Contacts of the helix formed by residues 37 - 57 (chain B) in PDB entry 1LI5
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 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU 3.7 2.5 + - - +
36B CYS* 1.3 75.6 - - - +
38B ILE* 1.3 57.7 + - - +
39B GLY* 3.0 31.0 - - - -
40B HIS* 2.8 70.7 + + - +
41B GLY 2.9 8.0 + - - -
267B MET* 3.8 20.1 - - + +
274B PHE* 4.0 28.3 - + + -
275B PHE 3.5 12.6 - - - +
276B THR* 3.6 6.7 - - - +
277B VAL* 3.5 3.3 - - - +
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 1.3 70.1 - - - +
39B GLY* 1.3 70.8 + - - +
41B GLY* 2.9 1.0 + - - -
42B ARG* 2.7 36.6 + - - +
260B VAL* 3.8 24.5 - - + -
262B VAL* 5.3 1.8 - - + -
267B MET* 3.3 35.7 - - + -
274B PHE 4.1 3.4 - - - +
275B PHE* 3.4 17.7 + - + +
277B VAL* 3.8 16.8 - - + +
280B VAL* 3.5 32.8 - - + -
289B VAL* 5.5 5.4 - - + -
292B PHE* 5.9 0.4 - - + -
293B LEU* 4.3 15.0 - - + +
304B TYR* 4.6 15.0 - - + -
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.0 16.5 + - - -
38B ILE* 1.3 92.8 - - - +
40B HIS* 1.3 61.9 + - - +
42B ARG* 3.3 4.0 + - - +
43B THR* 3.2 23.2 + - - -
259B MET* 6.0 0.8 - - - -
260B VAL* 4.1 18.8 - - - +
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.0 24.3 - - + +
31B THR 5.5 2.0 - - - -
36B CYS* 4.3 12.2 - - + -
37B HIS* 2.8 53.4 + + - +
39B GLY* 1.3 71.6 - - - -
41B GLY* 1.3 64.5 + - - +
43B THR* 3.4 7.5 + - - -
44B PHE* 2.9 47.4 + + + -
100B PHE* 5.3 0.4 - - - -
229B ASP* 5.6 4.0 + - - -
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Residues in contact with GLY 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS 2.9 8.7 + - - -
38B ILE* 2.9 8.3 + - - -
40B HIS* 1.3 76.8 - - - +
42B ARG* 1.3 64.6 + - - +
44B PHE* 3.6 3.6 + - - +
45B VAL* 3.1 29.5 + - - +
100B PHE* 5.1 5.4 - - - -
103B LEU* 4.7 6.3 - - - -
105B ILE* 4.4 1.0 - - - +
277B VAL* 4.1 15.2 - - - +
293B LEU* 4.1 10.5 - - - -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE 2.7 14.5 + - - +
39B GLY 3.5 9.4 - - - +
41B GLY* 1.3 72.2 - - - +
43B THR* 1.3 61.1 + - - +
45B VAL* 3.2 3.5 + - - +
46B ALA* 2.8 35.9 + - - +
257B SER* 4.7 1.6 - - - -
258B GLY 3.0 28.2 + - - +
259B MET 4.0 2.6 + - - -
260B VAL* 3.7 18.8 - - + -
293B LEU* 3.8 34.3 + - + +
296B GLY 3.9 8.3 + - - -
297B HIS 2.7 31.5 + - - -
298B TYR* 3.3 20.8 + - - +
300B SER* 2.9 22.8 + - - -
302B LEU* 3.9 29.4 - - + +
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.9 0.2 - - + -
28B CYS 5.6 0.7 - - - +
39B GLY 3.2 12.0 + - - -
40B HIS* 3.5 14.4 - - - -
42B ARG* 1.3 78.2 - - - +
44B PHE* 1.3 73.8 + - + +
46B ALA* 3.2 2.8 + - - +
47B PHE* 2.9 47.7 + - + -
226B GLY* 4.2 2.7 - - - -
227B GLY* 4.0 22.5 - - - +
257B SER* 3.2 29.0 + - - +
258B GLY 4.9 3.6 + - - -
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Residues in contact with PHE 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 4.0 13.5 - - + -
28B CYS 3.3 27.8 - - - -
