Contacts of the helix formed by residues 93 - 107 (chain E) in PDB entry 2BM9
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 GLY 93 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E LEU* 5.0 0.2 - - - -
90E VAL* 3.0 28.5 + - - +
91E TYR 3.4 0.8 - - - -
92E ASN* 1.3 78.9 + - - +
94E GLY* 1.3 63.8 + - - +
95E SER* 3.3 2.5 - - - -
96E LEU* 3.2 19.2 + - - +
97E ALA* 3.1 19.8 + - - +
122E CYS* 4.3 0.2 - - - -
124E ILE* 3.4 15.3 - - - +
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Residues in contact with GLY 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.8 2.3 - - - +
61E LEU* 4.2 14.1 - - - -
62E ARG 3.3 21.8 - - - -
63E MET* 3.7 9.7 - - - +
90E VAL 4.7 0.4 + - - -
92E ASN* 3.2 13.8 + - - +
93E GLY* 1.3 75.5 - - - +
95E SER* 1.3 65.2 + - - +
97E ALA* 3.5 2.4 + - - +
98E TRP* 3.2 25.3 + - - +
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Residues in contact with SER 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E MET* 4.1 11.1 - - - +
64E LEU 5.0 2.6 + - - -
65E LYS* 3.5 25.2 - - - +
87E GLU* 4.3 13.2 - - - -
90E VAL 5.6 0.6 + - - -
92E ASN* 4.9 0.8 + - - -
93E GLY* 3.3 0.8 - - - -
94E GLY* 1.3 76.1 - - - +
96E LEU* 1.3 64.3 + - - +
98E TRP* 4.0 3.9 - - - +
99E PHE* 3.1 32.3 + - - -
301E SAM 2.6 37.5 + - - -
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLU* 3.6 33.7 - - + +
90E VAL* 4.2 20.0 - - + +
93E GLY* 3.2 25.2 + - - +
95E SER* 1.3 83.5 - - - +
97E ALA* 1.3 63.5 + - - +
98E TRP 3.2 0.2 + - - -
99E PHE* 3.3 9.8 + - - +
100E ARG* 3.3 11.8 + - - +
112E VAL* 3.8 25.5 - - + +
114E GLY* 4.1 10.1 - - - +
122E CYS* 5.0 0.2 - - - -
124E ILE* 4.1 9.2 - - + -
132E ILE* 4.3 9.9 - - + -
134E LEU* 3.4 33.9 - - + -
301E SAM 5.8 0.4 - - - +
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Residues in contact with ALA 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 4.8 2.7 - - + -
59E ARG* 6.2 0.2 - - - +
61E LEU* 3.6 31.0 - - + -
93E GLY 3.1 6.5 + - - +
94E GLY 3.5 1.3 + - - +
96E LEU* 1.3 79.3 - - - +
98E TRP* 1.3 56.3 + - - +
100E ARG* 3.4 20.6 + - - +
101E ASP* 3.0 40.1 + - - +
124E ILE* 4.5 11.2 - - + +
128E ASP* 6.2 0.7 - - + -
132E ILE* 4.2 5.6 - - - -
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Residues in contact with TRP 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E TRP* 3.6 50.1 - + + +
63E MET* 3.4 26.5 - - + -
65E LYS* 5.2 4.5 - - + -
70E GLN* 3.6 50.1 + - + -
73E TYR* 3.7 20.9 - + + -
94E GLY 3.2 17.7 + - - +
95E SER* 4.1 6.1 - - - -
97E ALA* 1.3 76.5 - - - +
99E PHE* 1.3 94.4 + + - +
101E ASP* 3.9 0.4 - - - +
102E LEU* 3.1 59.9 + - + +
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Residues in contact with PHE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LYS* 4.3 6.3 - - - -
73E TYR* 3.8 28.9 - + + -
77E LEU* 4.1 15.7 - - + -
85E ILE* 3.7 29.4 - - + -
87E GLU* 4.0 18.8 - - + -
95E SER* 3.1 26.8 + - - +
96E LEU* 3.8 2.2 - - - +
98E TRP* 1.3 104.1 - + - +
100E ARG* 1.3 61.2 + - - +
101E ASP 3.2 0.2 - - - -
102E LEU* 4.1 1.7 - - - +
103E THR* 2.7 34.7 + - - +
112E VAL* 3.7 19.5 - - + +
158E ILE* 3.5 31.9 - - + -
