Contacts of the strand formed by residues 78 - 90 (chain E) in PDB entry 5FJV
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 MET 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ILE* 4.8 8.3 - - + -
71E ASP* 5.3 0.8 - - - +
72E VAL* 3.8 5.0 - - - +
73E ASP* 3.3 42.2 + - - +
76E ASN* 3.6 28.3 - - + +
77E GLN* 1.3 77.6 - - - +
79E MET* 1.3 67.8 + - - +
80E THR* 4.9 4.0 - - - +
124E ASN* 4.3 0.7 - - - +
126E ASP* 3.1 32.1 - - + +
154E LYS* 4.2 24.0 - - - -
155E SER 3.4 16.8 - - - +
156E SER* 4.7 1.3 - - - -
157E CYS* 4.4 3.4 - - - +
159E ILE* 4.4 3.8 - - - +
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Residues in contact with MET 79 (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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69E LEU* 4.2 14.1 - - + -
71E ASP 3.7 4.3 - - - +
72E VAL* 4.5 7.2 - - + +
78E MET* 1.3 75.2 - - - +
80E THR* 1.3 64.9 + - - +
81E THR* 4.0 23.3 - - + -
153E TYR 3.6 1.6 - - - +
154E LYS* 3.5 4.3 - - - +
155E SER* 2.9 56.7 + - - +
156E SER 5.0 1.6 - - - +
157E CYS* 4.7 0.4 - - + +
171E CYS* 3.6 45.1 - - + +
172E LYS 4.1 7.6 - - - +
173E MET* 4.0 17.7 - - + -
233E PHE* 4.8 13.0 - - - -
235E ILE* 6.0 3.6 - - - -
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Residues in contact with THR 80 (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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126D ASP* 6.1 1.1 - - + -
69E LEU* 3.6 2.1 - - - +
70E ILE* 2.6 59.4 + - + -
71E ASP* 2.7 32.5 + - - +
78E MET* 4.9 5.4 - - - +
79E MET* 1.3 74.3 - - - +
81E THR* 1.3 63.6 + - - +
152E ILE* 4.2 15.9 - - + -
153E TYR 3.5 6.1 - - - +
154E LYS* 3.6 23.2 - - + +
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Residues in contact with THR 81 (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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66E ILE* 5.3 3.1 - - + -
68E GLN 3.5 12.1 - - - +
69E LEU* 3.8 17.0 - - + -
70E ILE* 4.4 0.9 - - - +
79E MET* 4.0 15.7 - - + -
80E THR* 1.3 83.1 - - - +
82E ASN* 1.3 58.5 + - - +
83E VAL* 3.7 15.7 + - + +
151E ALA 3.7 0.2 - - - +
152E ILE* 3.1 8.6 - - - +
153E TYR* 2.7 42.0 + - - +
155E SER* 4.7 3.5 + - - -
173E MET* 3.7 26.1 - - - +
233E PHE* 5.2 9.2 - - + -
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Residues in contact with ASN 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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122D TYR 3.6 14.9 - - - +
124D ASN* 3.7 11.8 + - - -
129D PHE* 3.6 22.4 - - - -
66E ILE 3.8 0.2 - - - -
67E ALA* 2.9 46.0 + - - +
68E GLN* 3.1 29.5 + - + +
70E ILE* 4.4 2.9 - - + +
81E THR* 1.3 69.0 - - - +
83E VAL* 1.3 68.2 + - - +
84E TRP* 4.3 5.3 - - - +
151E ALA 3.1 14.6 + - - +
152E ILE* 3.2 17.3 - - + -
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Residues in contact with VAL 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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64E LEU* 3.9 19.3 - - + -
65E SER 3.4 9.4 - - - +
66E ILE* 3.8 18.2 - - + -
81E THR* 3.7 26.2 - - - +
82E ASN* 1.3 79.0 + - - +
84E TRP* 1.3 69.2 + - - +
85E LEU* 4.7 2.9 - - + +
150E PRO 3.6 0.3 - - - -
151E ALA* 2.7 38.0 + - + +
153E TYR* 3.5 33.4 - - + -
173E MET* 4.6 10.3 - - + -
175E PHE* 5.1 1.8 - - + -
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Residues in contact with TRP 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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122D TYR* 4.3 14.1 + + + -
129D PHE* 5.9 0.4 - - - -
178D TRP* 3.4 33.3 - + - -
219D TYR* 3.8 42.0 - + + -
221D CYS* 4.9 9.4 - - - -
300D EPJ 3.9 17.7 - - + -
