Contacts of the helix formed by residues 44 - 64 (chain B) in PDB entry 5B6N
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 THR 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PRO* 4.0 21.1 - - + -
217A TYR* 3.8 2.0 - - - -
40B PRO* 6.3 0.2 - - + -
41B ARG* 2.9 28.2 + - + -
42B ASP 3.6 9.2 - - - +
43B PHE* 1.3 84.2 - - - +
45B PRO* 1.3 60.9 - - - +
46B VAL 3.6 0.7 - - - -
47B CSD 2.1 33.5 + - - +
48B THR* 2.0 38.6 + - - -
82B TRP* 4.2 1.0 - - - +
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Residues in contact with PRO 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 6.4 0.4 - - + -
188A MET* 4.0 22.2 - - + +
189A VAL 3.5 24.0 - - - +
190A LEU* 5.3 0.2 - - - -
191A PRO* 3.9 15.9 - - + -
217A TYR* 3.4 28.7 - - + +
218A LEU* 3.5 22.5 - - + +
219A ARG 4.6 0.4 - - - +
44B THR* 1.3 86.9 - - - +
46B VAL* 1.3 63.9 + - + +
48B THR* 3.5 6.8 + - - +
49B THR* 3.1 21.3 - - - +
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Residues in contact with VAL 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ALA* 3.7 28.0 - - + -
177A THR 3.4 22.4 - - - +
178A PRO* 3.7 10.1 - - + -
188A MET* 3.6 25.6 - - + -
44B THR* 4.9 1.0 - - - -
45B PRO* 1.3 75.8 - - + +
47B CSD 1.3 61.5 + - - +
48B THR 3.1 1.6 - - - -
49B THR* 2.2 31.4 + - - +
50B GLU* 2.9 11.0 + - - +
132B ARG* 3.4 30.7 - - - +
154B GLY* 4.1 5.8 - - - +
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Residues in contact with CSD 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 3.6 11.4 - - + -
40B PRO* 3.5 27.4 - - - +
41B ARG 3.4 10.8 + - - +
44B THR* 2.1 40.0 + - - +
46B VAL* 1.3 77.9 + - - +
48B THR* 1.3 56.1 + - - +
50B GLU* 4.0 6.5 - - - -
51B LEU* 3.0 34.9 + - - +
82B TRP* 3.7 18.3 - - + -
132B ARG* 2.3 40.7 + - - -
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Residues in contact with THR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 5.4 0.2 - - + -
217A TYR* 3.6 17.1 - - + +
218A LEU* 4.5 12.1 - - + -
44B THR 2.0 35.8 + - - -
45B PRO* 3.5 8.3 + - - +
46B VAL 3.1 0.4 - - - -
47B CSD 1.3 74.6 + - - -
49B THR* 1.3 64.4 + - - +
51B LEU* 4.1 0.7 - - - +
52B GLY* 3.2 20.3 + - - -
82B TRP* 3.7 23.8 + - - +
85B ASP 4.5 4.7 - - - +
86B ILE* 4.3 23.1 - - - +
89B TYR* 4.1 14.1 - - + -
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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
----------------------------------------------------------
178A PRO* 4.0 16.8 - - + -
179A VAL* 3.4 32.7 + - - +
188A MET* 4.7 9.6 - - + -
218A LEU* 4.8 1.3 - - + -
220A TYR* 4.8 1.8 - - + +
45B PRO 3.1 17.7 - - - +
46B VAL* 2.2 27.6 + - - -
48B THR* 1.3 75.1 - - - +
50B GLU* 1.3 62.5 + - - +
52B GLY 3.4 0.5 + - - -
53B ARG* 2.9 30.5 + - - +
89B TYR* 3.9 33.6 - - + +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 4.0 25.4 - - + -
39B HIS* 4.6 3.3 - - - +
46B VAL* 2.9 12.2 + - + +
47B CSD 3.6 9.6 + - - +
48B THR 3.3 0.2 - - - -
49B THR* 1.3 81.9 + - - +
51B LEU* 1.3 63.3 + - + +
53B ARG* 3.2 4.3 + - - +
54B ALA* 3.0 22.7 + - - +
132B ARG* 2.6 38.2 + - - +
