Contacts of the helix formed by residues 16 - 36 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.6 32.0 - - + +
13B SER* 3.2 17.7 + - - +
15B GLY* 1.3 76.3 - - - +
17B PRO* 1.3 84.7 - - + +
18B ASP* 3.1 51.6 + - + +
19B LYS* 2.9 5.5 + - - +
20B VAL* 2.8 19.3 + - - +
167B ASP* 3.4 17.0 + - - +
168B ALA 5.1 0.7 - - - -
169B LYS* 4.4 20.0 + - + -
249B LYS* 3.8 14.5 - - - -
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Residues in contact with PRO 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY 3.9 2.5 - - - +
16B HIS* 1.3 100.1 - - + +
18B ASP* 1.3 60.8 + - - +
20B VAL* 3.3 12.0 + - + +
21B ALA 3.2 16.6 + - - -
47B CYS* 3.7 2.9 - - - -
167B ASP* 3.6 16.8 - - - +
238B GLY* 3.6 11.7 - - - +
239B PRO* 4.0 10.8 - - + -
242B ASP* 3.1 40.8 - - + +
243B CYS 4.0 2.5 - - - +
244B GLY* 3.5 21.8 - - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B HIS* 3.1 20.9 + - - +
17B PRO* 1.3 76.0 - - - +
19B LYS* 1.3 57.9 + - - +
21B ALA* 3.2 6.9 + - - +
22B ASP* 3.0 27.0 + - - +
243B CYS 4.0 4.7 - - - +
244B GLY* 3.3 6.1 - - - -
245B LEU* 3.0 34.7 + - - +
248B ARG* 4.0 18.0 + - + +
249B LYS* 2.8 42.5 + - + +
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Residues in contact with LYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.4 28.7 - - + +
13B SER 3.6 15.5 - - - +
14B GLU* 4.0 0.9 - - - +
16B HIS* 2.9 12.4 + - - +
18B ASP* 1.3 69.3 - - - +
20B VAL* 1.3 61.7 + - - +
21B ALA 3.1 1.6 - - - -
22B ASP* 2.9 27.6 + - - +
23B GLN* 2.8 45.2 + - - +
249B LYS* 3.8 19.1 - - + -
252B VAL* 4.5 7.9 - - - -
253B ASP* 2.6 32.6 + - - -
359B ALA* 2.9 28.4 + - - +
360B ALA* 4.1 8.7 - - - +
361B TYR 5.1 2.2 - - - +
363B HIS* 4.9 0.2 + - - -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU 3.9 9.4 - - - +
15B GLY 3.7 15.0 - - - +
16B HIS 2.8 18.4 + - - +
17B PRO 3.3 6.9 + - - +
19B LYS* 1.3 76.5 - - - +
21B ALA* 1.3 58.3 + - - +
23B GLN* 3.9 6.2 - - - +
24B ILE* 2.9 47.4 + - + +
47B CYS* 4.0 12.6 - - + -
74B ILE* 4.3 11.4 - - + -
77B ILE* 4.2 16.3 - - + +
79B TYR* 4.3 9.4 - - + -
239B PRO* 3.9 21.5 - - + -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO 3.2 7.5 + - - +
18B ASP 3.4 3.8 - - - +
19B LYS 3.1 0.4 - - - -
20B VAL* 1.3 80.6 - - - +
22B ASP* 1.3 56.5 + - - +
24B ILE 3.4 0.3 + - - -
25B SER* 2.9 33.1 + - - -
45B THR* 3.5 26.6 - - + +
47B CYS* 4.0 3.7 - - - -
244B GLY 4.0 4.0 - - - +
245B LEU* 3.3 36.3 - - - +
246B THR* 3.3 5.1 + - - +
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Residues in contact with ASP 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ASP 3.0 18.5 + - - +
19B LYS* 2.9 40.3 + - - +
21B ALA* 1.3 74.7 - - - +
