Contacts of the helix formed by residues 42 - 58 (chain B) in PDB entry 5LUA
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 ASN 42 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 3.4 25.8 + - - +
38B ASN* 3.0 22.4 + - - +
39B GLY* 2.9 13.2 + - - +
41B TYR* 1.3 77.8 - - - +
43B TYR* 1.3 64.5 + - - +
44B ARG* 3.0 22.4 + - - +
45B HIS* 3.1 18.8 + - - +
46B GLN* 4.2 6.1 + - - +
74B ILE* 4.9 0.7 - - - -
148B HIS* 2.8 30.9 + - - -
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Residues in contact with TYR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 3.6 1.6 + - - -
40B TRP* 2.9 55.7 + + - +
41B TYR 3.3 1.2 - - - -
42B ASN* 1.3 75.3 - - - +
44B ARG* 1.3 65.4 + - - +
45B HIS 3.1 1.6 + - - -
46B GLN* 3.2 6.2 + - - +
47B ALA* 3.1 24.5 + - + -
74B ILE* 3.5 32.1 - - + +
80B ASN* 5.2 2.2 - - - -
85B ILE 4.3 1.4 + - - -
86B VAL* 3.4 12.6 - - + -
87B ILE* 3.0 42.4 + - - +
225B ARG* 3.7 23.6 + - - -
227B THR* 3.6 17.0 - - + +
228B TYR 3.6 11.4 - - - +
229B LEU* 3.6 13.9 - - + -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR 2.9 28.1 + - - -
42B ASN* 3.0 11.4 + - - +
43B TYR* 1.3 78.9 - - - +
45B HIS* 1.3 76.9 + - + +
47B ALA* 3.7 0.7 - - - +
48B ASP* 2.7 40.2 + - - +
148B HIS* 3.7 10.5 - - - -
218B ALA* 3.4 18.3 - - - +
228B TYR* 3.4 22.0 + - - +
229B LEU 3.6 11.7 - - - -
230B GLY* 3.3 33.2 - - - +
231B ASP* 3.3 22.9 + - - +
304B 5KN 3.5 41.9 + - - -
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Residues in contact with HIS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.7 6.5 - - + +
37B SER* 2.7 30.4 + - - +
42B ASN* 3.1 16.5 + - - +
43B TYR 3.1 0.4 + - - -
44B ARG* 1.3 113.5 + - + +
46B GLN* 1.3 59.5 + - + +
48B ASP* 3.3 4.4 - - - +
49B ALA* 3.0 22.7 + - - +
146B THR* 3.3 36.8 - - - +
147B SNN 3.5 22.0 - - - -
148B HIS* 3.9 8.3 - - - -
187B GLU* 5.2 0.4 - - + -
231B ASP* 3.2 19.3 - - - -
304B 5KN 3.4 14.9 - - - -
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 3.9 20.9 - - + -
37B SER 3.6 19.8 + - - +
38B ASN* 4.0 4.8 - - - +
42B ASN 5.1 3.7 + - - +
43B TYR 3.2 7.6 + - - +
45B HIS* 1.3 74.7 - - + +
47B ALA* 1.3 56.1 + - - +
49B ALA* 3.2 3.0 + - - +
50B CYS* 2.8 42.8 + - - -
70B MET* 4.1 12.5 - - + +
71B TYR* 3.9 8.0 + - - +
72B ASP* 2.9 31.4 + - - -
73B ASP* 2.9 25.2 + - - -
74B ILE* 3.5 24.4 - - + +
86B VAL* 5.0 0.9 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TYR* 3.1 15.6 + - + +
44B ARG 3.7 2.9 - - - +
46B GLN* 1.3 74.3 - - - +
48B ASP* 1.3 65.6 + - - +
50B CYS* 3.4 3.0 + - - +
51B HIS* 2.9 24.9 + - - +
86B VAL* 3.5 22.4 - - + +
87B ILE 3.4 26.9 - - - +
88B ASN* 3.5 5.3 - - - +
95B VAL* 3.9 3.0 - - - +
229B LEU 3.4 16.2 - - - +
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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 ARG 2.7 24.3 + - - +
45B HIS* 3.3 6.7 - - - +
47B ALA* 1.3 72.1 - - - +
49B ALA* 1.3 57.2 + - - +
51B HIS 3.2 1.7 + - - -
52B ALA* 2.9 25.6 + - - +
88B ASN* 3.0 21.7 + - - +
144B TYR* 3.3 15.7 - - - +
146B THR* 3.0 14.7 + - + -
230B GLY* 3.4 11.4 - - - -
231B ASP* 2.7 27.7 + - - +
234B SER* 3.5 20.7 + - - -
235B VAL* 4.2 0.5 - - - +
238B MET* 3.4 14.2 - - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.5 30.0 - - + +
35B ALA* 4.1 17.7 - - + +
45B HIS 3.0 13.2 + - - +
46B GLN* 3.2 5.6 + - - +
48B ASP* 1.3 79.7 - - - +
50B CYS* 1.3 62.4 + - - +
52B ALA* 3.2 6.5 + - - +
53B TYR* 3.0 20.8 + - - +
68B VAL* 5.5 2.1 - - + +
69B MET 5.3 0.4 - - - +
70B MET* 5.2 9.9 - - + -
99B VAL* 5.4 1.3 - - - +
144B TYR* 4.3 3.1 - - - -