154B GLY* 3.7 0.2 - - - -
155B ARG* 3.0 53.9 + - - +
157B PHE* 3.7 19.5 - - + -
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Residues in contact with LEU 51 (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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37B PHE* 3.9 24.0 - - + -
39B HIS* 3.5 36.8 - - + +
47B CSD 3.0 21.0 + - - +
48B THR 4.6 0.7 - - - +
50B GLU* 1.3 82.1 - - + +
52B GLY* 1.3 57.9 + - - +
54B ALA* 3.9 6.7 - - - -
55B ALA* 3.4 20.4 + - - +
70B ALA* 4.3 11.9 - - + -
82B TRP* 3.5 26.7 - - + -
86B ILE* 3.9 23.5 - - + +
98B LEU* 5.2 0.4 - - + -
100B PHE* 3.6 16.5 - - + -
102B ILE* 4.5 7.2 - - + -
155B ARG* 5.1 0.4 - - - +
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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 THR 3.2 17.5 + - - -
49B THR 3.8 1.8 - - - -
50B GLU 3.1 0.6 - - - -
51B LEU* 1.3 76.6 - - - +
53B ARG* 1.3 64.3 + - - +
54B ALA 3.3 0.2 - - - -
55B ALA* 3.6 1.7 + - - -
56B LYS* 3.4 12.5 + - - +
86B ILE* 4.0 7.2 - - - -
89B TYR* 4.5 4.5 - - - -
90B ASN* 2.8 42.8 + - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.9 19.1 - - + -
180A ASP* 3.3 25.5 + - - +
49B THR 2.9 17.9 + - - +
50B GLU 3.4 5.6 - - - +
52B GLY* 1.3 76.4 - - - +
54B ALA* 1.3 63.9 + - - +
56B LYS* 3.3 23.7 + - - +
57B LEU* 3.2 38.5 + - + +
89B TYR* 5.9 0.7 - - + -
90B ASN* 5.2 0.2 - - - +
157B PHE* 4.0 14.4 - - + -
158B ASP* 3.4 25.6 + - - -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.0 12.1 - - + -
50B GLU 3.0 15.5 + - - +
51B LEU 3.8 7.6 - - - +
53B ARG* 1.3 78.0 - - - +
55B ALA* 1.3 55.9 + - - +
57B LEU* 2.8 21.0 + - - +
58B ALA* 2.8 15.6 + - - +
68B LEU* 4.0 8.6 - - + +
100B PHE* 3.8 18.6 - - + -
157B PHE* 3.9 24.4 - - + -
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Residues in contact with ALA 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 LEU 3.4 15.9 + - - +
52B GLY* 3.9 7.2 - - - +
53B ARG 3.3 0.4 - - - -
54B ALA* 1.3 78.9 - - - +
56B LYS* 1.3 60.6 + - - +
57B LEU 3.3 0.2 - - - -
58B ALA 4.0 0.7 - - - -
59B PRO* 3.9 10.2 - - - +
86B ILE* 5.3 1.1 - - + -
87B ASN* 6.1 2.2 - - - +
90B ASN* 4.2 8.7 - - - +
98B LEU* 5.1 7.0 - - + -
99B PRO* 3.8 33.8 - - + +
100B PHE* 3.8 9.6 - - + -
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Residues in contact with LYS 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 3.4 15.0 - - - +
53B ARG* 3.3 27.1 + - - +
54B ALA 3.0 0.6 - - - -
55B ALA* 1.3 76.7 - - - +
57B LEU* 1.3 61.2 + - - +
58B ALA 3.4 0.9 - - - -
59B PRO* 3.4 15.7 - - - +
60B GLU* 5.6 1.9 - - - +
90B ASN* 3.5 40.9 + - - +
92B GLU* 4.3 14.6 + - - +
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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
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53B ARG* 3.2 38.9 + - - +
54B ALA* 2.8 8.1 + - - +
56B LYS* 1.3 79.9 - - - +
58B ALA* 1.3 57.4 + - - +
59B PRO* 3.2 3.4 - - - -
60B GLU* 3.0 37.3 + - + +
61B PHE* 3.0 29.2 + - + -
157B PHE* 3.6 44.2 - - + +
158B ASP* 4.6 3.6 - - - +
161B LEU* 4.7 17.7 - - + -
