Contacts of the helix formed by residues 14 - 34 (chain C) in PDB entry 1RG9
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 HIS 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 18.2 - - + +
11C SER* 3.0 19.4 + - - +
12C GLU 3.3 0.2 - - - -
13C GLY* 1.3 77.2 - - - +
15C PRO* 1.3 72.2 - - + +
16C ASP* 3.1 41.1 + - + +
17C LYS* 2.8 16.2 + - + -
18C ILE* 2.8 11.9 + - - -
163C ASP* 3.6 5.4 - - - +
164C ALA 4.4 0.9 - - - +
165C LYS* 3.7 17.4 - - + +
238C ASP* 4.6 1.1 - - - -
245C LYS* 3.8 8.7 - - - +
584C PPK 2.9 40.8 + - - -
585C SAM 3.0 34.1 + - - -
588C MG 4.4 0.2 - - - -
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Residues in contact with PRO 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLY 3.6 4.9 - - - +
14C HIS* 1.3 90.0 - - + +
16C ASP* 1.3 64.0 + - - +
18C ILE* 3.0 23.9 + - + +
19C ALA 3.1 9.5 + - - -
45C VAL* 4.8 2.0 - - + +
163C ASP* 3.8 11.2 - - - +
234C GLY* 3.7 19.5 - - - +
235C PRO* 4.6 4.3 - - + -
238C ASP* 3.0 30.5 - - + +
239C CYS 3.9 2.5 - - - +
240C GLY* 3.3 23.2 - - - +
585C SAM 3.6 17.3 - - - +
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Residues in contact with ASP 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C HIS* 3.1 14.0 + - + +
15C PRO* 1.3 76.8 - - - +
17C LYS* 1.3 64.7 + - - +
19C ALA* 3.0 20.1 + - - +
20C ASP* 3.2 8.2 + - - +
239C CYS 3.7 0.9 - - - +
240C GLY* 3.6 3.1 - - - -
241C LEU* 2.9 34.5 + - - +
244C ARG* 3.7 15.1 - - + +
245C LYS* 2.8 23.8 + - + -
584C PPK 2.7 12.8 + - - -
588C MG 2.1 31.7 - - - -
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Residues in contact with LYS 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 3.7 24.2 - - + +
11C SER 3.7 15.7 - - - +
12C GLU 4.3 0.7 - - - +
14C HIS* 2.8 16.0 + - + +
16C ASP* 1.3 73.5 - - - +
18C ILE* 1.3 58.8 + - - +
20C ASP* 3.1 13.4 + - - +
21C GLN* 2.7 43.9 + - - +
245C LYS* 3.8 24.9 - - + -
248C VAL* 4.4 5.9 - - - +
249C ASP* 2.5 31.2 + - - -
355C ALA* 2.6 34.0 + - - +
356C ALA* 3.7 12.3 - - + +
357C TYR 4.2 4.9 - - - +
358C GLY 4.9 1.2 - - - +
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU 4.0 13.0 - - - +
13C GLY 3.8 17.5 - - - +
14C HIS 2.8 13.5 + - - +
15C PRO* 3.0 18.6 + - + +
17C LYS* 1.3 75.1 - - - +
19C ALA* 1.3 65.7 + - - +
21C GLN* 3.3 7.6 + - - +
22C ILE* 2.9 35.8 + - + +
45C VAL* 4.3 15.5 - - + -
72C VAL* 4.0 26.9 - - + -
75C ILE* 4.1 12.8 - - + -
77C TYR* 4.0 20.9 - - + -
84C PHE* 6.0 1.1 - - + -
235C PRO* 4.2 17.0 - - + -
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Residues in contact with ALA 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PRO 3.1 5.8 + - - +
16C ASP 3.0 12.0 + - - +
18C ILE* 1.3 78.7 - - - +
20C ASP* 1.3 53.5 + - - +
22C ILE* 2.8 7.4 + - - +
23C SER* 2.6 33.8 + - - -
43C THR* 3.7 13.6 + - - +
45C VAL* 4.2 13.6 - - + +
241C LEU* 3.4 30.1 - - - +
242C THR* 3.5 12.8 - - - +