29B GLY* 3.8 15.5 - - - -
30B ILE* 4.2 8.1 - - + -
40B HIS* 2.9 40.9 + + + +
41B GLY 4.3 0.2 - - - +
43B THR* 1.3 82.0 - - + +
45B VAL* 1.3 59.9 + - - +
47B PHE* 3.9 2.6 - - - +
48B ASP* 2.9 28.0 + - - +
63B TYR* 4.6 3.9 + - - +
65B ARG* 3.5 29.6 - - - +
100B PHE* 3.3 34.8 - + + -
105B ILE* 3.9 25.2 - - + +
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Residues in contact with VAL 45 (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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41B GLY 3.1 22.7 + - - +
42B ARG 3.5 4.0 - - - +
44B PHE* 1.3 73.8 - - - +
46B ALA* 1.3 58.2 + - - +
48B ASP* 2.8 7.6 + - - +
49B VAL* 2.8 37.2 + - - +
103B LEU* 4.5 5.6 - - + -
105B ILE* 3.7 22.7 - - + -
290B ARG* 4.0 20.4 - - + +
293B LEU* 3.8 28.7 - - + +
294B MET* 3.4 33.9 - - + -
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Residues in contact with ALA 46 (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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42B ARG* 2.8 17.9 + - - +
43B THR* 3.3 12.8 - - - +
45B VAL* 1.3 80.7 - - - +
47B PHE* 1.3 60.7 + - + +
49B VAL* 3.1 9.7 + - - +
50B VAL* 3.1 27.9 + - - +
257B SER* 4.4 9.4 - - - -
293B LEU 6.0 1.1 - - - +
294B MET* 6.0 0.9 - - - -
298B TYR* 3.8 31.9 - - + +
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Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.9 10.7 - - + +
27B VAL* 3.7 23.3 - - + -
43B THR* 2.9 41.4 + - + +
44B PHE* 4.5 2.5 - - - +
46B ALA* 1.3 75.8 - - + +
48B ASP* 1.3 64.7 + - - +
50B VAL* 3.6 14.7 - - + +
51B ALA* 3.0 23.4 + - - +
63B TYR* 3.9 20.3 + - + +
223B ILE* 4.3 0.7 - - + -
225B GLY* 3.4 22.2 - - - -
226B GLY 3.3 23.1 - - - -
255B MET* 3.4 46.2 - - + -
256B HIS 4.5 1.1 - - - -
257B SER* 4.0 12.1 - - - -
298B TYR* 5.4 4.0 - + - -
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PHE 2.9 20.1 + - - +
45B VAL* 2.8 11.5 + - - +
47B PHE* 1.3 76.6 - - - +
49B VAL* 1.3 58.6 + - - +
51B ALA* 3.3 6.4 + - - +
52B ARG* 2.8 53.0 + - - +
63B TYR* 5.2 5.8 - - + -
104B ASN 3.4 2.1 - - - +
105B ILE* 3.8 9.2 - - + +
106B LEU* 2.7 43.0 + - - +
290B ARG* 2.8 20.0 + - - +
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Residues in contact with VAL 49 (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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45B VAL 2.8 17.7 + - - +
46B ALA* 3.3 10.5 - - - +
48B ASP* 1.3 78.4 - - - +
50B VAL* 1.3 56.8 + - + +
52B ARG* 3.7 7.5 - - - +
53B TYR* 2.9 28.9 + - - +
290B ARG* 4.0 8.1 - - - +
294B MET* 3.3 35.9 - - + -
346B MET* 3.6 28.9 - - + -
350B PHE* 5.2 5.8 - - + -
352B THR* 4.1 10.3 - - + -
390B VAL 4.7 1.2 - - - +
391B LEU* 3.9 14.1 - - + +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 5.9 0.7 - - + -
25B MET* 3.7 26.0 - - + -
46B ALA 3.1 18.7 + - - +
47B PHE* 3.6 15.7 - - + +
48B ASP 3.2 0.2 - - - -
49B VAL* 1.3 77.0 - - + +
