Contacts of the helix formed by residues 43 - 64 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.3 40.2 - - + -
42A ALA* 1.3 71.7 - - - +
44A TYR* 1.3 72.6 + - + +
45A GLY 3.2 2.2 - - - -
46A TRP* 2.9 30.2 + - + +
47A LEU* 3.2 8.2 + - + +
183A ASN* 5.9 0.4 - - - +
240A VAL* 5.7 6.5 - - + -
243A THR 6.0 1.3 - - - +
244A THR* 5.0 22.0 - - + -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.3 3.8 - - - -
43A ILE* 1.3 80.7 - - + +
45A GLY* 1.3 57.0 + - - +
47A LEU* 2.4 37.2 + - + +
48A VAL* 3.0 13.3 + - + +
183A ASN* 4.7 14.8 + - - -
189A THR* 3.6 27.3 - - + +
193A ILE* 3.1 34.1 - - + -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.9 2.2 + - - -
43A ILE 3.2 1.4 - - - -
44A TYR* 1.3 76.4 - - - +
46A TRP* 1.3 56.2 + - - +
48A VAL* 3.4 1.4 + - - -
49A THR* 3.0 17.6 + - - +
193A ILE* 3.8 9.5 - - - +
196A THR* 2.9 31.9 + - - -
197A LEU* 2.9 32.9 - - - +
200A THR* 4.4 0.7 - - - -
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Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.4 35.0 - - + -
35A LEU* 4.2 17.6 - - + +
42A ALA 4.5 5.2 - - - -
43A ILE* 2.9 31.3 + - + +
44A TYR 2.6 3.4 + - - -
45A GLY* 1.3 70.9 - - - +
47A LEU* 1.3 64.2 + - - +
49A THR* 3.2 17.9 - - + +
50A ILE* 2.9 41.1 + - + +
196A THR* 5.0 0.7 - - + -
200A THR* 3.6 37.7 - - + +
204A PHE* 4.6 3.1 - + - -
239A TYR* 3.7 35.2 - + + -
240A VAL* 4.5 18.4 - - + -
243A THR* 3.2 28.7 + - + -
244A THR* 6.6 0.2 - - + -
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.2 6.2 + - + +
44A TYR* 2.4 31.4 + - + +
46A TRP* 1.3 67.4 - - - +
48A VAL* 1.3 71.2 + - + +
50A ILE* 4.2 3.8 - - + +
51A ILE* 3.3 37.7 + - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 3.0 16.1 + - + +
45A GLY 3.6 6.3 - - - +
47A LEU* 1.3 83.5 - - + +
49A THR* 1.3 67.4 + - - +
51A ILE* 2.9 15.9 + - - +
52A GLY* 3.0 10.7 + - - +
193A ILE* 4.8 11.4 - - + -
197A LEU* 3.5 29.8 - - + -
201A LEU* 5.9 1.1 - - + -
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.0 10.8 + - - +
46A TRP* 3.2 33.4 - - + +
48A VAL* 1.3 81.4 - - - +
50A ILE* 1.3 61.6 + - + +
52A GLY* 3.2 1.5 + - - +
53A ALA* 2.8 30.4 + - - +
197A LEU* 4.1 0.9 - - - -
200A THR* 3.2 34.5 + - - +
201A LEU* 3.0 30.1 - - - +
204A PHE* 4.1 5.5 - - + -
397A TYR* 3.6 7.1 + - - -
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TRP* 2.9 27.8 + - + +
47A LEU* 4.4 4.9 - - + +
49A THR* 1.3 75.7 - - + +
51A ILE* 1.3 65.2 + - - +
53A ALA* 4.8 0.7 - - - -
54A LEU* 2.9 43.0 + - + +
204A PHE* 4.1 15.9 - - + -
236A ALA* 3.5 39.0 - - + +
240A VAL* 3.5 32.1 - - + -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.3 34.2 + - + +
48A VAL* 2.9 10.7 + - - +
50A ILE* 1.3 80.0 - - - +
52A GLY* 1.3 64.7 + - - +
54A LEU* 3.5 7.4 - - - +
55A GLY* 3.1 18.7 + - - -
58A MET* 5.5 0.2 - - - +
393A ILE* 4.1 26.6 - - + +
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.0 13.6 + - - -
49A THR* 3.2 0.9 + - - -
51A ILE* 1.3 75.9 - - - +
53A ALA* 1.3 57.2 + - - +
55A GLY* 3.1 4.2 + - - -
56A LEU* 3.0 23.0 + - - +
393A ILE* 3.8 20.6 - - - +
394A ALA* 4.8 0.5 - - - -
397A TYR* 3.2 25.6 - - - +
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Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR 2.8 19.1 + - - +
50A ILE 4.4 0.2 - - - +
52A GLY* 1.3 69.4 - - - -
54A LEU* 1.3 56.8 + - - +
56A LEU* 3.0 8.4 + - + +
57A SER* 2.7 35.6 + - - -
204A PHE* 3.5 40.8 - - + +
207A VAL* 4.6 3.8 - - + +
232A VAL* 4.5 2.0 - - - +
397A TYR* 3.2 19.5 - - + +
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Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 2.9 37.2 + - + +
51A ILE* 3.5 6.1 - - - +
53A ALA* 1.3 75.9 - - - +
55A GLY* 1.3 56.5 + - - +
57A SER* 2.9 12.6 + - - +
58A MET* 2.9 46.4 + - + +
204A PHE* 5.6 0.2 - - - -
232A VAL* 4.4 15.7 - - + +
233A LEU* 3.4 34.8 - - + -
