Contacts of the helix formed by residues 66 - 81 (chain I) in PDB entry 2BM8
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 ASP 66 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56I TYR* 3.4 22.0 - - + -
64I LEU 3.5 3.2 + - - +
65I LYS* 1.3 74.2 - - - +
67I PRO* 1.3 75.3 - - + +
68I ASP* 3.4 24.2 + - - +
69I THR* 3.0 14.7 + - - -
70I GLN* 2.9 21.1 + - - +
221I SER* 5.1 0.2 + - - -
222I SER* 4.6 8.5 + - - -
223I GLN* 3.2 28.1 + - - +
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Residues in contact with PRO 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TYR* 3.4 37.9 - - + +
66I ASP* 1.3 91.3 - - + +
68I ASP* 1.3 64.9 + - - +
70I GLN* 3.6 16.6 - - + +
71I ALA* 3.0 18.7 + - - +
67L PRO* 3.4 39.4 - - + +
68L ASP* 4.1 10.3 - - - +
71L ALA* 3.9 16.4 - - + -
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Residues in contact with ASP 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I ASP* 3.2 16.3 - - - +
67I PRO* 1.3 80.8 - - - +
69I THR* 1.3 61.4 + - - +
71I ALA* 3.4 8.0 - - - +
72I VAL* 3.4 23.0 + - - +
220I ALA 4.2 6.1 - - - +
221I SER* 3.8 21.1 - - - -
222I SER* 5.2 3.1 - - - +
56L TYR* 5.7 0.7 + - - -
67L PRO* 4.6 6.6 - - - +
68L ASP* 4.3 14.6 - - - +
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Residues in contact with THR 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I LYS* 4.2 11.9 - - + -
66I ASP* 3.0 11.5 + - - -
68I ASP* 1.3 75.5 - - - +
70I GLN* 1.3 65.0 + - - +
71I ALA 3.2 0.4 - - - -
72I VAL* 3.2 5.0 + - - +
73I TYR* 3.0 47.0 + - + -
186I GLU* 4.6 1.3 - - - +
221I SER* 2.9 21.4 + - - -
223I GLN* 2.7 33.5 + - + +
224I LEU* 3.8 17.9 - - + -
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Residues in contact with GLN 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I TYR* 4.8 5.1 - - - +
57I GLN 5.3 5.2 + - - +
58I TRP* 5.3 4.3 - - - -
63I MET* 3.9 28.2 - - + +
65I LYS* 2.9 25.6 + - + +
66I ASP* 2.9 19.1 + - - +
67I PRO* 3.6 18.2 - - + +
69I THR* 1.3 75.1 - - - +
71I ALA* 1.3 63.7 + - - +
73I TYR* 3.2 1.3 + - - -
74I HIS* 2.9 24.8 + - - +
98I TRP* 3.5 41.7 + - + -
71L ALA* 6.1 0.8 - - - +
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Residues in contact with ALA 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I PRO 3.0 13.1 + - - +
68I ASP 3.4 10.8 - - - +
69I THR 3.2 0.4 - - - -
70I GLN* 1.3 76.5 - - - +
72I VAL* 1.3 62.8 + - + +
74I HIS* 3.2 7.8 + - - +
75I ASP* 3.1 31.1 + - - +
56L TYR* 4.3 17.0 - - + -
67L PRO* 4.0 19.3 - - + -
70L GLN* 6.3 0.4 - - - +
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Residues in contact with VAL 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I ASP 3.4 13.0 + - - +
69I THR 3.2 7.5 + - - +
71I ALA* 1.3 76.4 - - + +
73I TYR* 1.3 64.6 + - - +
75I ASP* 3.2 8.8 + - - +
76I MET* 3.1 28.8 + - + +
217I TYR* 3.8 35.2 - - + +
220I ALA* 3.5 37.5 - - + +
221I SER* 4.3 5.8 - - - -
224I LEU* 3.7 22.7 - - + -
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Residues in contact with TYR 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I LYS* 3.9 14.6 - - + -
69I THR* 3.0 38.4 + - + +
72I VAL* 1.3 73.6 - - - +
74I HIS* 1.3 65.3 + - - +
76I MET* 4.0 17.7 - - + -
77I LEU* 3.0 34.6 + - + +
98I TRP* 3.6 25.4 - + + -
99I PHE* 3.8 16.8 - + + -
156I ILE* 4.6 3.4 - - + -
158I ILE* 3.5 24.5 - - + +
184I ILE* 3.3 41.1 - - + +
186I GLU* 2.9 29.7 + - - -
224I LEU* 4.0 9.9 - - + -