51B ALA* 1.3 63.6 + - - +
53B TYR* 3.3 1.6 + - - +
54B LEU* 3.0 37.0 + - + +
223B ILE* 5.4 0.7 - - + -
255B MET* 3.6 31.6 - - + -
298B TYR* 5.8 3.1 - - + -
350B PHE* 3.9 32.7 - - + -
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.8 11.2 - - + -
47B PHE 3.0 17.2 + - - +
48B ASP* 3.6 8.1 - - - +
50B VAL* 1.3 78.5 - - - +
52B ARG* 1.3 63.9 + - + +
54B LEU* 3.3 2.5 + - - +
55B ARG* 3.2 35.0 + - - +
61B LEU* 3.6 25.9 - - + +
63B TYR* 4.2 14.6 - - + -
106B LEU* 6.1 2.9 - - + -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 2.8 41.5 + - - +
49B VAL* 3.7 2.2 - - - +
51B ALA* 1.3 73.7 - - - +
53B TYR* 1.3 57.0 + - - +
55B ARG* 3.5 8.1 + - - +
56B PHE* 3.0 27.5 + - - +
104B ASN* 2.8 43.6 + - - -
106B LEU* 3.4 38.2 - - + +
290B ARG* 3.5 10.5 - - - +
389B ALA 3.2 18.2 + - - -
390B VAL* 3.2 31.6 - - + +
392B GLY* 4.0 8.7 - - - +
395B GLU* 4.4 4.8 + - - -
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Residues in contact with TYR 53 (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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2B LEU* 4.3 6.5 - - + -
49B VAL 2.9 18.7 + - - +
50B VAL 3.8 2.9 - - - +
52B ARG* 1.3 75.6 - - - +
54B LEU* 1.3 66.4 + - - +
56B PHE* 3.2 29.5 + + - +
57B LEU* 3.0 51.0 + - + +
342B PHE* 4.5 2.5 - + - -
343B ILE* 3.2 19.3 + - - +
346B MET* 3.5 46.7 - - + -
347B ASP* 2.4 30.7 + - - -
350B PHE* 3.9 21.1 - + + -
390B VAL* 4.0 13.4 - - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.8 29.4 - - + -
4B ILE* 5.5 1.6 - - + -
15B PHE* 4.7 5.6 - - + -
23B VAL* 4.1 27.8 - - + -
25B MET* 4.8 4.5 - - - -
50B VAL* 3.0 39.4 + - + +
51B ALA* 3.8 5.6 - - - +
53B TYR* 1.3 75.0 - - - +
55B ARG* 1.3 62.4 + - - +
57B LEU* 3.2 9.3 + - + -
59B TYR* 3.1 50.5 + - + -
61B LEU* 4.5 14.1 - - + -
223B ILE* 5.5 4.5 - - + -
350B PHE* 5.0 6.7 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA* 3.2 23.7 + - - +
52B ARG* 3.8 6.3 - - - +
54B LEU* 1.3 73.7 - - - +
56B PHE* 1.3 58.9 + - - +
58B GLY* 2.6 25.8 + - - -
59B TYR 3.9 17.2 - - - +
61B LEU* 2.8 42.8 + - + +
63B TYR* 5.1 4.2 - - - +
106B LEU* 4.8 16.9 - - - +
107B ARG 5.3 6.1 + - - -
109B ASP* 2.6 40.7 + - - -
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG 3.0 14.3 + - - +
53B TYR* 3.3 29.4 - + - +
55B ARG* 1.3 76.1 - - - +
57B LEU* 1.3 64.7 + - + +
58B GLY* 3.2 1.4 + - - -
339B GLU* 3.9 18.8 - - - -
342B PHE* 4.4 16.2 - + - -
343B ILE* 4.5 16.4 - - + -
386B LYS* 3.9 23.8 - - + -
387B LEU* 4.0 17.3 - - + -
390B VAL* 3.5 32.3 - - + -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.2 16.4 - - + -
53B TYR* 3.0 62.6 + - + +
54B LEU* 3.5 8.3 - - - +
55B ARG 3.0 0.4 - - - -
56B PHE* 1.3 80.3 - - + +
58B GLY* 1.3 58.5 + - - +
59B TYR* 3.6 25.5 - - + -
343B ILE* 4.9 12.8 - - + -
347B ASP* 4.3 5.6 - - - +
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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