Contacts of the helix formed by residues 16 - 36 (chain C) in PDB entry 3IML
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 16 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.7 31.4 - - + +
13C SER* 3.2 18.6 + - - +
15C GLY* 1.3 76.9 - - - +
17C PRO* 1.3 83.9 - - + +
18C ASP* 3.2 48.8 + - + +
19C LYS 2.8 15.2 + - - +
20C VAL* 2.9 9.4 + - - +
167C ASP* 3.5 16.6 - - - +
168C ALA 5.2 1.1 - - - -
169C LYS* 3.9 23.8 + - + -
249C LYS* 3.6 13.9 - - - -
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Residues in contact with PRO 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY 3.5 0.6 - - - -
16C HIS* 1.3 100.6 - - + +
18C ASP* 1.3 61.1 + - - +
20C VAL* 3.2 9.0 + - + +
21C ALA 3.2 17.5 + - - -
47C CYS* 3.8 2.8 - - - -
167C ASP* 3.8 7.2 - - - +
238C GLY* 3.6 22.0 - - - +
239C PRO* 3.8 14.4 - - + -
242C ASP* 3.3 39.7 - - + +
243C CYS 4.0 2.2 - - - +
244C GLY* 3.5 22.1 - - - +
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C HIS* 3.2 18.5 + - - +
17C PRO* 1.3 76.5 - - - +
19C LYS* 1.3 58.9 + - - +
21C ALA* 3.4 5.7 - - - +
22C ASP* 3.1 29.1 + - - +
243C CYS 4.0 5.4 - - - +
244C GLY* 3.4 5.9 - - - -
245C LEU* 2.9 34.3 + - - +
248C ARG* 3.8 20.7 + - + +
249C LYS* 2.9 39.3 + - + -
44D GLU* 5.7 0.2 - - - +
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Residues in contact with LYS 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C VAL* 3.5 26.2 - - + +
13C SER 3.6 19.1 - - - +
14C GLU* 4.4 0.7 - - - -
16C HIS* 2.8 9.7 + - + +
18C ASP* 1.3 71.1 - - - +
20C VAL* 1.3 58.4 + - - +
22C ASP* 3.1 24.4 + - - +
23C GLN* 2.6 47.0 + - - +
249C LYS* 3.9 15.9 - - + -
252C VAL* 4.5 11.7 - - - -
253C ASP* 2.4 33.9 + - - -
359C ALA* 2.9 32.2 + - - +
360C ALA* 4.1 9.0 - - - +
361C TYR 5.1 2.7 - - - +
362C GLY 5.9 0.2 - - - +
363C HIS* 4.7 0.2 + - - -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU 3.7 15.0 - - - +
15C GLY* 3.9 14.8 - - - +
16C HIS 2.9 18.4 + - - +
17C PRO* 3.2 10.5 + - + +
19C LYS* 1.3 76.4 - - - +
21C ALA* 1.3 57.9 + - - +
23C GLN* 3.3 7.0 + - - +
24C ILE* 2.9 51.7 + - + +
47C CYS* 4.2 10.3 - - - -
74C ILE* 4.3 12.6 - - + -
77C ILE* 4.1 17.0 - - + -
79C TYR* 4.3 12.1 - - + -
239C PRO* 4.3 10.1 - - + -
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO 3.2 10.6 + - - +
18C ASP 3.4 4.5 - - - +
20C VAL* 1.3 74.0 - - - +
22C ASP* 1.3 66.4 + - - +
24C ILE 3.3 1.2 + - - -
25C SER* 3.0 26.3 + - - -
45C THR* 3.5 25.8 - - + +
47C CYS* 4.1 3.9 - - - -
244C GLY 4.1 3.6 - - - +
245C LEU* 3.3 36.6 - - - +
246C THR* 3.3 6.0 + - - +
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASP 3.1 19.0 + - - +
19C LYS* 3.1 36.6 + - - +
20C VAL 3.4 0.2 - - - -
21C ALA* 1.3 79.2 - - - +
23C GLN* 1.3 57.5 + - - +
25C SER* 3.4 1.7 + - - -
26C ASP* 3.0 24.8 + - - +
246C THR* 3.3 6.8 - - - +
247C GLY* 2.8 31.9 + - - -
249C LYS* 4.3 8.3 + - - +
253C ASP* 4.1 6.5 - - - +
267C SER* 3.4 32.3 + - - +
