Contacts of the strand formed by residues 100 - 115 (chain E) in PDB entry 3B4V
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 100 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E ILE* 4.1 19.5 - - + -
92E LEU* 3.5 34.8 - - + -
93E TYR 3.8 2.7 - - - -
94E TYR* 4.2 3.1 - - + +
99E ASN* 1.3 70.6 - - - +
101E ILE* 1.3 65.9 + - - +
157H VAL* 4.0 21.5 - - + -
158H VAL 3.7 25.4 - - - +
159H ASP* 3.7 2.8 - - - -
160H GLN* 3.2 23.4 + - - +
202H THR* 4.0 17.9 - - + +
203H CYS* 5.4 0.9 - - - -
207H ARG* 3.9 11.7 - - - +
208H SER* 2.8 33.0 + - - +
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Residues in contact with ILE 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E MET 3.6 1.0 - - - +
92E LEU* 3.3 6.5 - - - +
93E TYR* 2.8 68.8 + - + +
95E ASP* 3.5 33.4 - - + +
99E ASN* 3.5 19.3 - - + +
100E ILE* 1.3 79.9 - - - +
102E LYS* 1.3 65.5 + - - +
103E LYS* 4.1 8.1 - - + -
160H GLN* 3.4 24.9 - - + +
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Residues in contact with LYS 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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90E SER* 3.6 26.0 - - - +
91E MET 3.3 7.9 - - - +
92E LEU* 3.8 6.1 - - + -
101E ILE* 1.3 73.4 - - - +
103E LYS* 1.3 65.7 + - - +
112H ASP 4.8 13.6 + - - -
113H GLY* 4.8 9.6 + - - -
159H ASP* 3.3 29.8 - - + +
160H GLN* 2.8 29.2 + - - +
161H THR* 5.4 7.4 + - + +
163H SER* 4.2 12.5 + - - -
165H HIS* 4.0 20.7 - - + -
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Residues in contact with LYS 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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90E SER* 4.3 2.5 - - - -
91E MET* 2.8 32.5 + - - +
93E TYR* 3.3 31.2 + - + +
101E ILE* 4.1 9.3 - - + -
102E LYS* 1.3 79.4 - - - +
104E ASP* 1.3 75.9 + - - +
105E ILE* 3.5 11.0 + - + +
60G PHE 5.1 0.8 + - - -
61G LEU 3.6 17.8 + - - -
62G GLY* 4.7 4.9 + - - -
160H GLN* 4.8 3.6 - - - +
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Residues in contact with ASP 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E PRO* 4.6 8.6 - - + +
89E MET 3.5 3.6 - - - +
90E SER* 3.4 26.5 + - - -
103E LYS* 1.3 80.2 - - - +
105E ILE* 1.3 67.8 + - - +
106E GLN* 4.1 22.2 + - - +
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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
----------------------------------------------------------
88E PRO* 3.2 2.8 - - - +
89E MET 2.8 32.0 + - - -
91E MET* 3.8 19.5 - - + -
93E TYR* 4.0 12.3 - - + -
103E LYS* 3.8 18.6 - - - +
104E ASP* 1.3 84.2 - - - +
106E GLN* 1.3 65.4 + - - +
108E MET* 3.3 16.8 - - + +
58F PHE* 4.0 30.7 - - + -
60G PHE* 3.9 25.8 - - + +
61G LEU* 3.8 26.0 - - + -
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Residues in contact with GLN 106 (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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86E LEU 5.7 0.5 - - - +
87E ARG* 5.0 0.3 - - - -
88E PRO* 3.4 38.4 - - - +
104E ASP* 4.2 17.9 + - - +
105E ILE* 1.3 78.9 - - - +
107E ASN* 1.3 87.2 + - - +
108E MET* 3.1 9.0 + - - +
58F PHE* 3.9 8.5 - - - +
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Residues in contact with ASN 107 (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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86E LEU* 3.9 38.9 + - + +
87E ARG* 4.0 6.5 + - - +
106E GLN* 1.3 84.5 + - - +
108E MET* 1.3 59.3 + - - +
109E ILE 3.7 0.9 - - - -
57F SER* 4.0 20.0 - - - -
58F PHE* 3.5 4.6 - - - +
59F HIS* 3.0 30.3 + - - +
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Residues in contact with MET 108 (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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35E TYR* 2.7 63.4 + - + -