64E LEU* 3.0 9.2 - - - +
65E SER* 2.7 62.1 + - - -
66E ILE 5.7 0.2 - - - -
67E ALA* 3.6 28.1 - - + +
82E ASN* 4.3 6.6 + - - +
83E VAL* 1.3 84.1 - - - +
85E LEU* 1.3 58.9 + - - +
86E LYS 3.5 3.5 + - - -
148E VAL* 4.1 15.7 - - + -
149E PRO 3.7 5.6 - - - +
150E PRO* 4.3 5.1 - - + +
194E VAL* 5.7 0.2 - - + -
199E TYR* 4.4 14.1 - - + -
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Residues in contact with LEU 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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62E PHE* 3.3 35.0 - - + -
63E GLY 3.9 1.3 - - - +
64E LEU* 3.9 13.2 - - + -
83E VAL* 4.1 1.8 + - + -
84E TRP* 1.3 69.2 - - - +
86E LYS* 1.3 65.1 + - - +
87E GLN* 3.4 15.1 + - - +
119E ILE* 4.8 9.4 - - + +
131E VAL* 3.7 27.1 - - + -
147E TRP 3.2 12.5 - - - +
148E VAL* 3.3 9.4 - - - -
149E PRO* 3.4 17.9 + - + +
151E ALA* 5.7 1.3 - - + +
153E TYR* 3.8 18.4 - - + +
175E PHE* 3.9 29.8 - - + -
231E TYR* 5.9 0.2 - - + -
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Residues in contact with LYS 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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221D CYS* 4.1 16.2 - - + +
222D CYS* 5.8 0.2 - - - -
61E ARG* 3.1 15.1 - - - +
62E PHE* 3.5 4.0 - - - -
63E GLY 2.6 43.3 + - - +
84E TRP 3.5 2.0 + - - -
85E LEU* 1.3 73.7 - - - +
87E GLN* 1.3 71.9 + - - +
88E GLU* 2.5 41.2 + - - +
146E HIS* 3.3 20.3 - - - -
148E VAL* 3.4 25.4 - - + -
190E MET* 3.2 22.0 - - - +
194E VAL* 3.5 28.5 - - + -
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Residues in contact with GLN 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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60E VAL* 4.2 4.7 - - + -
61E ARG 3.6 2.9 - - - -
62E PHE* 3.7 20.4 - - + -
85E LEU* 3.7 24.8 + - - +
86E LYS* 1.3 84.9 - - - +
88E GLU* 1.3 65.2 + - - +
89E TRP* 3.9 14.8 - - + -
117E PRO* 3.9 14.0 - - - +
119E ILE* 3.0 32.0 - - + +
131E VAL* 4.9 1.0 - - - +
146E HIS* 3.4 3.5 - - - -
147E TRP* 2.7 66.8 + - - +
149E PRO* 4.1 3.2 - - - +
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Residues in contact with GLU 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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59E ILE 3.6 0.7 - - - +
60E VAL* 3.2 6.5 - - - +
61E ARG* 2.9 62.5 + - + +
86E LYS* 2.5 38.4 + - - +
87E GLN* 1.3 74.8 - - - +
89E TRP* 1.3 66.5 + - - +
144E THR* 3.8 17.1 - - + +
145E VAL 3.1 13.5 - - - +
146E HIS* 2.6 23.0 + - + +
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Residues in contact with TRP 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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52E PRO* 4.4 7.8 - - + +
58E VAL* 4.0 12.6 - - + -
59E ILE 3.7 15.7 - - - +
60E VAL* 4.2 6.7 - - + -
87E GLN* 3.9 20.4 - - + -
88E GLU* 1.3 84.4 - - - +
90E SER* 1.3 73.1 + - - +
91E ASP* 4.5 1.8 + - - +
114E ILE* 4.7 1.1 - - + -
115E TRP* 3.3 48.6 + + - -
116E ILE* 3.9 13.5 - - + -
117E PRO* 3.4 33.0 - - + -
144E THR* 3.7 4.4 - - - +
145E VAL* 2.7 69.6 + - + +
147E TRP* 4.0 15.3 - + + -
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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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52E PRO* 4.1 9.4 - - - +
58E VAL* 4.8 6.3 - - - +
59E ILE 4.8 1.2 + - - -
89E TRP* 1.3 84.6 - - - +
91E ASP* 1.3 62.2 + - - +
92E TYR 3.8 2.4 + - - -
95E ARG* 5.6 2.1 - - - -
142E THR 4.3 5.5 + - - -
143E GLY* 3.3 17.9 + - - -
144E THR* 4.3 9.2 + - - +
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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