359C ALA* 3.9 4.9 - - - +
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Residues in contact with GLN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 2.9 46.2 + - - +
19C LYS* 2.6 31.5 + - - +
20C VAL 3.7 3.8 - - - +
21C ALA 3.2 0.2 - - - -
22C ASP* 1.3 74.4 - - - +
24C ILE* 1.3 54.9 + - - +
26C ASP* 3.6 0.4 - - - -
27C ALA* 2.7 36.4 + - - +
73C THR* 3.9 13.0 - - + -
76C ARG* 2.9 29.4 + - - +
77C ILE* 3.9 5.1 - - + +
356C GLU* 3.9 9.1 - - + +
359C ALA* 3.6 25.8 - - + +
360C ALA* 3.9 12.3 - - - +
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 2.9 40.2 + - + +
21C ALA 3.8 4.3 - - - +
23C GLN* 1.3 72.6 - - - +
25C SER* 1.3 68.0 + - - +
27C ALA* 3.2 3.8 + - - +
28C ILE* 2.9 43.4 + - + +
45C THR* 3.8 21.8 - - + +
47C CYS* 4.9 3.1 - - - -
52C VAL* 4.7 9.9 - - + -
54C LEU* 3.9 10.8 - - + -
70C ALA* 4.1 16.8 - - + +
73C THR* 3.9 23.1 - - + -
74C ILE* 4.1 19.7 - - + -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 3.0 12.0 + - - -
22C ASP 3.5 5.2 - - - -
24C ILE* 1.3 77.0 - - - +
26C ASP* 1.3 56.4 + - - +
28C ILE* 3.4 5.3 + - - +
29C LEU* 3.0 24.9 + - - +
43C ALA* 2.7 34.9 + - - +
45C THR* 2.8 14.0 + - - -
246C THR* 2.7 27.3 + - - -
268C GLY* 3.8 16.7 - - - -
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Residues in contact with ASP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ASP 3.0 11.6 + - - +
23C GLN 4.1 1.1 - - - +
25C SER* 1.3 72.4 - - - +
27C ALA* 1.3 60.6 + - - +
28C ILE 3.3 0.2 - - - -
29C LEU* 3.4 9.4 - - - +
30C ASP* 3.0 32.6 + - - -
267C SER* 2.6 26.9 + - - -
268C GLY 3.0 8.8 + - - -
276C ARG* 2.8 43.2 + - - -
355C TYR* 3.3 22.9 - - - +
356C GLU* 3.7 9.2 - - - -
358C THR* 3.8 0.5 + - - -
359C ALA* 3.6 5.9 - - + +
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Residues in contact with ALA 27 (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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23C GLN 2.7 23.2 + - - +
24C ILE* 3.5 4.7 - - - +
26C ASP* 1.3 71.9 - - - +
28C ILE* 1.3 62.1 + - - +
30C ASP* 3.5 3.9 + - - +
31C ALA* 3.2 23.2 + - - +
69C ILE* 3.8 13.1 - - + +
73C THR* 3.2 25.1 - - - +
356C GLU* 3.6 25.2 - - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 2.9 37.7 + - + +
25C SER* 3.7 4.9 - - - +
27C ALA* 1.3 74.3 - - - +
29C LEU* 1.3 66.2 + - - +
31C ALA* 3.5 4.1 + - - +
32C ILE* 3.1 40.2 + - + +
43C ALA* 4.3 10.5 - - + -
45C THR* 5.2 0.7 - - - +
54C LEU* 3.9 17.3 - - + -
58C ILE* 4.9 0.2 - - + -
64C ILE* 5.3 0.4 - - + +
66C TYR* 4.0 26.2 - - + +
69C ILE* 3.7 20.9 - - + -
97C TYR* 3.2 34.1 - - + +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C SER 3.0 14.7 + - - +
26C ASP* 3.4 13.9 - - - +
28C ILE* 1.3 77.1 - - - +
30C ASP* 1.3 57.7 + - - +
32C ILE* 3.2 9.9 + - - +
33C LEU* 2.9 47.2 + - + +
41C VAL* 3.8 34.3 - - + +
268C GLY* 4.9 1.1 - - - -
269C LYS 3.5 13.7 - - - +
270C ASP* 4.0 11.9 - - + +
276C ARG* 3.3 29.8 - - - +