87E ARG 3.1 9.7 + - - +
89E MET* 3.7 15.9 - - + +
91E MET* 3.6 44.0 - - + +
105E ILE* 3.3 26.7 - - - +
106E GLN 3.7 6.7 - - - +
107E ASN* 1.3 78.5 - - - +
109E ILE* 1.3 65.8 + - + +
58F PHE* 3.7 23.6 - - + -
59F HIS* 3.6 17.0 - - - +
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Residues in contact with ILE 109 (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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35E TYR* 3.7 18.6 - - + -
36E HIS 3.4 16.4 - - - +
37E ALA 3.9 2.9 - - - -
38E ASN* 3.7 7.0 - - - +
86E LEU* 3.3 7.3 - - - -
87E ARG* 2.8 67.9 + - + +
88E PRO 3.6 24.2 - - - +
89E MET* 3.8 22.4 - - + -
107E ASN 3.7 0.2 - - - -
108E MET* 1.3 83.7 - - + +
110E VAL* 1.3 76.2 + - - +
111E GLU 3.3 0.3 + - - -
132H ASP* 5.7 2.2 - - - +
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Residues in contact with VAL 110 (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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13E LYS* 3.5 15.7 + - + +
37E ALA 3.0 11.4 + - - +
38E ASN* 3.0 31.7 + - + +
39E TYR* 4.2 3.8 - - - -
40E CYS* 3.8 3.4 - - - -
83E PRO* 3.8 17.0 - - + -
86E LEU* 3.9 7.2 - - + -
87E ARG* 5.7 0.2 + - - -
109E ILE* 1.3 73.7 - - - +
111E GLU* 1.3 61.9 + - - +
112E GLU 4.0 7.4 - - - +
113E CYS* 3.7 30.7 - - - -
59F HIS* 3.0 42.4 - - + +
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Residues in contact with GLU 111 (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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13E LYS* 3.1 28.5 + - - -
85E LYS* 2.8 37.5 + - + +
87E ARG* 2.7 56.8 + - + +
109E ILE 3.3 0.6 + - - -
110E VAL* 1.3 75.6 - - - +
112E GLU* 1.3 72.0 + - + +
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Residues in contact with GLU 112 (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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1E GLY* 4.0 29.5 + - - +
13E LYS* 4.6 2.5 - - - +
83E PRO* 3.4 6.1 - - - +
84E THR* 2.8 37.0 + - - +
85E LYS* 3.4 36.4 + - + +
110E VAL* 3.8 2.2 - - - +
111E GLU* 1.3 92.3 - - + +
113E CYS* 1.3 66.0 + - - +
16H GLN* 6.0 1.1 - - - -
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Residues in contact with CYS 113 (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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1E GLY* 4.8 14.9 + - - -
2E LEU* 5.1 4.7 + - - +
11E CYS* 4.2 10.1 - - - +
12E CYS* 3.9 17.9 - - - -
13E LYS* 3.4 26.0 - - - +
40E CYS* 2.0 55.2 - - + -
82E VAL 3.6 3.8 - - - -
84E THR* 4.0 5.6 + - - -
110E VAL* 3.7 8.3 - - - -
112E GLU* 1.3 75.1 - - - +
114E GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 114 (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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11E CYS* 3.6 13.6 - - - -
55E SER 6.0 2.0 - - - -
82E VAL* 3.1 35.1 + - - +
84E THR* 3.7 15.3 - - - +
113E CYS* 1.3 75.0 - - - +
115E CYS* 1.3 63.9 + - - -
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Residues in contact with CYS 115 (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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11E CYS* 3.7 15.3 - - - -
43E GLU 4.0 1.8 - - - -
44E CYS* 2.0 50.9 - - - -
45E PRO* 3.7 3.6 - - + -
55E SER 5.7 4.1 + - - -
56E LEU* 3.6 22.0 - - + +
57E SER* 5.1 2.8 + - - -
60E SER* 2.5 28.2 + - - -
79E SER* 3.5 9.4 - - - +
80E CYS 3.4 4.0 - - - -
82E VAL* 5.0 0.2 - - - -
84E THR* 5.4 2.9 - - - +
114E GLY* 1.3 73.2 - - - -
116E SER* 1.3 54.0 + - - +
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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