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Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ASP* 3.2 8.7 + - - +
17C LYS* 3.1 23.0 + - - +
19C ALA* 1.3 77.3 - - - +
21C GLN* 1.3 55.1 + - - +
23C SER* 3.1 4.0 + - - -
24C ASP* 2.7 37.8 + - - +
241C LEU 5.2 0.2 - - - -
242C THR* 3.4 2.5 + - - +
243C GLY* 3.0 30.6 + - - -
244C ARG 5.1 0.2 + - - -
245C LYS* 4.5 6.1 + - - +
249C ASP* 3.6 18.5 - - - +
263C SER* 3.3 30.1 - - - +
355C ALA* 3.9 13.9 - - - +
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Residues in contact with GLN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU* 2.9 51.1 + - - +
17C LYS* 2.7 27.8 + - - +
18C ILE* 3.6 4.7 - - - +
20C ASP* 1.3 72.1 - - - +
22C ILE* 1.3 53.4 - - - +
24C ASP* 3.6 0.9 - - - +
25C ALA* 2.7 38.2 + - - +
71C THR* 4.1 15.6 - - + +
75C ILE* 3.8 12.3 - - + +
352C LYS* 4.2 13.5 - - + +
355C ALA* 3.6 20.7 - - + +
356C ALA* 3.9 17.3 + - - +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 2.9 28.7 + - + +
19C ALA* 2.8 12.3 + - - +
21C GLN* 1.3 70.8 - - - +
23C SER* 1.3 64.8 + - - +
25C ALA* 2.9 17.6 + - + +
26C VAL* 3.0 17.0 + - + +
43C THR* 3.9 19.7 - - + +
45C VAL* 5.0 0.7 - - + -
50C VAL* 3.6 14.8 - - + -
52C VAL* 4.2 10.8 - - + -
67C ILE* 5.7 0.4 - - + -
68C THR* 3.5 43.1 - - + +
71C THR* 4.1 13.7 - - + -
72C VAL* 4.1 18.2 - - + -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA 2.6 12.0 + - - -
20C ASP* 3.4 9.6 - - - -
22C ILE* 1.3 77.6 - - - +
24C ASP* 1.3 59.5 + - - +
26C VAL* 3.2 11.3 + - - +
27C LEU* 3.3 11.8 + - - +
41C CYS* 3.1 29.1 + - - +
43C THR* 2.7 23.5 + - - -
242C THR* 2.9 19.0 + - - -
263C SER 4.2 3.6 - - - -
264C GLY* 3.9 16.8 - - - -
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Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ASP 2.7 15.8 + - - +
21C GLN 4.2 0.7 - - - +
23C SER* 1.3 72.2 - - - +
25C ALA* 1.3 63.2 + - - +
26C VAL 3.3 0.2 - - - -
27C LEU* 3.9 9.2 - - - +
28C ASP* 3.2 28.9 + - - +
263C SER* 2.9 22.1 + - - -
264C GLY* 2.6 24.9 + - - -
272C ARG* 2.6 38.1 + - - -
351C TYR* 3.7 9.7 - - - +
352C LYS* 3.8 20.2 - - - +
354C THR* 3.8 2.1 - - - +
355C ALA* 4.1 3.6 - - + +
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLN 2.7 22.9 + - - +
22C ILE* 2.9 8.0 + - - +
24C ASP* 1.3 75.1 - - - +
26C VAL* 1.3 62.8 + - - +
28C ASP* 3.7 2.7 + - - +
29C ALA* 3.2 22.0 + - - +
67C ILE* 3.8 13.5 - - + +
71C THR* 3.3 25.4 - - - +
352C LYS* 3.8 20.4 - - + +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.0 16.8 + - + +
23C SER 3.6 7.9 - - - +
25C ALA* 1.3 74.5 - - - +
27C LEU* 1.3 62.2 + - - +
29C ALA* 3.3 5.7 + - - +
30C ILE* 2.9 48.1 + - + +
39C VAL* 5.1 0.2 - - + -
41C CYS* 4.5 9.9 - - + -
52C VAL* 4.3 21.1 - - + -
56C ILE* 4.1 14.8 - - + -
62C VAL* 5.3 1.1 - - + -
64C ILE* 4.3 25.4 - - + -
67C ILE* 4.0 20.6 - - + +
68C THR* 5.2 0.4 - - - +
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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
