Contacts of the helix formed by residues 86 - 99 (chain B) in PDB entry 1MF8
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 ASP 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B HIS* 5.3 4.3 - - - -
84B LYS 3.6 4.0 + - - +
85B GLY* 1.3 78.6 - - - +
87B LYS* 1.3 67.3 + - - +
88B GLU* 4.3 9.7 - - + +
89B GLN* 3.4 28.9 + - - +
90B LYS* 3.8 18.7 + - - +
162B HIS* 4.3 1.7 - - - -
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Residues in contact with LYS 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 ASP* 1.3 73.9 - - - +
88B GLU* 1.3 67.4 + - - +
90B LYS* 2.9 15.6 + - - +
91B LEU* 3.2 33.0 + - + +
157B GLY* 3.1 31.1 + - - -
158B GLY* 5.0 1.2 - - - -
160B ASP* 3.6 9.9 + - - -
162B HIS* 3.6 41.8 - - + +
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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 ASP* 3.6 6.4 - - + +
87B LYS* 1.3 80.3 - - - +
89B GLN* 1.3 60.3 + - - +
91B LEU* 3.1 12.3 + - - +
92B ARG* 2.8 34.3 + - + +
149B PHE* 4.2 18.3 - - + -
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Residues in contact with GLN 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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13B HIS* 3.5 27.8 + - - -
79B SER* 5.3 0.6 + - - -
80B GLN* 3.8 46.7 + - - +
85B GLY* 3.9 9.9 - - - -
86B ASP* 3.4 29.4 + - - +
87B LYS 3.2 1.4 - - - -
88B GLU* 1.3 83.3 - - + +
90B LYS* 1.3 56.8 + - - +
92B ARG* 3.3 9.8 - - + +
93B PHE* 3.0 25.8 + - - +
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Residues in contact with LYS 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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80B GLN 3.6 24.2 - - - +
81B PHE 4.2 0.7 - - - -
82B SER 3.6 20.3 + - - -
83B VAL* 3.9 6.7 + - - +
85B GLY* 3.8 16.8 + - - -
86B ASP 3.8 8.7 - - - +
87B LYS 2.9 4.2 + - - +
89B GLN* 1.3 76.1 - - + +
91B LEU* 1.3 62.4 + - - +
93B PHE* 3.7 7.5 + - + +
94B ALA* 3.3 17.8 + - - +
162B HIS* 2.8 51.5 + - + +
163B LYS* 5.4 0.6 - - - +
165B MET* 3.2 30.9 - - + +
166B VAL* 3.3 24.2 - - - +
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Residues in contact with LEU 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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354A LEU* 6.2 0.4 - - + -
87B LYS* 3.2 52.7 + - + +
88B GLU* 3.1 9.7 + - - +
90B LYS* 1.3 73.9 - - - +
92B ARG* 1.3 58.0 + - - +
94B ALA* 2.7 9.0 + - - +
95B PHE* 2.5 35.7 + - - +
149B PHE* 4.0 11.7 - - + -
152B PHE* 4.1 4.0 - - + -
153B CYS* 4.3 22.9 - - + -
156B VAL* 3.8 31.2 - - + +
157B GLY* 4.5 11.4 - - - +
162B HIS* 5.3 5.4 - - + +
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Residues in contact with ARG 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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80B GLN* 6.2 0.7 - - - +
88B GLU* 2.8 18.2 + - + +
89B GLN* 3.3 16.8 - - + +
91B LEU* 1.3 76.8 - - - +
93B PHE* 1.3 64.5 + - - +
95B PHE* 3.1 24.7 + - - +
96B ARG* 3.0 69.6 + - - +
99B ASP* 5.7 0.4 + - - -
104B GLY* 4.4 13.1 - - - -
149B PHE* 3.5 46.2 - - + +
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Residues in contact with PHE 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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361A VAL* 4.2 12.3 - - + -
57B VAL* 4.1 20.2 - - + -
60B ILE* 3.7 26.9 - - + +
61B PHE* 4.1 9.6 - + - -
80B GLN* 4.0 21.3 - - + +
81B PHE* 3.2 44.6 - + + -
89B GLN 3.0 16.3 + - - +