23B GLN* 1.3 58.5 + - - +
25B SER* 3.2 5.7 + - - -
26B ASP* 2.9 25.6 + - - +
245B LEU 4.9 0.2 - - - -
246B THR* 3.5 6.6 - - - +
247B GLY* 2.9 31.2 + - - -
248B ARG 4.9 0.3 + - - -
249B LYS* 4.3 8.3 + - - +
253B ASP* 4.2 6.1 - - - +
267B SER* 3.5 26.8 + - - +
359B ALA* 4.0 7.0 - - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 2.8 51.9 + - - +
19B LYS* 2.8 28.5 + - - +
20B VAL 4.0 2.2 - - - +
22B ASP* 1.3 74.6 - - - +
24B ILE* 1.3 56.0 + - - +
26B ASP* 3.2 1.1 + - - +
27B ALA* 2.7 36.6 + - - +
73B THR* 3.9 6.8 - - + +
76B ARG* 3.1 37.2 + - - +
77B ILE* 3.8 7.0 - - + +
356B GLU* 4.3 9.6 - - + +
359B ALA* 3.7 26.0 - - + +
360B ALA* 4.1 7.6 - - - +
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 2.9 39.4 + - + +
21B ALA 3.8 3.1 - - - +
23B GLN* 1.3 73.6 - - - +
25B SER* 1.3 66.4 + - - +
27B ALA* 3.2 3.4 + - - +
28B ILE* 3.0 31.5 + - + +
45B THR* 3.7 24.7 - - + +
47B CYS* 4.9 4.5 - - + -
52B VAL* 4.6 6.1 - - + -
54B LEU* 3.8 20.9 - - + -
69B ILE 5.6 0.2 - - - -
70B ALA* 4.0 19.1 - - + +
73B THR* 3.9 22.4 - - + +
74B ILE* 4.1 20.0 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 2.9 12.7 + - - -
22B ASP 3.2 5.4 + - - -
24B ILE* 1.3 78.1 - - - +
26B ASP* 1.3 55.0 + - - +
28B ILE* 3.7 5.2 - - - +
29B LEU* 3.2 17.2 + - - +
43B ALA* 2.7 33.5 + - - +
45B THR* 2.7 21.7 + - - -
246B THR* 2.8 20.7 + - - -
268B GLY* 3.6 21.5 - - - -
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP 2.9 10.5 + - - +
23B GLN 4.0 1.1 - - - +
25B SER* 1.3 73.4 - - - +
27B ALA* 1.3 60.6 + - - +
28B ILE 3.2 1.3 - - - -
29B LEU* 3.5 8.5 - - - +
30B ASP* 2.9 33.6 + - - -
267B SER* 2.8 27.9 + - - -
268B GLY 3.0 9.5 + - - -
276B ARG* 2.8 41.8 + - - -
355B TYR* 3.4 20.9 - - - +
356B GLU* 3.7 10.1 - - - +
359B ALA* 3.5 6.8 - - + +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN 2.7 20.0 + - - +
24B ILE* 3.2 3.8 + - - +
26B ASP* 1.3 72.3 - - - +
28B ILE* 1.3 63.4 - - - +
30B ASP* 3.5 4.1 + - - +
31B ALA* 3.0 24.1 + - - +
69B ILE* 3.8 14.6 - - + +
73B THR* 3.1 27.6 - - - +
356B GLU* 3.8 25.0 - - - +
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.0 36.0 + - + +
25B SER* 3.7 4.0 - - - +
27B ALA* 1.3 78.8 - - - +
29B LEU* 1.3 63.8 + - - +
31B ALA* 3.3 4.3 + - - +
32B ILE* 3.0 41.2 + - + +
43B ALA* 4.1 13.7 - - + -
45B THR* 5.3 0.4 - - - +
54B LEU* 3.9 16.8 - - + -
58B ILE* 5.0 0.4 - - + -
64B ILE* 5.4 1.5 - - + +
66B TYR* 4.3 23.6 - - + +
69B ILE* 4.0 20.0 - - + -
70B ALA 5.2 0.2 - - - +
97B TYR* 3.1 34.1 - - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER 3.2 12.3 + - - +
26B ASP* 3.2 14.6 + - - +
28B ILE* 1.3 80.7 - - - +
30B ASP* 1.3 53.1 + - - +
32B ILE* 3.1 8.4 + - - +