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 4.6 3.0 - - - +
96E LEU 3.3 7.9 + - - +
97E ALA* 3.7 24.8 + - - +
98E TRP 3.4 0.2 - - - -
99E PHE* 1.3 77.0 - - - +
101E ASP* 1.3 90.3 + - - +
103E THR* 3.1 15.0 + - - +
104E LYS* 3.2 29.0 + - + +
110E CYS 5.2 2.5 - - - +
112E VAL* 3.7 17.0 - - + +
128E ASP* 3.3 33.0 + - - +
130E GLU* 2.8 57.7 + - - +
131E ASN* 3.9 15.7 - - + +
132E ILE* 3.2 22.4 - - + +
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Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 4.1 13.0 - - + +
58E TRP* 2.8 40.3 + - + +
59E ARG* 3.4 27.0 + - - -
97E ALA* 3.0 24.2 + - - +
98E TRP 3.9 2.2 - - - +
99E PHE 3.2 0.2 - - - -
100E ARG* 1.3 99.0 + - - +
102E LEU* 1.3 62.9 + - - +
104E LYS* 3.1 20.2 + - - +
105E ILE* 3.1 18.3 - - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP* 3.9 30.5 - - + -
58E TRP* 4.8 8.7 - - + -
74E HIS* 4.1 29.4 - - + -
77E LEU* 4.1 19.7 - - + -
98E TRP* 3.1 55.3 + - + +
99E PHE* 4.1 3.1 - - - +
100E ARG 3.3 0.2 - - - -
101E ASP* 1.3 78.0 - - - +
103E THR* 1.3 64.5 + - - +
105E ILE* 3.2 11.9 + - + +
106E MET* 3.0 31.0 + - + +
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Residues in contact with THR 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 3.8 20.4 - - + -
82E PRO* 4.9 2.5 - - + +
85E ILE* 4.1 4.5 - - + -
99E PHE 2.7 23.4 + - - +
100E ARG* 3.1 17.3 + - - +
102E LEU* 1.3 73.7 - - - +
104E LYS* 1.3 60.4 + - - +
106E MET* 3.1 9.2 + - - -
107E GLY 3.0 18.9 + - - -
108E ILE* 3.1 27.8 + - + -
110E CYS* 3.6 41.3 + - + +
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Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ILE* 5.4 5.2 - - + -
100E ARG* 3.2 22.6 + - + +
101E ASP* 3.1 16.2 + - - +
103E THR* 1.3 80.8 + - - +
105E ILE* 1.3 61.7 + - + +
107E GLY* 3.3 12.2 + - - -
108E ILE 4.8 4.0 - - - -
130E GLU* 3.6 26.6 + - - +
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Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D TRP* 4.0 24.7 - - + -
59D ARG* 3.2 30.1 + - - +
101D ASP* 3.5 34.5 - - + +
102D LEU* 5.4 2.0 - - + -
104D LYS* 6.1 3.1 - - - +
105D ILE* 3.3 35.9 - - + -
58E TRP* 5.6 1.8 - - + -
101E ASP 3.1 16.1 + - - +
102E LEU* 3.2 13.0 + - + +
104E LYS* 1.3 75.4 - - - +
106E MET* 1.3 63.6 + - - +
107E GLY* 3.1 2.3 + - - -
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Residues in contact with MET 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ARG* 4.5 17.2 + - + +
74E HIS* 3.4 56.3 - - + +
77E LEU* 3.8 24.7 - - + -
78E TRP* 3.7 41.3 - - + -
81E ARG* 3.5 16.1 + - - -
102E LEU* 3.0 23.4 + - + +
103E THR 3.1 1.1 + - - +
105E ILE* 1.3 76.3 - - + +
107E GLY* 1.3 58.9 + - - +
108E ILE* 3.4 24.7 - - + -
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Residues in contact with GLY 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E ARG* 3.6 10.2 + - - -
103E THR 3.0 2.8 + - - -
104E LYS 3.3 8.9 + - - -
105E ILE 3.1 6.5 - - - -
106E MET* 1.3 78.2 - - - +
108E ILE* 1.3 59.2 + - - +
109E ASP 4.1 0.5 + - - -
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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