Contacts of the helix formed by residues 43 - 64 (chain B) in PDB entry 3LRB
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 ILE 43 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 3.3 41.5 - - + -
42B ALA* 1.3 71.7 - - - +
44B TYR* 1.3 73.0 + - + +
45B GLY 3.1 2.2 - - - -
46B TRP* 2.9 29.5 + - + +
47B LEU* 3.2 8.2 + - + +
183B ASN* 5.9 0.4 - - - +
240B VAL* 5.7 6.7 - - + -
243B THR 6.0 1.1 - - - +
244B THR* 5.0 20.4 - - + -
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 3.3 3.1 - - - -
43B ILE* 1.3 80.0 - - + +
45B GLY* 1.3 56.8 + - - +
47B LEU* 2.4 36.8 + - + +
48B VAL* 3.0 14.1 + - + +
183B ASN* 4.7 14.5 + - - -
189B THR* 3.6 27.7 - - + +
193B ILE* 3.1 34.8 - - + -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 3.9 1.6 + - - -
43B ILE 3.1 1.4 - - - -
44B TYR* 1.3 77.5 - - - +
46B TRP* 1.3 56.4 + - - +
48B VAL* 3.5 1.4 + - - -
49B THR* 3.0 16.7 + - - +
193B ILE* 3.8 9.5 - - - +
196B THR* 2.9 32.9 + - - -
197B LEU* 2.8 33.5 - - - +
200B THR* 4.4 0.9 - - - -
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Residues in contact with TRP 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.4 33.7 - - + -
35B LEU* 4.1 17.6 - - + +
42B ALA 4.5 4.9 - - - -
43B ILE* 2.9 30.8 + - + +
44B TYR 2.7 3.4 + - - -
45B GLY* 1.3 71.3 - - - +
47B LEU* 1.3 65.0 + - - +
49B THR* 3.2 18.9 - - + +
50B ILE* 2.9 40.3 + - + +
196B THR* 5.0 0.7 - - + -
200B THR* 3.6 37.7 - - + +
204B PHE* 4.6 3.4 - + - -
239B TYR* 3.8 35.4 - + + -
240B VAL* 4.4 19.5 - - + -
243B THR* 3.2 28.7 + - + -
244B THR* 6.6 0.2 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.2 6.3 + - + +
44B TYR* 2.4 31.0 + - + +
46B TRP* 1.3 68.0 - - - +
48B VAL* 1.3 70.8 + - + +
50B ILE* 4.3 3.7 - - + +
51B ILE* 3.3 37.1 + - + +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.0 17.2 + - + +
45B GLY 3.6 7.0 - - - +
47B LEU* 1.3 83.0 - - + +
49B THR* 1.3 67.2 + - - +
51B ILE* 2.9 16.2 + - - +
52B GLY* 3.0 11.1 + - - +
193B ILE* 4.8 11.4 - - + -
197B LEU* 3.5 29.6 - - + -
201B LEU* 5.9 0.9 - - + -
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLY 3.0 11.5 + - - +
46B TRP* 3.2 34.1 - - + +
48B VAL* 1.3 81.1 - - - +
50B ILE* 1.3 61.8 + - + +
52B GLY* 3.2 1.3 + - - +
53B ALA* 2.8 30.4 + - - +
197B LEU* 4.1 0.9 - - - -
200B THR* 3.3 30.9 + - - +
201B LEU* 3.0 29.7 - - - +
204B PHE* 4.1 5.2 - - + -
397B TYR* 3.6 7.1 + - - -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TRP* 2.9 27.6 + - + +
47B LEU* 4.4 4.5 - - + +
49B THR* 1.3 76.0 - - + +
51B ILE* 1.3 61.8 + - - +
54B LEU* 2.9 47.8 + - + +
204B PHE* 4.2 15.5 - - + -
236B ALA* 3.6 38.1 - - + +
237B VAL* 5.7 0.2 - - - -
240B VAL* 3.4 32.8 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.3 34.9 + - + +
48B VAL* 2.9 11.5 + - - +
