4 39.6 - - + +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 5.5 4.7 - - + -
17C PHE* 6.3 0.4 - - + -
23C MET* 2.9 19.4 + - - +
24C HIS* 3.2 21.5 - - + +
25C LEU 3.2 0.2 - - - -
26C ARG* 1.3 75.5 - - - +
28C PHE* 1.3 57.7 + - - +
30C LEU* 3.5 7.6 + - + +
31C ALA* 3.0 31.5 + - - +
154C LEU* 3.9 26.8 - - + +
155C CYS* 4.7 8.3 - - - +
186C VAL* 4.1 19.0 - - + +
811C TAD 3.5 66.0 - - + +
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Residues in contact with PHE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.7 11.2 - - + -
13C ALA* 3.6 24.0 - - + -
17C PHE* 5.8 1.6 - + - -
24C HIS 3.5 18.2 - - - -
25C LEU* 3.2 12.4 + - + +
26C ARG 3.1 0.8 - - - -
27C LEU* 1.3 77.4 - - + +
29C GLU* 1.3 62.1 + - - +
31C ALA* 4.0 0.8 - - - +
32C LYS* 2.9 33.1 + - - +
46C GLY* 3.6 15.7 - - - -
47C ILE 3.5 39.3 - - - -
48C ILE* 3.6 25.4 - - + -
79C TRP* 3.2 22.7 - + + -
80C VAL* 4.0 15.9 - - + -
154C LEU* 3.7 18.8 - - + -
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU 3.6 12.9 - - - +
26C ARG* 2.9 24.3 + - - +
28C PHE* 1.3 77.3 - - - +
30C LEU* 1.3 64.5 + - - +
32C LYS* 3.7 3.2 - - - +
33C ASP* 3.0 30.7 + - - -
77C SER* 5.4 0.2 + - - -
78C LYS* 4.3 6.6 + - - -
79C TRP* 3.4 33.6 + - - -
80C VAL* 4.7 2.8 - - - +
235D SER* 2.7 32.8 + - - +
237D ARG* 3.7 16.3 - - - +
238D TYR* 3.9 23.2 - - + -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C MET* 5.5 1.8 - - - -
26C ARG* 2.9 53.4 + - + +
27C LEU* 3.8 5.4 - - + +
29C GLU* 1.3 76.2 - - - +
31C ALA* 1.3 58.5 + - - +
33C ASP* 3.2 8.6 + - + +
34C TYR* 2.8 29.8 + - - +
186C VAL* 4.0 23.6 - - + -
213C VAL* 4.2 14.6 - - + +
214C ASN 4.3 16.4 - - - +
215C GLU* 4.0 23.1 - - + +
216C TRP 5.8 0.2 - - - +
217C ILE* 6.2 2.5 - - + -
234D GLN* 5.8 5.8 - - - +
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Residues in contact with ALA 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.7 21.3 - - + -
27C LEU 3.0 15.9 + - - +
28C PHE 4.0 0.2 - - - +
30C LEU* 1.3 78.9 - - - +
32C LYS* 1.3 57.5 + - - +
34C TYR* 3.7 6.0 - - - +
35C MET* 2.9 34.7 + - - +
154C LEU* 3.9 10.1 - - + -
184C ILE* 3.8 25.4 - - + -
186C VAL* 4.8 1.8 - - + +
213C VAL* 4.6 3.1 - - - +
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Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.1 1.5 - - - +
28C PHE 2.9 19.4 + - - +
29C GLU* 3.7 5.4 - - - +
31C ALA* 1.3 78.8 - - - +
33C ASP* 1.3 67.5 + - - +
35C MET* 4.0 0.3 - - - +
36C ASN* 2.9 46.3 + - - +
43C VAL* 3.9 29.9 + - + -
79C TRP* 3.6 55.5 - - + +
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 5.0 1.9 + - - -
29C GLU 3.0 18.2 + - - +
30C LEU* 3.6 9.1 - - + +
32C LYS* 1.3 79.4 - - - +
34C TYR* 1.3 54.9 + - - +
36C ASN* 3.8 3.0 - - - +
37C GLY* 2.7 32.9 + - - -
233D GLY 4.5 3.9 - - - +
234D GLN* 3.4 29.2 + - + +
235D SER* 2.8 37.3 + - - +
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Residues in contact with TYR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A TRP* 6.3 3.4 - + - -
207A ARG* 5.3 6.1 + - - +
30C LEU 2.8 16.6 + - - +
31C ALA 3.7 2.7 - - - +
33C ASP* 1.3 76.7 - - - +
35C MET* 1.3 82.4 + - + +
37C GLY* 3.0 3.3 + - - -
38C THR* 3.0 43.9 + - + +
40C ARG* 5.6 2.3 + - - -
211C HIS* 3.7 31.5 + - + +
212C VAL 4.2 15.8 + - - -
213C VAL* 3.6 35.2 - - + -
214C ASN 5.7 0.2 - - - -
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Residues in contact with MET 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C VAL* 4.3 9.9 - - + -
11C LEU* 4.8 0.4 - - + -
31C ALA 2.9 25.5 + - - +
34C TYR* 1.3 96.2 - - + +
36C ASN* 1.3 59.2 + - - +
38C THR* 2.9 26.2 + - - -
41C TYR* 3.4 60.5 - - + +
43C VAL* 3.7 21.3 - - + -
152C LYS* 5.0 3.1 - - - -
184C ILE* 3.8 35.2 - - + -
211C HIS* 4.1 18.2 - - + +
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C LYS* 5.0 3.6 + - - -
32C LYS* 2.9 46.5 + - - +
33C ASP* 4.3 2.2 - - - +
35C MET* 1.3 76.8 - - - +
37C GLY* 1.3 63.3 + - - +
39C GLY* 3.1 14.7 + - - -
41C TYR 3.4 7.7 - - - +
42C THR* 3.3 12.2 - - - +
43C VAL* 2.8 32.3 + - - +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.8 25.7 + - - -
208A SER* 6.1 1.0 - - - -
33C ASP 2.7 19.7 + - - -
34C TYR 3.0 2.4 + - - -
36C ASN* 1.3 79.7 - - - +
38C THR* 1.3 60.3 + - - +
39C GLY* 2.9 3.0 + - - -
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 5.6 6.8 - - - -
34C TYR* 3.0 43.3 + - + +
35C MET* 2.9 16.0 + - - +
37C GLY* 1.3 75.1 - - - +
39C GLY* 1.3 56.4 + - - +
40C ARG* 2.8 52.0 + - - +
41C TYR* 3.5 14.8 - - + -
211C HIS* 5.9 0.4 - - - +
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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
------------------------------------------------------------
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