90B LYS* 3.9 9.4 - - + +
91B LEU 3.1 0.2 - - - -
92B ARG* 1.3 74.7 - - - +
94B ALA* 1.3 64.7 + - - +
96B ARG* 3.0 26.3 + - - +
97B ILE* 3.3 30.2 + - + +
165B MET* 4.0 15.0 - - + -
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Residues in contact with ALA 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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354A LEU* 4.4 17.7 - - + -
357A VAL* 5.4 1.1 - - + -
90B LYS 3.3 12.2 + - - +
91B LEU* 2.7 17.3 + - + +
93B PHE* 1.3 75.2 - - - +
95B PHE* 1.3 63.9 + - - +
97B ILE* 2.8 28.3 + - - +
98B TYR* 3.4 8.9 - - + -
152B PHE* 4.2 13.9 - - + -
161B ILE* 6.5 0.2 - - + -
165B MET* 4.0 18.4 - - + -
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Residues in contact with PHE 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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91B LEU 2.5 14.6 + - - +
92B ARG* 3.3 23.6 - - - +
94B ALA* 1.3 72.0 - - - +
96B ARG* 1.3 62.6 + - + +
98B TYR* 3.2 15.7 + - - +
99B ASP* 3.3 17.8 + - + -
104B GLY* 3.5 33.7 - - - -
106B ILE* 3.5 25.8 - - + -
147B ILE 3.7 6.5 - - - -
148B SER 3.6 9.2 - - - -
149B PHE* 3.4 55.2 - + + -
152B PHE* 3.4 32.4 - + + -
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Residues in contact with ARG 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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56B ARG* 2.9 24.1 + - - -
60B ILE* 3.5 32.1 + - + +
80B GLN* 4.0 21.8 - - - +
92B ARG* 3.0 62.0 + - - +
93B PHE* 3.3 14.4 - - - +
94B ALA 3.0 0.6 + - - -
95B PHE* 1.3 77.6 - - + +
97B ILE* 1.3 56.9 + - - +
98B TYR 2.9 6.6 + - - -
99B ASP* 3.3 16.2 - - + +
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Residues in contact with ILE 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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357A VAL* 3.7 36.8 - - + -
361A VAL* 4.2 11.2 - - + -
53B LEU* 4.7 11.2 - - + +
56B ARG* 3.4 25.6 + - + +
57B VAL* 4.8 3.1 - - + +
60B ILE* 3.4 22.4 - - + -
93B PHE* 3.3 30.0 + - + +
94B ALA* 2.8 13.9 + - - +
96B ARG* 1.3 77.5 - - - +
98B TYR* 1.3 62.3 + - + +
114B VAL* 3.3 31.3 - - + +
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Residues in contact with TYR 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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350A PHE* 4.0 15.5 - + - -
353A SER* 2.7 28.3 + - - -
354A LEU* 3.6 18.7 - - + +
357A VAL* 3.4 21.8 - - + +
94B ALA* 3.4 18.8 - - + -
95B PHE 3.2 1.9 + - - +
96B ARG 2.9 0.2 - - - -
97B ILE* 1.3 85.5 - - + +
99B ASP* 1.3 61.7 + - - +
100B MET* 3.0 18.0 + - - +
106B ILE* 3.3 27.6 - - + -
110B GLU* 3.7 14.7 - - - +
111B LEU* 4.3 9.4 - - + -
114B VAL* 3.7 29.4 - - + +
115B LEU* 4.4 11.0 - - + -
118B MET* 4.5 2.2 - - + -
152B PHE* 3.8 29.2 - + - -
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Residues in contact with ASP 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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56B ARG* 3.5 2.6 + - - -
92B ARG* 5.7 0.5 + - - -
95B PHE* 3.3 23.2 + - + +
96B ARG* 3.3 19.0 + - + +
98B TYR* 1.3 74.9 - - - +
100B MET* 1.3 62.0 + - - +
102B LYS* 2.9 24.4 + - - +
103B ASP* 2.6 6.0 - - - +
104B GLY* 2.8 23.8 + - - -
105B TYR 2.3 40.0 - - - +
106B ILE* 4.1 2.4 - - + +
110B GLU* 3.9 4.0 - - - -
403B CA 2.3 16.0 - - - -
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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