146B THR* 4.2 4.0 - - + +
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLN* 2.8 29.5 + - - +
47B ALA* 3.8 2.2 - - - +
49B ALA* 1.3 69.5 - - - +
51B HIS* 1.3 64.7 + - - +
53B TYR* 3.3 6.0 + - - +
54B GLN* 3.2 25.1 + - - +
70B MET* 3.8 25.1 - - - -
86B VAL* 5.3 3.4 - - - -
95B VAL* 3.5 29.8 - - + +
96B TYR* 4.0 20.6 - - - -
99B VAL* 3.9 19.1 - - - -
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA 2.9 14.0 + - - +
48B ASP 3.4 7.9 - - - +
50B CYS* 1.3 72.1 - - - +
52B ALA* 1.3 66.4 + - - +
54B GLN* 3.1 16.2 + - + +
55B ILE* 3.1 21.9 + - + +
88B ASN* 2.9 35.8 + - + +
89B ARG* 6.3 3.6 - - + -
95B VAL* 3.9 19.4 - - + +
235B VAL* 5.8 0.2 - - - -
238B MET* 3.7 20.2 - - + +
239B GLU* 4.5 12.3 - - + -
242B ASP* 2.6 32.7 + - - -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 4.0 11.2 - - + -
48B ASP 2.9 10.0 + - - +
49B ALA 3.2 10.3 + - - +
51B HIS* 1.3 76.5 - - - +
53B TYR* 1.3 62.3 + - - +
55B ILE* 3.3 7.0 + - - +
56B ILE* 3.1 26.0 + - + +
142B PHE* 6.1 0.9 - - + -
144B TYR* 3.6 32.3 - - + -
237B TRP* 4.2 11.1 - - + -
238B MET* 3.4 11.1 - - - -
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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
----------------------------------------------------------
33B ILE* 3.6 12.7 - - + +
49B ALA 3.0 12.2 + - - +
50B CYS 3.5 7.9 - - - +
51B HIS 3.2 0.2 - - - -
52B ALA* 1.3 77.0 - - - +
54B GLN* 1.3 63.6 + - - +
56B ILE* 3.0 3.3 + - + -
57B HIS* 2.7 66.1 + + + +
63B ASP* 2.6 34.1 + - - -
66B ILE* 3.9 29.8 - - + -
68B VAL* 4.4 2.5 - - + -
98B GLY* 3.2 23.4 + - - -
99B VAL* 3.7 25.6 - - + -
100B PRO* 3.4 25.8 - - + -
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B CYS 3.4 10.8 - - - +
51B HIS* 3.1 11.9 + - + +
53B TYR* 1.3 87.8 - - - +
55B ILE* 1.3 62.2 + - - +
57B HIS* 4.1 10.4 - - - +
58B ARG* 3.1 30.7 + - - +
94B ASP 5.3 1.3 - - - +
95B VAL* 2.8 41.7 + - + +
97B GLN 3.0 25.3 + - - +
99B VAL* 3.7 10.5 - - - +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 3.1 18.4 + - + +
52B ALA* 3.5 7.2 - - - +
54B GLN* 1.3 77.2 - - - +
56B ILE* 1.3 54.6 - - + +
58B ARG* 2.2 33.9 - - - +
59B ASN* 2.8 25.9 + - - +
237B TRP* 4.2 4.9 - - + -
238B MET* 3.4 53.6 - - + +
241B SER* 4.0 14.4 - - - +
242B ASP* 3.5 19.1 - - - +
246B LEU* 4.9 0.7 - - + -
284B GLN* 3.9 26.0 - - + +
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Residues in contact with ILE 56 (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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31B VAL* 3.8 33.9 - - + -
33B ILE* 4.5 3.4 - - + -
52B ALA* 3.1 17.7 + - + +
53B TYR* 3.0 9.3 + - - +
55B ILE* 1.3 75.1 - - + +
57B HIS* 1.3 58.8 + - - +
58B ARG 2.7 16.0 - - - +
60B GLY 3.8 0.5 + - - -
61B ILE* 3.5 30.1 + - + +
66B ILE* 3.6 26.9 - - + -
142B PHE* 4.2 10.5 - - + -
237B TRP* 5.8 1.3 - - + -
284B GLN* 3.6 45.4 - - + +
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 2.7 57.9 + + + +
54B GLN* 4.1 12.1 - - - +
56B ILE* 1.3 72.0 - - - +
58B ARG* 1.3 67.7 + - + +
59B ASN 3.7 0.2 + - - -
60B GLY* 3.4 12.5 + - - -
61B ILE 4.0 12.7 + - - +
62B PRO* 6.0 0.4 - - - +
63B ASP* 3.9 9.8 + - - -
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Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 3.1 16.0 + - - +
55B ILE* 2.2 38.5 - - - +
56B ILE 2.7 7.8 - - - +
57B HIS* 1.3 82.7 - - + +
59B ASN* 1.3 82.4 + - - +
241B SER 4.8 3.2 + - - -
242B ASP* 2.8 48.2 + - - +
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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