Contacts of the helix formed by residues 85 - 97 (chain C) in PDB entry 1M6X
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 LYS 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C THR* 3.8 42.9 + - + +
83C THR* 3.2 12.5 + - - +
84C GLN* 1.3 78.8 - - + +
86C ALA* 1.3 65.5 + - - +
87C THR* 3.3 2.9 - - - -
88C ILE* 3.3 42.7 + - + +
89C LEU* 3.5 8.7 + - - +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C THR* 4.2 10.2 + - + -
84C GLN 3.3 5.1 + - - +
85C LYS* 1.3 75.2 - - - +
87C THR* 1.3 66.0 + - - +
89C LEU* 2.9 8.0 + - - +
90C GLU* 2.8 32.4 + - - +
104C ILE* 3.5 35.6 - - + +
106C PRO* 5.0 10.1 - - + -
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Residues in contact with THR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LYS 3.3 1.3 - - - -
86C ALA* 1.3 77.2 - - - +
88C ILE* 1.3 67.7 + - + +
90C GLU* 2.9 15.0 + - + +
91C ALA* 2.8 27.0 + - + +
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Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER* 6.0 5.8 - - - -
45C ILE* 5.3 7.0 - - + -
46C THR* 6.4 1.6 - - + -
85C LYS* 3.3 43.4 + - + +
86C ALA 3.3 0.2 + - - -
87C THR* 1.3 78.9 - - + +
89C LEU* 1.3 59.8 + - - +
91C ALA* 3.5 7.6 + - - +
92C SER* 2.9 31.3 + - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C CYS* 3.7 40.6 - - + +
45C ILE* 3.6 42.6 - - + -
46C THR* 4.0 12.8 - - + -
81C TYR* 4.3 13.5 - - + -
83C THR* 4.4 5.8 - - + +
85C LYS 3.5 7.0 + - - +
86C ALA* 2.9 9.3 + - - +
88C ILE* 1.3 78.8 - - - +
90C GLU* 1.3 65.7 + - - +
92C SER* 3.2 6.1 + - - -
93C LEU* 2.9 28.2 + - + +
104C ILE* 3.9 27.4 - - + -
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 2.8 32.1 + - - +
87C THR* 3.4 12.4 + - + +
89C LEU* 1.3 75.3 - - - +
91C ALA* 1.3 65.1 + - - +
93C LEU* 3.3 4.8 + - - +
94C LYS* 3.0 23.8 + - - +
101C GLU* 4.9 2.1 - - - +
102C PHE* 2.7 37.1 - - + +
103C THR* 3.6 7.1 + - - +
104C ILE* 3.3 38.9 + - + +
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C THR* 2.8 14.5 + - + +
88C ILE* 3.6 12.3 - - - +
90C GLU* 1.3 77.2 - - - +
92C SER* 1.3 63.3 + - - +
94C LYS* 3.0 9.1 + - - +
95C LYS* 3.0 31.4 + - - +
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER* 4.1 11.9 + - - -
116B ILE* 2.8 26.7 - - - +
45C ILE* 3.5 34.4 - - - +
88C ILE* 2.9 16.7 + - - +
89C LEU 3.2 8.0 + - - -
91C ALA* 1.3 77.7 - - - +
93C LEU* 1.3 65.2 + - - +
95C LYS* 3.1 22.7 + - - +
96C LEU 3.4 2.6 + - - -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 3.7 4.7 - - + +
19C PHE* 4.6 8.1 - - + -
38C LEU* 4.0 17.5 - - + -
41C LEU* 4.6 20.4 - - + -
42C CYS* 4.5 7.2 - - - -
45C ILE* 4.5 14.6 - - + -
79C PHE* 3.9 11.4 - - + -
89C LEU* 2.9 17.3 + - + +
90C GLU 3.6 6.5 - - - +
92C SER* 1.3 75.9 - - - +
94C LYS* 1.3 63.3 + - - +
96C LEU* 3.0 19.8 + - + +
97C ILE* 3.2 5.4 + - - +
102C PHE* 3.8 36.1 - - + -
104C ILE* 3.7 30.3 - - + -
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU 3.0 13.5 + - - +
91C ALA* 3.0 11.6 + - - +
93C LEU* 1.3 72.3 - - - +
95C LYS* 1.3 57.4 + - - +
96C LEU 2.9 1.8 - - - -
97C ILE 2.6 26.6 + - - -
98C PRO* 2.7 47.0 + - + +
100C TRP 3.1 16.9 + - - +
101C GLU* 3.4 26.7 + - - +
102C PHE* 3.8 9.6 - - + +
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER 5.3 2.8 + - - -
115B ASP* 3.7 34.5 + - - +
116B ILE* 5.3 3.8 - - + +
91C ALA* 3.0 23.8 + - - +
92C SER* 3.1 14.1 + - - +
94C LYS* 1.3 76.1 - - - +
96C LEU* 1.3 59.7 + - - +
98C PRO* 3.7 14.2 - - - +
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ILE* 4.2 25.1 - - + +
117B THR* 4.1 24.7 - - + -
16C VAL* 3.8 33.9 - - + -
19C PHE* 4.0 11.0 - - + -
20C VAL* 4.4 19.7 - - + +
41C LEU* 3.9 25.6 - - + -
92C SER 3.4 4.6 + - - +
93C LEU* 3.0 15.4 + - - +
94C LYS 2.9 0.8 - - - -
95C LYS* 1.3 81.7 - - - +
97C ILE* 1.3 65.4 + - + +
98C PRO* 3.7 4.1 - - - +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.6 29.2 - - + +
20C VAL* 4.4 12.8 - - + -
23C PHE* 3.4 44.0 - - + -
93C LEU 3.2 2.6 + - - +
94C LYS* 2.6 15.1 + - - +
96C LEU* 1.3 86.0 - - + +
98C PRO* 1.3 62.2 - - + +
99C ALA* 3.2 4.7 - - + +
100C TRP* 3.0 56.0 + - + +
102C PHE* 3.9 10.5 - - + -
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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