50B ILE* 1.3 79.3 - - - +
52B GLY* 1.3 64.5 + - - +
54B LEU* 3.5 7.8 - - - +
55B GLY* 3.0 19.1 + - - -
58B MET* 5.5 0.2 - - - +
393B ILE* 4.1 26.0 - - + +
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Residues in contact with GLY 52 (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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48B VAL* 3.0 13.6 + - - -
49B THR* 3.2 1.1 + - - -
51B ILE* 1.3 78.3 - - - +
53B ALA* 1.3 55.7 + - - +
55B GLY* 3.0 5.0 + - - -
56B LEU* 3.0 23.2 + - - +
393B ILE* 3.8 20.5 - - - +
394B ALA* 4.8 0.3 - - - -
397B TYR* 3.2 26.1 - - - +
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B THR 2.8 18.9 + - - +
50B ILE 4.3 0.4 - - - +
52B GLY* 1.3 70.0 - - - +
54B LEU* 1.3 56.2 + - - +
56B LEU* 3.0 8.4 + - + +
57B SER* 2.7 36.2 + - - -
204B PHE* 3.5 39.7 - - + +
207B VAL* 4.5 3.4 - - + +
232B VAL* 4.5 2.5 - - + +
397B TYR* 3.2 20.2 - - + +
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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
----------------------------------------------------------
50B ILE* 2.9 37.5 + - + +
51B ILE* 3.5 6.5 - - - +
53B ALA* 1.3 75.3 - - - +
55B GLY* 1.3 58.4 + - - +
57B SER* 2.8 12.4 + - - +
58B MET* 2.8 45.6 + - + +
232B VAL* 4.4 16.1 - - + +
233B LEU* 3.4 35.4 - - + -
236B ALA* 5.1 1.3 - - + -
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Residues in contact with GLY 55 (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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51B ILE 3.0 13.2 + - - -
52B GLY 3.0 4.9 + - - -
54B LEU* 1.3 79.1 - - - +
56B LEU* 1.3 56.3 + - - +
58B MET* 3.1 15.8 + - - +
59B VAL* 2.8 35.6 + - - +
390B VAL* 3.8 17.5 - - - +
393B ILE* 4.7 4.0 - - - -
394B ALA* 4.4 4.0 - - - -
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Residues in contact with LEU 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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52B GLY 3.0 11.6 + - - +
53B ALA* 3.0 12.3 + - + +
55B GLY* 1.3 75.7 - - - +
57B SER* 1.3 63.4 - - - +
59B VAL* 3.3 2.8 + - + -
60B TYR* 3.1 31.1 + - + -
207B VAL* 4.2 9.4 - - + -
362B LEU* 5.9 0.7 - - + -
365B TYR* 3.2 50.0 - - + -
369B CYS* 4.0 27.1 - - - -
394B ALA* 4.1 11.5 - - + +
397B TYR* 4.5 18.8 - - + -
398B CYS* 4.3 12.3 - - - -
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA 2.7 18.8 + - - -
54B LEU* 2.8 17.3 + - - +
56B LEU* 1.3 73.9 - - - +
58B MET* 1.3 50.2 + - - +
60B TYR* 3.5 2.9 + - - +
61B ALA* 2.7 35.3 + - - +
207B VAL* 4.0 11.2 - - - +
228B THR* 3.3 8.6 + - - -
229B ILE* 3.9 16.3 - - - +
232B VAL* 3.3 37.3 - - - +
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Residues in contact with MET 58 (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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51B ILE 5.5 0.2 - - - +