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Residues in contact with HIS 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I GLN 2.9 14.2 + - - +
71I ALA* 3.4 12.6 - - - +
72I VAL 3.2 0.2 - - - -
73I TYR* 1.3 78.5 - - - +
75I ASP* 1.3 73.0 + - - +
78I TRP* 3.1 20.7 + - + +
98I TRP* 4.3 1.2 - - + -
102I LEU* 4.2 16.4 - - + -
106I MET* 3.4 27.6 - - + +
57L GLN* 3.6 20.9 + - - +
58L TRP* 3.3 44.5 - + - -
59L ARG* 3.2 32.3 + - - +
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Residues in contact with ASP 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71I ALA* 3.1 19.2 + - - +
72I VAL* 3.2 7.7 + - - +
74I HIS* 1.3 78.6 + - - +
76I MET* 1.3 57.5 - - - +
78I TRP* 3.4 3.8 + - - +
79I GLU* 3.0 29.8 + - - +
217I TYR* 3.5 20.8 + - + +
24L TYR* 4.5 6.4 + - - +
27L PRO* 5.9 2.6 - - - +
55L PRO 4.6 10.2 - - - +
56L TYR* 5.6 2.3 - - - -
57L GLN* 3.2 42.0 + - - +
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Residues in contact with MET 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I VAL* 3.1 23.1 + - + +
73I TYR* 3.9 16.8 - - + +
75I ASP* 1.3 74.7 - - - +
77I LEU* 1.3 58.8 + - - +
79I GLU* 3.9 1.5 - - - +
80I LEU* 2.9 36.7 + - + +
156I ILE* 4.0 24.5 - - + -
182I TYR* 3.9 22.7 - - + -
184I ILE* 3.7 32.5 - - + -
217I TYR* 3.7 41.9 + - + -
224I LEU* 5.7 0.4 - - + -
228I VAL* 3.9 16.4 - - + -
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Residues in contact with LEU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I TYR* 3.0 30.5 + - + +
74I HIS 3.7 3.4 - - - +
76I MET* 1.3 74.0 - - + +
78I TRP* 1.3 62.3 + - - +
81I ARG* 2.8 32.7 + - - +
82I PRO* 3.7 15.0 - - + +
85I ILE* 3.9 10.8 - - + -
99I PHE* 4.2 23.6 - - + +
102I LEU* 4.2 27.4 - - + -
103I THR* 4.1 21.1 - - + -
106I MET* 3.9 12.8 - - + -
108I ILE* 3.7 3.9 - - + +
156I ILE* 3.8 25.1 - - + -
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Residues in contact with TRP 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I HIS 3.1 17.7 + - - +
75I ASP 3.5 5.4 - - - +
77I LEU* 1.3 78.5 - - - +
79I GLU* 1.3 61.9 + - + +
81I ARG* 3.6 25.3 + - - +
106I MET* 3.9 43.2 - - + -
24L TYR* 4.8 7.7 - + - -
57L GLN* 3.7 25.8 - - - +
59L ARG* 3.4 42.0 - - + -
60L GLY* 3.5 19.0 - - - -
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Residues in contact with GLU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ASP 3.0 16.6 + - - +
76I MET* 3.9 2.3 - - - +
78I TRP* 1.3 81.2 - - + +
80I LEU* 1.3 67.3 + - + +
81I ARG* 4.6 3.1 - - - +
182I TYR* 4.2 4.8 + - - -
216I LEU* 4.7 2.1 - - - +
217I TYR* 2.7 29.9 + - - +
230I ARG* 5.5 2.2 - - - -
34L ARG* 3.1 38.0 + - - -
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I MET* 2.9 22.3 + - + +
79I GLU* 1.3 77.6 - - + +
81I ARG* 1.3 69.8 + - - +
82I PRO* 3.9 12.3 - - + -
154I PRO* 3.5 40.1 - - + +
155I LEU 4.4 3.6 - - - +
156I ILE* 3.9 27.6 - - + -
180I GLY* 3.9 17.5 - - - +
182I TYR* 4.1 25.1 - - + -
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Residues in contact with ARG 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I LEU 2.8 20.9 + - - +
78I TRP* 3.6 34.7 + - - +
79I GLU 4.6 2.5 - - - +
80I LEU* 1.3 77.1 - - - +
82I PRO* 1.3 72.3 - - - +
83I ARG* 3.7 3.8 + - - +
106I MET 3.4 18.2 + - - -
107I GLY 3.5 26.3 + - - -
108I ILE* 3.4 27.7 - - + +
154I PRO* 3.9 8.5 - - - +
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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