----------------------------------------------------------
23C SER 3.3 9.0 + - - +
24C ASP* 3.9 17.5 - - - +
25C ALA 3.4 0.4 - - - -
26C VAL* 1.3 80.1 - - - +
28C ASP* 1.3 51.2 + - - +
30C ILE* 3.0 6.8 + - - +
31C LEU* 2.6 54.7 + - + +
39C VAL* 3.5 42.6 - - + +
264C GLY 4.9 2.2 - - - +
265C LYS 3.9 15.0 - - - +
266C ASP* 3.8 18.6 - - + +
351C TYR* 3.4 39.3 - - + -
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Residues in contact with ASP 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP 3.2 14.7 + - - +
25C ALA* 3.8 5.6 - - - +
27C LEU* 1.3 78.3 - - - +
29C ALA* 1.3 65.6 + - - +
31C LEU* 3.1 1.1 + - - -
32C GLU* 2.8 23.7 + - - +
349C PRO* 3.1 42.8 - - + +
350C ILE 3.2 0.9 + - - -
351C TYR* 3.1 23.4 + - - +
352C LYS* 2.9 32.1 + - + +
353C GLU 4.6 0.2 + - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA 3.2 8.8 + - - +
26C VAL 3.5 7.6 - - - +
27C LEU 3.3 0.2 - - - -
28C ASP* 1.3 79.4 - - - +
30C ILE* 1.3 65.9 + - - +
32C GLU* 3.4 16.8 + - - +
33C GLN* 3.6 7.8 + - - +
62C VAL* 4.1 10.6 - - + +
67C ILE* 3.5 32.5 - - + -
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Residues in contact with ILE 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL* 2.9 24.6 + - + +
27C LEU* 3.3 8.3 - - - +
29C ALA* 1.3 76.0 - - - +
31C LEU* 1.3 63.7 + - + +
33C GLN* 2.8 9.0 + - - +
34C ASP 2.8 17.5 + - - -
37C ALA* 3.6 28.3 - - + -
39C VAL* 3.8 13.2 - - + -
56C ILE* 3.6 43.3 - - + -
58C THR* 3.6 18.2 - - + +
60C ALA* 3.7 2.8 - - + +
62C VAL* 3.9 29.6 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.6 56.4 + - + +
28C ASP 3.7 3.6 - - - +
30C ILE* 1.3 73.8 - - + +
32C GLU* 1.3 65.0 + - - +
34C ASP 2.8 28.1 + - - +
35C PRO* 3.1 40.3 - - + +
37C ALA* 4.4 12.1 - - + +
266C ASP* 5.2 2.7 - - + -
267C PRO* 4.7 9.2 - - + -
347C LEU 5.3 2.2 - - - -
348C HIS* 3.7 25.1 - - - +
349C PRO* 4.4 12.3 - - + +
351C TYR* 4.0 7.9 - - + -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ASP 2.8 16.2 + - - +
29C ALA* 3.4 14.0 - - - +
30C ILE 3.2 0.2 - - - -
31C LEU* 1.3 73.6 - - - +
33C GLN* 1.3 61.5 + - - +
35C PRO* 5.3 1.7 - - - +
349C PRO* 3.9 24.1 - - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA 3.6 5.3 + - - +
30C ILE 2.8 9.0 + - - +
32C GLU* 1.3 85.3 - - - +
34C ASP* 1.3 59.3 + - - +
35C PRO* 4.3 3.6 - - - +
59C SER* 4.5 2.3 + - - -
60C ALA* 3.1 16.4 - - + +
61C TRP* 2.6 54.4 + - - +
62C VAL* 4.4 4.9 - - - +
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Residues in contact with ASP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ILE 2.8 6.5 + - - +
31C LEU* 2.8 22.3 + - - +
33C GLN* 1.3 81.5 - - - +
35C PRO* 1.3 67.0 - - - +
36C LYS* 2.8 22.2 + - - +
37C ALA* 3.0 22.8 + - - +
58C THR* 3.0 27.3 + - - +
59C SER* 3.6 23.7 + - - +
60C ALA* 4.3 2.5 - - + -
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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