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Residues in contact with ALA 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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54B ALA 2.8 12.9 + - - +
55B ALA 4.0 0.7 - - - +
57B LEU* 1.3 76.6 - - - +
59B PRO* 1.3 67.2 - - + +
61B PHE* 4.1 9.5 - - - +
62B ALA* 3.0 25.3 + - - +
68B LEU* 4.4 12.6 - - + -
99B PRO* 3.8 35.2 - - + +
100B PHE* 4.8 1.3 - - + -
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Residues in contact with PRO 59 (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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55B ALA 3.9 5.8 - - - +
56B LYS* 3.4 21.1 - - - +
57B LEU 3.5 0.2 - - - -
58B ALA* 1.3 93.8 - - + +
60B GLU* 1.3 63.3 + - + +
62B ALA* 3.4 5.3 + - + +
63B LYS* 3.2 26.0 + - - +
99B PRO* 6.1 0.4 - - + -
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Residues in contact with GLU 60 (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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56B LYS 5.6 1.6 - - - +
57B LEU* 3.0 23.9 + - + +
59B PRO* 1.3 79.0 - - + +
61B PHE* 1.3 65.8 + - - +
62B ALA 3.4 0.3 + - - -
63B LYS* 3.2 37.2 + - - +
64B ARG* 2.6 50.1 + - - +
161B LEU* 3.9 21.8 - - + +
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Residues in contact with PHE 61 (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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35B ILE* 3.7 23.1 - - + -
57B LEU* 3.0 49.9 + - + +
58B ALA* 4.1 6.1 - - - +
60B GLU* 1.3 75.3 - - - +
62B ALA* 1.3 54.5 + - - +
64B ARG* 4.0 1.1 - - - -
65B ASN 3.6 1.6 + - - -
66B VAL* 2.7 61.3 + - + +
68B LEU* 3.9 25.8 - - + -
157B PHE* 4.6 9.9 - + - -
160B ILE* 3.9 20.9 - - + -
161B LEU* 3.8 38.4 - - + -
164B VAL* 4.1 10.5 - - + -
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Residues in contact with ALA 62 (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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58B ALA 3.0 19.7 + - - +
59B PRO* 3.5 7.6 - - + +
60B GLU 3.1 0.2 - - - -
61B PHE* 1.3 74.6 - - - +
63B LYS* 1.3 55.4 + - - +
64B ARG 2.9 4.3 - - - -
65B ASN* 2.7 27.4 + - - -
66B VAL 3.8 8.0 + - - -
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Residues in contact with LYS 63 (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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59B PRO 3.2 16.1 + - - +
60B GLU* 3.2 42.7 + - - +
62B ALA* 1.3 78.0 - - - +
64B ARG* 1.3 78.1 + - + +
65B ASN* 3.3 2.0 + - - +
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Residues in contact with ARG 64 (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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60B GLU* 2.6 46.0 + - - +
61B PHE* 4.2 3.8 - - - +
62B ALA 2.9 1.6 + - - -
63B LYS* 1.3 97.9 - - + +
65B ASN* 1.3 65.1 + - - +
66B VAL* 3.4 5.1 - - + +
161B LEU* 4.8 8.6 - - - +
164B VAL* 4.9 7.6 - - + -
165B ILE* 3.5 44.0 - - - +
168B GLN* 2.5 49.1 + - - +
183B ASP* 3.9 12.1 + - - -
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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