Contacts of the helix formed by residues 86 - 97 (chain E) in PDB entry 3IFS
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 TYR 86 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E GLY 3.8 5.2 - - - +
82E ILE* 3.8 15.3 - - - -
83E GLY 2.9 12.9 + - - +
84E GLY 3.1 1.0 - - - -
85E SER* 1.3 81.1 - - - +
87E LEU* 1.3 89.9 + - + +
88E GLY 3.5 2.1 + - - -
89E ALA* 3.5 6.2 + - - +
90E ARG* 2.8 56.5 + - - +
116E PHE* 3.4 47.0 - + + -
119E GLN* 3.8 25.7 + - + +
280E TYR* 3.8 9.7 + + - -
309F THR* 3.9 23.6 - - + +
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Residues in contact with LEU 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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83E GLY* 2.9 20.5 + - - +
84E GLY* 5.4 0.4 - - - -
86E TYR* 1.3 98.5 - - + +
88E GLY* 1.3 59.0 + - - +
90E ARG* 3.4 2.6 + - - +
91E ALA* 2.9 31.5 + - - +
280E TYR* 4.3 14.9 - - + +
283E GLU* 3.5 44.0 - - + +
284E TRP* 4.2 16.1 - - + +
287E GLN* 3.4 28.3 - - + +
309F THR* 5.7 2.2 - - + -
310F ASP* 5.9 2.0 - - - +
313F SER* 4.1 12.6 - - - -
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Residues in contact with GLY 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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84E GLY* 4.5 9.0 + - - -
86E TYR 3.5 0.6 - - - -
87E LEU* 1.3 78.9 - - - +
89E ALA* 1.3 62.3 + - - +
91E ALA* 3.4 3.7 + - - +
92E ALA* 3.2 20.1 + - - +
211E VAL* 3.6 28.9 - - - +
284E TRP* 3.6 22.8 - - - -
394E PHE* 4.0 2.6 - - - -
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Residues in contact with ALA 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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79E VAL* 5.8 0.4 - - + -
84E GLY 5.6 0.4 + - - -
85E SER 5.4 3.8 - - - +
86E TYR* 3.5 9.4 + - - +
87E LEU 3.3 0.2 - - - -
88E GLY* 1.3 75.3 - - - +
90E ARG* 1.3 57.4 + - - +
92E ALA* 3.3 2.1 + - - +
93E ILE* 2.8 36.6 + - + +
116E PHE* 4.4 9.4 - - + -
211E VAL* 4.1 2.2 - - - +
215E VAL* 4.5 2.2 - - + +
216E GLY* 4.4 11.3 - - - +
219E PRO* 3.8 33.2 - - + -
220E ILE* 4.2 12.1 - - + -
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Residues in contact with ARG 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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86E TYR* 2.8 60.8 + - + +
87E LEU* 4.0 3.8 - - - +
89E ALA* 1.3 79.2 - - - +
91E ALA* 1.3 63.4 + - - +
93E ILE* 4.4 2.5 - - - -
94E GLU* 2.9 51.4 + - + +
116E PHE* 3.7 32.5 - - + +
119E GLN* 4.5 8.7 - - - +
125E TYR* 5.1 3.4 + - - -
280E TYR* 3.4 42.7 + - + +
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Residues in contact with ALA 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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87E LEU 2.9 18.3 + - - +
88E GLY* 3.5 6.7 - - - +
90E ARG* 1.3 77.6 - - - +
92E ALA* 1.3 56.9 + - - +
94E GLU* 4.4 0.3 - - - +
95E MSE 2.9 33.4 + - - +
277E ALA 4.8 1.2 - - - +
280E TYR* 3.8 15.2 - - - +
281E PHE* 3.6 32.5 + - + +
284E TRP* 4.3 8.1 - - + -
394E PHE* 4.2 9.4 - - + -
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Residues in contact with ALA 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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88E GLY 3.2 5.2 + - - +
91E ALA* 1.3 75.4 - - - +
93E ILE* 1.3 67.2 + - - +
95E MSE 4.5 0.2 - - - -
96E LEU* 3.0 30.9 + - + +
220E ILE* 3.4 36.3 - - + -
225E LEU* 3.8 3.2 - - + +
230E MSE 4.5 6.5 - - + -
394E PHE* 3.5 32.5 - - + -
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Residues in contact with ILE 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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89E ALA 2.8 23.5 + - - +
90E ARG* 3.9 4.5 - - - +
92E ALA* 1.3 75.5 - - - +
94E GLU* 1.3 68.0 + - + +
97E ASN* 3.0 45.1 + - + +
101E TYR* 4.8 16.2 - - + -
114E VAL* 3.7 34.3 - - + +
116E PHE* 4.1 14.1 - - + -
219E PRO* 3.8 21.1 - - + +
220E ILE* 4.3 9.0 - - + -
223E SER* 3.7 18.6 - - - +
225E LEU* 4.3 1.3 - - - -
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Residues in contact with GLU 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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90E ARG* 2.9 51.8 + - + +
91E ALA 4.4 0.7 - - - +
93E ILE* 1.3 81.2 - - + +
95E MSE 1.3 66.1 + - - +
96E LEU 3.4 0.3 + - - -
97E ASN* 3.8 12.5 - - - +
98E HIS 5.2 1.5 - - - +
99E SER* 5.8 1.2 - - - -
277E ALA* 3.8 22.2 - - - +
279E GLN* 5.4 2.6 - - - +
280E TYR* 3.1 32.7 + - + +
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Residues in contact with MSE 95 (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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91E ALA 2.9 21.5 + - - +
92E ALA 3.9 2.7 - - - +
94E GLU* 1.3 78.6 - - - +
96E LEU* 1.3 78.0 + - + +
97E ASN 4.0 1.6 + - - +
277E ALA* 3.5 19.1 + - - +
278E LEU* 4.0 23.1 - - + -
281E PHE* 3.4 47.1 - - + -
386E ILE* 6.2 0.2 - - + -
389E LEU* 4.0 32.6 - - + +
390E ASN 5.5 0.2 - - - +
394E PHE* 3.8 28.5 - - + -
397E LEU* 4.7 9.9 - - + -
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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
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92E ALA 3.0 16.4 + - - +
95E MSE 1.3 100.5 - - + +
97E ASN* 1.3 64.2 + - - +
225E LEU* 3.6 26.0 - - + +
230E MSE 4.3 5.4 - - + -
389E LEU* 3.6 10.8 - - + +
390E ASN* 3.5 31.9 - - - +
391E GLU* 3.8 36.6 - - + +
394E PHE* 4.1 14.4 - - + -
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Residues in contact with ASN 97 (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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93E ILE* 3.0 23.8 + - - +
94E GLU* 3.8 10.7 - - - +
95E MSE 3.7 1.9 - - - +
96E LEU* 1.3 83.9 + - - +
98E HIS* 1.3 71.2 + - - +
99E SER* 3.4 1.6 + - - -
101E TYR* 3.8 31.0 - - + -
111E THR* 5.2 0.2 + - - -
223E SER* 3.3 40.6 + - - -
224E GLY* 5.5 0.4 - - - -
225E LEU* 3.7 15.3 - - - +
277E ALA* 5.7 1.0 - - - +
128F ASP* 4.9 0.3 - - - +
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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