Contacts of the helix formed by residues 86 - 95 (chain B) in PDB entry 5IFM
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 THR 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B ASP 3.7 10.8 - - - +
85B ILE* 1.3 78.1 - - - +
87B GLU* 1.4 65.6 + - - +
88B GLU* 3.7 8.4 + - - +
89B GLU* 3.2 37.2 + - - +
90B MET 3.2 17.8 + - - -
105B ILE* 3.4 11.9 - - - +
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Residues in contact with GLU 87 (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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86B THR* 1.4 71.5 - - - +
88B GLU* 1.3 62.8 + - + +
90B MET* 3.4 4.8 + - - +
91B ARG* 2.7 67.4 + - + +
103B VAL* 3.8 26.5 - - + +
104B PHE* 5.6 0.2 - - - -
105B ILE* 3.6 16.1 + - + +
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Residues in contact with GLU 88 (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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86B THR* 3.2 8.7 + - - +
87B GLU* 1.3 80.6 - - + +
89B GLU* 1.3 58.1 + - - +
91B ARG* 3.8 24.0 - - - +
92B LYS* 3.0 54.0 + - - +
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Residues in contact with GLU 89 (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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84B ASP 4.4 1.4 - - - +
85B ILE* 3.6 17.2 - - + +
86B THR* 3.2 40.6 + - - +
88B GLU* 1.3 73.5 - - + +
90B MET* 1.4 57.8 + - - +
92B LYS* 3.3 8.6 + - - +
93B LEU* 3.0 34.1 + - + +
134B LEU* 4.9 5.4 - - + +
135B ARG* 2.8 37.3 + - - -
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Residues in contact with MET 90 (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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78B VAL* 4.2 18.6 - - + -
81B LEU* 4.5 7.4 - - + -
85B ILE* 4.1 13.0 - - + -
86B THR 3.2 4.5 + - - +
87B GLU 3.4 9.0 - - - +
89B GLU* 1.4 75.7 - - - +
91B ARG* 1.3 64.2 + - - +
93B LEU* 3.2 12.9 + - + +
94B PHE* 3.2 45.4 - - - +
103B VAL* 3.9 19.1 - - + -
104B PHE 4.1 9.6 - - - +
105B ILE* 3.7 21.3 - - + -
112B GLY* 4.4 3.8 - - - -
113B PHE 3.7 33.4 - - - +
114B ILE* 4.3 10.5 - - + +
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Residues in contact with ARG 91 (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 GLU* 2.7 54.0 + - - +
88B GLU* 3.8 25.1 - - - +
89B GLU 3.4 0.2 - - - -
90B MET* 1.3 74.6 - - - +
92B LYS* 1.3 57.8 + - + +
94B PHE* 3.3 3.0 + - - +
95B GLU* 2.9 30.0 + - - +
100B ALA* 4.1 18.4 + - + +
101B GLY 2.8 28.9 + - - -
103B VAL* 3.5 24.3 - - + +
114B ILE* 4.8 6.7 - - + -
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Residues in contact with LYS 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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88B GLU* 3.0 38.1 + - - +
89B GLU* 3.6 7.4 - - - +
91B ARG* 1.3 74.6 - - + +
93B LEU* 1.4 63.7 + - - +
95B GLU* 3.2 43.3 - - - +
96B LYS* 3.9 9.2 - - - -
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Residues in contact with LEU 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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78B VAL* 5.3 0.2 - - + -
81B LEU* 5.2 1.6 - - + -
85B ILE* 4.9 4.0 - - + -
89B GLU* 3.0 19.5 + - + +
90B MET* 3.2 21.3 + - - +
92B LYS* 1.4 76.2 - - - +
94B PHE* 1.3 73.9 + - + +
96B LYS* 2.9 32.9 + - - +
129B LEU* 3.5 21.7 - - + +
134B LEU* 4.1 29.4 - - + -
139B LEU* 3.9 26.7 - - + -
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Residues in contact with PHE 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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76B LEU* 3.9 17.9 - - + -
78B VAL* 3.6 34.5 - - + -
90B MET* 3.2 32.9 + - - +
91B ARG 3.6 2.2 - - - +
92B LYS 3.3 0.4 - - - -
93B LEU* 1.3 90.2 - - + +
95B GLU* 1.3 64.2 + - - +
96B LYS 3.2 2.7 - - - -
97B TYR* 3.0 27.6 + + - +
98B GLY 4.2 3.3 - - - +
100B ALA* 5.9 2.4 - - + +
114B ILE* 3.7 42.0 - - + -
116B LEU* 4.3 13.2 - - + +
125B ALA* 4.1 14.4 - - + -
129B LEU* 3.5 23.8 - - + -
141B VAL* 4.5 9.4 - - + -
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Residues in contact with GLU 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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55A LEU* 5.8 0.2 - - - +
91B ARG 2.9 11.8 + - - +
92B LYS* 3.2 40.6 + - - +
93B LEU 3.6 0.2 - - - -
94B PHE* 1.3 74.6 - - - +
96B LYS* 1.4 63.2 - - + +
97B TYR 3.4 0.5 + - - -
98B GLY* 3.7 16.4 + - - +
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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