Contacts of the strand formed by residues 81 - 94 (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 CYS 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E CYS* 2.0 63.7 - - + -
12E CYS 3.8 0.2 - - - -
40E CYS* 3.8 14.9 - - - +
41E GLU* 3.5 25.8 - - - -
42E GLY 3.7 19.7 + - - +
44E CYS* 3.4 6.3 - - - -
80E CYS* 1.3 71.2 - - - +
82E VAL* 1.3 62.5 + - - +
114E GLY 3.9 0.2 - - - -
77F LEU* 6.0 3.1 - - + +
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Residues in contact with VAL 82 (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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40E CYS* 3.4 7.2 - - - -
80E CYS* 3.5 30.3 - - + +
81E CYS* 1.3 81.5 - - - +
83E PRO* 1.3 80.9 - - + +
84E THR* 3.3 3.4 + - + +
113E CYS* 3.6 0.3 - - - -
114E GLY 3.1 33.0 + - - +
115E CYS 5.0 0.2 - - - -
116E SER* 4.4 6.1 - - - +
80F CYS* 5.0 0.2 - - - -
82F VAL* 3.7 31.9 - - + -
83F PRO* 5.4 1.6 - - + +
116F SER* 3.5 28.0 - - - +
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Residues in contact with PRO 83 (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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40E CYS* 3.5 17.5 - - + +
82E VAL* 1.3 94.4 - - + +
84E THR* 1.3 61.4 + - - +
85E LYS 4.5 0.9 - - - +
86E LEU* 3.7 31.9 - - + +
110E VAL* 3.8 19.1 - - + -
112E GLU 3.4 9.6 - - - +
59F HIS* 4.5 10.1 - - + +
82F VAL* 5.3 1.5 - - + +
83F PRO 4.2 13.0 - - - +
84F THR* 5.6 1.6 - - - +
116F SER* 4.4 14.4 - - - +
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Residues in contact with THR 84 (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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82E VAL* 3.9 4.7 - - + +
83E PRO* 1.3 76.4 - - - +
85E LYS* 1.3 69.3 + - - +
86E LEU* 5.9 0.2 - - - -
112E GLU* 2.8 32.3 + - - +
113E CYS 4.0 3.3 + - - -
114E GLY* 3.7 30.5 - - - +
115E CYS 5.4 2.7 - - - +
83F PRO 5.5 2.2 - - - -
84F THR 5.1 8.4 - - - +
86F LEU* 5.9 9.2 - - + -
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Residues in contact with LYS 85 (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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83E PRO* 3.5 1.4 - - - +
84E THR* 1.3 89.8 + - - +
86E LEU* 1.3 65.3 + - - +
87E ARG* 6.1 1.1 - - + -
110E VAL* 3.8 2.3 - - - +
111E GLU* 2.8 45.7 + - + +
112E GLU* 3.4 42.6 + - + +
107F ASN* 5.5 4.6 + - - -
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Residues in contact with LEU 86 (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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83E PRO* 3.7 31.2 - - + -
85E LYS* 1.3 80.8 - - - +
87E ARG* 1.3 62.5 + - - +
88E PRO* 4.8 0.5 - - - +
106E GLN* 5.7 0.5 - - - +
107E ASN* 3.9 43.3 + - + +
109E ILE 3.3 13.9 - - - +
110E VAL* 3.9 14.1 - - + -
57F SER* 4.3 14.1 - - - +
59F HIS* 4.3 12.3 - - + -
84F THR* 5.7 12.6 - - + +
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Residues in contact with ARG 87 (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* 6.1 0.2 - - - +
85E LYS* 6.1 1.1 - - + -
86E LEU* 1.3 76.0 - - - +
88E PRO* 1.3 79.0 + - + +
106E GLN* 5.4 0.2 - - - -
107E ASN 4.3 2.7 - - - +
108E MET 3.1 7.2 + - - -
109E ILE* 2.8 70.5 + - + +
111E GLU* 2.7 40.9 + - + -
129H GLY* 2.9 31.5 + - - -
130H HIS* 4.0 25.2 + - - +
131H PRO* 5.5 2.0 - - - +
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Residues in contact with PRO 88 (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 4.8 0.4 - - - +