355C TYR* 3.8 19.7 - - + -
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Residues in contact with ASP 30 (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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26C ASP 3.0 15.8 + - - +
27C ALA* 3.8 5.8 - - - +
28C ILE 3.3 0.4 - - - -
29C LEU* 1.3 72.7 - - - +
31C ALA* 1.3 62.3 + - - +
33C LEU* 3.2 1.7 + - - +
34C ALA* 2.8 31.9 + - - +
353C PRO* 3.2 37.6 - - + +
354C ILE 3.3 1.0 + - - -
355C TYR* 3.0 31.5 + - - +
356C GLU* 3.0 29.4 + - - +
357C LYS 4.9 0.2 + - - -
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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
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27C ALA 3.2 12.5 + - - +
28C ILE 3.9 4.0 - - - +
29C LEU 3.4 0.2 - - - -
30C ASP* 1.3 80.3 - - - +
32C ILE* 1.3 62.1 + - - +
34C ALA* 3.5 16.8 + - - +
35C GLN* 3.6 8.0 + - - +
64C ILE* 3.7 19.3 - - + +
69C ILE* 3.4 33.7 - - + -
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Residues in contact with ILE 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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28C ILE* 3.1 35.4 + - + +
29C LEU 3.4 6.3 - - - +
31C ALA* 1.3 74.9 - - - +
33C LEU* 1.3 61.0 + - + +
35C GLN* 3.2 3.5 + - - -
36C ASP* 2.8 26.0 + - - +
39C SER* 3.2 33.9 - - - +
41C VAL* 3.8 24.0 - - + -
58C ILE* 4.2 21.3 - - + -
60C THR* 3.5 13.0 - - + +
62C ALA* 4.0 9.6 - - + +
64C ILE* 3.9 17.0 - - + -
66C TYR* 4.4 6.7 - - + +
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 2.9 46.4 + - + +
30C ASP* 3.2 5.4 + - - +
32C ILE* 1.3 76.9 - - - +
34C ALA* 1.3 62.7 + - - +
35C GLN 3.2 0.7 + - - -
36C ASP 3.7 5.2 - - - +
37C LYS* 3.3 58.2 + - + +
39C SER* 4.4 15.3 - - - +
270C ASP* 4.9 3.8 - - + -
271C PRO* 4.7 9.0 - - + -
350C LEU 4.9 0.2 - - - +
351C LEU* 5.2 1.6 - - + -
352C ARG* 3.9 24.0 - - - +
353C PRO* 4.4 13.5 - - + +
355C TYR* 3.9 13.9 - - + -
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASP 2.8 18.1 + - - +
31C ALA* 3.5 11.0 - - - +
32C ILE 3.2 0.2 - - - -
33C LEU* 1.3 77.5 - - - +
35C GLN* 1.3 61.3 + - + +
37C LYS* 4.6 7.8 + - - +
353C PRO* 4.4 17.0 - - + +
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ALA 3.6 5.3 + - - +
32C ILE 3.2 2.3 + - - +
33C LEU 3.1 0.6 - - - -
34C ALA* 1.3 82.8 - - + +
36C ASP* 1.3 59.5 + - - +
37C LYS* 4.0 9.5 + - - -
61C THR* 4.8 2.1 + - - -
62C ALA* 3.6 13.7 - - + -
63C ASN* 3.1 33.2 + - - +
64C ILE* 3.3 28.0 - - - +
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Residues in contact with ASP 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE 2.8 13.5 + - - +
33C LEU* 3.6 4.4 - - - -
35C GLN* 1.3 76.2 - - - +
37C LYS* 1.3 59.9 + - - +
38C TYR* 3.4 21.7 + - - +
39C SER* 2.6 47.7 + - - +
60C THR* 3.6 10.9 - - - +
61C THR* 2.9 44.3 + - - +
62C ALA* 4.3 2.9 - - + -
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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