54B LEU* 2.8 50.7 + - + +
55B GLY* 3.1 13.2 + - - +
57B SER* 1.3 78.9 + - - +
59B VAL* 1.3 67.4 + - - +
61B ALA* 3.3 5.6 - - + +
62B LYS* 2.8 32.5 + - + +
229B ILE* 4.5 15.5 - - + -
390B VAL* 3.8 25.6 - - + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 2.8 21.3 + - - +
56B LEU* 3.3 7.8 + - + +
58B MET* 1.3 71.2 - - - +
60B TYR* 1.3 58.9 + - - +
63B MET* 2.9 30.1 + - - +
368B THR* 3.7 23.1 - - + -
369B CYS* 3.9 16.6 - - - -
372B LEU* 3.3 29.4 - - + +
390B VAL* 4.4 4.2 - - + +
391B THR* 3.6 26.5 - - + +
394B ALA* 3.6 22.9 - - + -
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.1 18.6 + - + +
57B SER* 3.8 6.3 - - - +
59B VAL* 1.3 75.8 - - - +
61B ALA* 1.3 68.5 + - - +
62B LYS 2.8 1.7 + - - -
63B MET* 2.9 12.1 + - - -
64B SER* 2.8 20.4 + - - -
73B SER* 2.8 32.0 + - - -
76B TYR* 4.1 2.7 - + - -
207B VAL* 4.4 10.1 - - + +
208B GLU* 4.0 24.0 + - + +
211B SER* 3.2 35.2 + - - -
212B VAL* 5.3 0.2 - - + -
228B THR* 5.0 2.2 - - + -
364B PRO 3.6 7.6 + - - -
365B TYR* 3.4 32.7 - + - -
368B THR* 2.5 43.4 + - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 2.7 23.7 + - - +
58B MET* 2.9 8.0 + - - +
60B TYR* 1.3 73.0 - - - +
62B LYS* 1.3 64.6 + - + +
64B SER* 3.3 6.6 + - - -
65B PHE* 3.6 2.6 - - - +
225B PRO* 3.1 36.5 - - + +
228B THR* 3.4 12.7 + - - +
229B ILE* 3.3 33.0 - - + -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MET* 2.8 17.7 + - + +
59B VAL 3.7 1.8 - - - +
61B ALA* 1.3 85.3 - - + +
63B MET* 1.3 61.2 + - - +
64B SER 3.5 0.2 - - - -
65B PHE* 3.7 26.5 + - + +
66B LEU* 3.5 23.4 + - - +
225B PRO* 4.1 13.9 - - - +
226B ILE 5.6 0.2 - - - +
229B ILE* 3.9 21.1 - - + +
372B LEU* 4.0 11.9 - - + +
387B TYR* 3.8 33.2 - - + +
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Residues in contact with MET 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A PRO* 6.3 0.2 - - + -
59B VAL 2.9 17.9 + - - +
60B TYR* 2.9 7.0 + - - +
62B LYS* 1.3 78.3 - - - +
64B SER* 1.3 62.1 + - - +
65B PHE 3.2 0.2 - - - -
66B LEU* 3.2 14.6 + - + +
67B ASP* 3.0 29.7 + - + +
76B TYR* 3.6 41.3 - - + -
368B THR* 4.7 4.9 - - + +
371B ALA* 3.7 18.8 - - + +
372B LEU* 3.8 29.6 - - + +
375B LEU* 3.4 35.4 - - + -
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR 2.8 19.1 + - - -
61B ALA* 3.3 7.8 + - - -
63B MET* 1.3 75.4 - - - +
65B PHE* 1.3 59.7 + - - +
66B LEU 3.0 5.9 + - - -
67B ASP 4.0 4.0 - - - -
68B PRO* 2.7 38.7 - - - +
76B TYR* 3.6 19.0 + - - -
211B SER* 3.8 7.1 - - - -
220B PRO 5.0 0.2 - - - +
221B LYS* 4.7 1.0 - - - +
224B VAL* 3.1 34.0 - - - +
225B PRO* 4.2 1.7 - - - +
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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