33B LEU* 2.8 51.1 + - + +
41B VAL* 3.6 37.0 - - + -
268B GLY* 4.8 2.0 - - - -
269B LYS 3.4 11.9 - - - +
270B ASP* 3.8 19.5 - - + +
276B ARG* 3.4 29.8 - - - +
355B TYR* 3.7 20.6 - - + -
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP 2.9 17.6 + - - +
27B ALA* 3.8 4.7 - - - +
29B LEU* 1.3 72.8 - - - +
31B ALA* 1.3 57.8 + - - +
33B LEU* 4.3 0.7 - - - -
34B ALA* 2.8 31.2 + - - +
353B PRO* 3.2 34.3 - - + +
354B ILE 3.2 1.0 + - - -
355B TYR* 2.9 31.4 + - - +
356B GLU* 2.8 33.9 + - - +
357B LYS 4.8 0.2 + - - -
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.0 10.8 + - - +
28B ILE 3.6 8.5 - - - +
30B ASP* 1.3 76.5 - - - +
32B ILE* 1.3 63.6 + - - +
34B ALA* 3.4 15.9 + - - +
35B GLN* 3.7 6.6 + - - -
64B ILE* 3.5 25.7 - - + +
69B ILE* 3.1 35.7 - - + -
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Residues in contact with ILE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 3.0 38.3 + - + +
29B LEU 3.4 5.4 - - - +
31B ALA* 1.3 76.3 - - - +
33B LEU* 1.3 59.4 + - + +
35B GLN* 3.1 5.0 + - - +
36B ASP 2.9 24.9 + - - -
39B SER* 3.3 34.3 - - - +
41B VAL* 3.9 28.0 - - + -
58B ILE* 4.1 19.5 - - + -
60B THR* 3.5 11.4 - - + +
62B ALA* 3.9 9.2 - - + +
64B ILE* 4.0 17.0 - - + -
66B TYR* 4.4 6.3 - - + +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.8 40.8 + - + +
30B ASP* 3.9 5.4 - - - +
32B ILE* 1.3 71.7 - - + +
34B ALA* 1.3 65.9 + - - +
35B GLN 3.3 0.5 + - - -
36B ASP 3.9 4.9 - - - +
37B LYS* 3.4 52.7 + - + +
39B SER* 4.6 13.7 - - - +
270B ASP* 4.9 0.2 - - + -
271B PRO* 4.6 13.5 - - + -
350B LEU 4.8 0.2 - - - +
351B LEU* 5.1 1.1 - - + -
352B ARG* 3.6 27.3 - - - +
353B PRO* 4.3 13.2 - - + +
355B TYR* 3.7 22.4 - - + -
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP 2.8 18.1 + - - +
31B ALA* 3.6 9.4 - - - +
32B ILE 3.2 0.2 - - - -
33B LEU* 1.3 78.1 - - - +
35B GLN* 1.3 60.9 + - + +
353B PRO* 4.3 15.6 - - + +
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Residues in contact with GLN 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.7 2.8 + - - +
32B ILE 3.1 2.6 + - - +
34B ALA* 1.3 82.3 - - + +
36B ASP* 1.3 60.1 + - - +
37B LYS 4.1 0.9 - - - -
61B THR* 4.9 2.0 + - - +
62B ALA* 3.6 16.0 - - + -
63B ASN* 3.2 33.5 + - - +
64B ILE* 3.0 33.9 - - - +
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE 2.9 12.3 + - - +
33B LEU* 3.8 2.5 - - - -
35B GLN* 1.3 78.2 - - - +
37B LYS* 1.3 61.4 + - - +
38B TYR* 3.1 23.2 + - - +
39B SER* 2.5 45.6 + - - +
60B THR* 3.7 10.5 - - - +
61B THR* 3.2 41.7 + - - +
62B ALA 4.2 2.7 - - - +
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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