236A ALA* 5.0 1.3 - - + -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE 3.1 12.8 + - - -
52A GLY 3.1 5.3 + - - -
54A LEU* 1.3 75.5 - - - +
56A LEU* 1.3 59.2 + - - +
58A MET* 3.1 16.6 + - - +
59A VAL* 2.8 34.9 + - - +
390A VAL* 3.8 17.4 - - - +
393A ILE* 4.8 4.0 - - - -
394A ALA* 4.4 3.8 - - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 3.0 11.3 + - - +
53A ALA* 3.0 12.5 + - - +
55A GLY* 1.3 75.6 - - - +
57A SER* 1.3 62.5 + - - +
59A VAL* 3.2 2.3 + - + -
60A TYR* 3.1 32.7 + - + -
207A VAL* 4.1 9.4 - - + -
362A LEU* 5.9 0.4 - - + -
365A TYR* 3.2 49.4 - - + -
369A CYS* 4.0 27.4 - - - -
394A ALA* 4.0 10.4 - - + +
397A TYR* 4.5 18.8 - - + -
398A CYS* 4.3 12.6 - - - -
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Residues in contact with SER 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ALA 2.7 18.8 + - - -
54A LEU* 2.9 13.0 + - - +
56A LEU* 1.3 72.4 - - - +
58A MET* 1.3 53.8 + - - +
60A TYR* 3.6 3.1 + - - +
61A ALA* 2.7 34.4 + - - +
207A VAL* 4.0 11.8 - - - +
228A THR* 3.2 8.7 + - - -
229A ILE* 3.9 17.5 - - - +
232A VAL* 3.3 37.9 - - - +
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE 5.5 0.4 - - - +
54A LEU* 2.9 50.0 + - + +
55A GLY* 3.1 13.2 + - - +
57A SER* 1.3 80.4 + - - +
59A VAL* 1.3 67.7 + - - +
61A ALA* 3.3 5.5 - - + +
62A LYS* 2.8 32.6 + - + +
229A ILE* 4.5 15.5 - - + -
390A VAL* 3.8 23.8 - - + -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLY 2.8 21.1 + - - +
56A LEU* 3.2 8.3 + - + +
58A MET* 1.3 71.3 - - - +
60A TYR* 1.3 64.8 + - - +
63A MET* 2.9 24.8 + - - +
368A THR* 3.7 23.3 - - + -
369A CYS* 3.9 16.6 - - - -
372A LEU* 3.4 28.8 - - + +
390A VAL* 4.4 3.8 - - + +
391A THR* 3.6 26.7 - - + +
394A ALA* 3.6 23.1 - - + -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.1 20.1 + - + +
57A SER* 3.8 3.4 - - - +
59A VAL* 1.3 79.7 - - - +
61A ALA* 1.3 65.3 + - - +
62A LYS 2.8 1.7 + - - -
63A MET* 2.9 13.9 + - - -
64A SER* 2.9 18.2 + - - -
73A SER* 2.8 32.9 + - - -
76A TYR* 4.1 1.8 - + - -
207A VAL* 4.4 10.8 - - + +
208A GLU* 4.0 24.6 + - + +
211A SER* 3.2 35.3 + - - -
212A VAL* 5.3 0.2 - - + -
228A THR* 5.0 2.2 - - + -
364A PRO 3.5 7.6 + - - -
365A TYR* 3.4 33.2 - + - -
368A THR* 2.5 44.8 + - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A SER 2.7 23.5 + - - +
58A MET* 2.9 8.5 + - - +
60A TYR* 1.3 72.8 - - - +
62A LYS* 1.3 63.4 + - + +
64A SER* 3.3 6.9 + - - -
65A PHE* 3.6 1.9 - - - +
225A PRO* 3.1 36.0 - - + +
228A THR* 3.4 11.9 + - - +
229A ILE* 3.3 34.1 - - + -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 2.8 18.3 + - + +
59A VAL 3.7 1.8 - - - +
61A ALA* 1.3 86.9 - - + +
63A MET* 1.3 62.8 + - - +
64A SER 3.5 0.4 - - - -
65A PHE* 3.7 26.7 + - + +
66A LEU* 3.5 23.0 + - - +
225A PRO* 4.1 14.5 - - - +
229A ILE* 3.9 21.1 - - + +
372A LEU* 4.0 11.9 - - + +
387A TYR* 3.8 31.9 - - + +
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Residues in contact with MET 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL 2.9 18.5 + - - +
60A TYR* 2.9 7.0 + - - +
62A LYS* 1.3 78.4 - - - +
64A SER* 1.3 61.4 + - - +
65A PHE 3.2 0.2 - - - -
66A LEU* 3.2 13.6 + - + +
67A ASP* 3.0 28.9 + - + +
76A TYR* 3.6 41.5 - - + -
368A THR* 4.6 6.1 - - + +
371A ALA* 3.7 19.1 - - + +
372A LEU* 3.7 28.7 - - + -
375A LEU* 3.4 36.3 - - + -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR 2.9 18.7 + - - -
61A ALA* 3.3 7.8 + - - -
63A MET* 1.3 75.5 - - - +
65A PHE* 1.3 60.1 + - - +
66A LEU 3.0 5.9 + - - -
67A ASP 4.0 0.4 - - - -
68A PRO* 2.7 41.9 - - - +
76A TYR* 3.7 18.5 + - - -
211A SER* 3.8 7.7 - - - -
220A PRO 5.5 0.2 - - - -
221A LYS* 4.7 1.6 - - - +
224A VAL* 3.1 34.4 - - - +
225A PRO* 4.1 2.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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