87E ARG* 1.3 101.2 + - + +
89E MET* 1.3 62.7 + - - +
104E ASP* 4.6 11.2 - - + -
105E ILE 3.2 13.9 - - - +
106E GLN* 3.4 43.5 - - - +
108E MET* 4.5 0.2 - - - -
109E ILE* 3.6 9.6 - - - +
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Residues in contact with MET 89 (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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32E PRO* 4.2 22.0 - - + -
35E TYR* 3.7 32.8 - - + -
88E PRO* 1.3 74.8 - - - +
90E SER* 1.3 72.4 + - - +
91E MET* 3.5 5.0 + - - +
104E ASP* 3.9 4.3 - - - -
105E ILE 2.8 30.8 + - - +
108E MET* 3.7 18.3 - - - -
109E ILE* 3.8 16.2 - - + -
132H ASP* 4.0 29.4 - - + +
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Residues in contact with SER 90 (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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31E ALA 4.8 0.2 - - - +
32E PRO* 4.3 9.5 - - - +
89E MET* 1.3 84.1 - - - +
91E MET* 1.3 61.9 + - - +
102E LYS* 3.6 31.2 - - - +
103E LYS 3.6 4.0 - - - -
104E ASP* 3.4 20.1 + - - -
111H SER 6.1 0.7 - - - -
112H ASP* 5.4 10.8 + - - -
165H HIS* 5.8 0.2 - - - -
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Residues in contact with MET 91 (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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20E PHE* 4.1 11.0 - - + -
29E ILE* 3.6 36.1 - - + -
31E ALA 3.9 2.9 - - - +
32E PRO* 4.1 16.6 - - - -
89E MET* 3.7 11.7 - - - +
90E SER* 1.3 78.6 + - - +
92E LEU* 1.3 60.9 + - - +
93E TYR* 3.8 10.0 - - + -
101E ILE 3.6 1.2 - - - +
102E LYS* 3.3 4.8 - - - +
103E LYS 2.8 35.1 + - - +
105E ILE* 3.8 16.4 - - + -
108E MET* 3.6 23.6 - - + -
58F PHE* 3.8 27.6 - - + -
61G LEU* 4.7 4.9 - - + -
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Residues in contact with LEU 92 (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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29E ILE* 3.7 3.1 - - - +
30E ILE* 2.8 31.0 + - + -
31E ALA* 3.0 26.8 + - + +
91E MET* 1.3 71.2 - - - +
93E TYR* 1.3 63.1 + - - +
100E ILE* 3.5 27.4 - - + -
101E ILE 3.3 3.1 - - - +
102E LYS* 3.8 24.2 - - + -
157H VAL* 4.1 8.1 - - + -
159H ASP* 3.9 4.5 - - + -
165H HIS* 3.6 41.5 - - + +
167H VAL* 3.8 24.2 - - + -
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Residues in contact with TYR 93 (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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28E TRP 3.2 15.5 - - - +
29E ILE* 4.1 8.1 - - + -
30E ILE* 3.8 8.3 - - - -
91E MET* 3.8 19.1 - - + -
92E LEU* 1.3 76.4 - - - +
94E TYR* 1.3 70.5 + - - +
99E ASN 3.4 0.7 - - - +
100E ILE* 3.7 1.7 - - - -
101E ILE* 2.8 58.8 + - + +
103E LYS* 3.3 43.5 + - + +
105E ILE* 4.0 5.4 - - + -
61G LEU* 3.2 53.6 + - + -
63G LEU* 3.8 22.5 - - + +
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Residues in contact with TYR 94 (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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27E ASP 3.6 12.8 - - - -
28E TRP* 2.9 20.6 + - + +
30E ILE* 3.3 33.6 - - + +
93E TYR* 1.3 77.0 - - - +
95E ASP* 1.3 66.4 + - - +
98E GLN* 3.4 34.3 - - - +
99E ASN 3.3 5.2 - - - -
100E ILE* 4.2 3.7 - - + +
63G LEU* 3.5 15.4 - - - +
199H ARG* 2.9 62.9 + - + +
202H THR* 4.0 17.5 - - + -
203H CYS* 3.4 21.8 + - - +
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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