Contacts of the helix formed by residues 91 - 102 (chain B) in PDB entry 4IF8
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 GLN 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA* 1.3 78.6 - - - +
92B ASP* 1.3 82.3 + - - +
95B LEU* 3.3 18.9 + - - -
336B GLY 5.1 4.3 - - - +
337B ASP* 2.9 32.1 + - - +
339B THR* 3.8 16.5 + - - -
340B LYS* 3.8 33.4 - - + +
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 1.3 83.0 - - - +
93B SER* 1.4 61.1 + - - +
95B LEU* 3.3 5.0 + - - +
96B ASP* 2.9 42.3 + - - +
336B GLY 5.7 0.3 - - - +
337B ASP* 3.8 13.8 - - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN 3.6 0.2 + - - -
92B ASP* 1.4 77.2 - - - +
94B THR* 1.3 55.8 + - - +
96B ASP* 3.8 7.6 + - - +
97B GLU* 3.0 32.1 + - - +
330B LYS* 3.7 29.9 + - - +
335B HIS* 4.5 7.6 + - - +
337B ASP* 2.9 19.9 + - - -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ALA* 4.2 9.9 - - + -
91B GLN 3.8 0.2 - - - -
92B ASP 3.3 0.4 - - - -
93B SER* 1.3 74.2 + - - +
95B LEU* 1.4 64.7 + - - +
97B GLU* 3.8 2.3 - - - +
98B ILE* 3.1 25.8 + - + +
330B LYS* 3.6 26.1 + - - +
331B ILE* 3.6 44.8 + - + +
333B GLU 5.2 0.2 + - - -
335B HIS* 4.0 4.9 - - - +
337B ASP* 2.7 35.7 + - + +
338B LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B CYS* 3.7 48.2 - - + +
90B ALA* 3.7 17.3 - - - +
91B GLN* 3.3 28.9 + - + +
92B ASP 3.3 2.4 + - - +
94B THR* 1.4 78.2 - - - +
96B ASP* 1.3 70.0 + - - +
98B ILE* 3.3 6.3 + - - +
99B LYS* 3.1 44.9 + - - +
109B GLU* 3.6 26.5 - - - +
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASP* 2.9 27.8 + - - +
93B SER* 3.8 7.4 + - - +
95B LEU* 1.3 83.7 - - - +
97B GLU* 1.3 57.6 + - - +
99B LYS* 3.4 14.0 + - - +
100B GLN* 3.0 33.4 + - + +
105B ARG* 5.8 2.9 + - - +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B SER 3.0 18.8 + - - +
94B THR 3.8 3.5 - - - +
96B ASP* 1.3 74.0 - - - +
98B ILE* 1.4 65.4 + - - +
100B GLN* 3.3 6.6 + - + +
101B GLY* 3.0 21.7 + - - -
327B GLY 3.2 26.2 - - - +
328B VAL* 3.5 7.3 - - - +
329B SER* 2.8 28.9 + - - -
330B LYS* 2.8 39.2 + - + +
331B ILE 4.5 0.7 + - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 3.7 27.1 - - + +
86B LEU* 4.6 5.4 - - + -
87B CYS* 3.6 25.6 - - - -
90B ALA* 4.7 6.3 - - + -
94B THR* 3.1 24.3 + - + +
95B LEU* 3.3 6.0 + - - +
97B GLU* 1.4 73.7 - - - +
99B LYS* 1.3 56.1 - - - +
101B GLY 3.3 0.2 + - - -
102B PHE* 2.8 49.2 + - + +
104B PHE* 4.3 5.2 - - + -
328B VAL* 4.5 18.4 - - + -
331B ILE* 3.9 41.3 - - + +
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B CYS* 4.6 9.9 - - - -
95B LEU* 3.1 33.8 + - - +
96B ASP* 3.6 16.0 + - - +
98B ILE* 1.3 76.0 - - - +
100B GLN* 1.4 56.4 + - - +
103B ASN* 3.1 8.0 + - - -
104B PHE* 2.8 54.6 + - + +
105B ARG* 3.4 38.7 + - + +
107B MET 5.4 4.2 + - - +
108B PRO* 6.3 0.2 - - - +
109B GLU* 2.8 45.8 + - - +
112B LEU* 5.7 3.1 - - + -
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LYS* 4.4 2.1 + - - -
96B ASP* 3.0 20.4 + - + +
97B GLU* 3.3 8.3 + - + +
99B LYS* 1.4 73.7 - - - +
101B GLY* 1.3 63.9 + - - +
103B ASN* 3.3 18.4 + - - +
105B ARG* 3.9 28.5 - - - +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.6 10.8 - - - +
58B LYS* 2.8 29.4 + - - -
97B GLU 3.0 9.9 + - - -
98B ILE 3.7 0.2 - - - -
100B GLN* 1.3 77.7 - - - +
102B PHE* 1.3 61.9 + - - +
103B ASN* 3.7 0.3 + - - +
326B ILE* 3.9 10.8 - - - +
328B VAL* 3.7 22.7 - - - -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLN* 4.1 9.7 - - - +
55B LEU* 3.6 33.0 - - + +
79B ILE* 3.8 20.2 - - + -
80B SER* 3.7 29.6 + - - -
83B PHE* 3.7 32.5 - + + -
98B ILE* 2.8 33.6 + - + +
101B GLY* 1.3 72.5 - - - -
103B ASN* 1.4 74.3 + - - +
104B PHE* 3.5 32.8 + + + -
323B LEU* 3.9 22.2 - - + -
326B ILE* 4.5 2.5 - - + -
328B VAL* 4.3 12.3 - - + -
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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