Contacts of the helix formed by residues 85 - 97 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D THR* 3.8 42.7 + - + +
83D THR* 3.6 12.5 + - - +
84D GLN* 1.3 78.7 - - + +
86D ALA* 1.3 65.9 + - - +
87D THR* 3.3 3.1 - - - -
88D ILE* 3.3 43.1 + - + +
89D LEU* 3.5 8.8 + - - +
18H A 5.8 1.8 + - - -
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Residues in contact with ALA 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D THR* 4.2 10.4 + - + -
84D GLN* 3.3 4.2 + - - +
85D LYS* 1.3 75.2 - - - +
87D THR* 1.3 65.0 + - - +
89D LEU* 2.9 8.7 + - - +
90D GLU* 2.9 32.2 + - - +
104D ILE* 3.5 35.4 - - + +
106D PRO* 5.0 10.8 - - + -
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Residues in contact with THR 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D LYS 3.3 1.0 - - - -
86D ALA* 1.3 78.0 - - - +
88D ILE* 1.3 68.1 + - + +
90D GLU* 2.9 15.3 + - + +
91D ALA* 2.9 26.3 + - + +
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER* 6.1 5.4 - - - -
45D ILE* 5.3 7.0 - - + -
46D THR* 6.4 1.6 - - + -
85D LYS* 3.3 43.2 + - + +
87D THR* 1.3 78.9 - - + +
89D LEU* 1.3 61.2 + - - +
91D ALA* 3.5 7.5 + - - +
92D SER* 3.0 30.9 + - - +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D CYS* 3.8 40.8 - - + +
45D ILE* 3.6 41.7 - - + -
46D THR* 4.0 13.2 - - + -
81D TYR* 4.3 13.0 - - + -
83D THR* 4.4 6.3 - - + +
85D LYS 3.5 6.4 + - - +
86D ALA 2.9 9.7 + - - +
88D ILE* 1.3 78.3 - - - +
90D GLU* 1.3 66.1 + - - +
92D SER* 3.2 6.1 + - - -
93D LEU* 2.9 28.6 + - + +
104D ILE* 3.9 26.5 - - + -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ALA* 2.9 31.8 + - - +
87D THR* 3.5 11.8 + - + +
89D LEU* 1.3 74.5 - - - +
91D ALA* 1.3 64.6 + - - +
93D LEU* 3.3 3.9 + - - +
94D LYS* 3.0 23.8 + - - +
101D GLU* 4.9 2.3 - - - +
102D PHE* 2.7 41.7 - - + +
103D THR* 3.6 8.3 + - - +
104D ILE* 3.3 35.8 + - + +
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D THR* 2.9 14.8 + - + +
88D ILE* 3.5 11.9 - - - +
90D GLU* 1.3 76.4 - - - +
92D SER* 1.3 64.3 + - - +
94D LYS* 3.0 17.5 + - - +
95D LYS* 3.0 23.0 + - - +
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER 4.6 7.1 + - - -
116A ILE* 2.9 37.9 - - - +
45D ILE* 3.5 24.4 - - - +
88D ILE* 3.0 16.4 + - - +
89D LEU 3.2 9.3 + - - -
91D ALA* 1.3 78.0 - - - +
93D LEU* 1.3 64.7 + - - +
95D LYS* 3.1 20.7 + - - +
96D LEU 3.4 3.3 + - - -
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 3.8 3.8 - - + +
19D PHE* 4.6 8.2 - - + -
38D LEU* 4.0 18.2 - - + -
41D LEU* 4.6 19.3 - - + -
42D CYS* 4.5 6.3 - - - -
45D ILE* 4.5 15.5 - - + -
79D PHE* 3.9 11.4 - - + -
89D LEU* 2.9 18.3 + - + +
90D GLU 3.6 6.3 - - - +
92D SER* 1.3 75.5 - - - +
94D LYS* 1.3 63.1 + - - +
96D LEU* 3.0 21.1 + - + +
97D ILE* 3.2 5.4 + - - +
102D PHE* 3.8 36.6 - - + -
104D ILE* 3.8 30.3 - - + -
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Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLU 3.0 13.1 + - - +
91D ALA* 3.0 11.4 + - - +
93D LEU* 1.3 72.9 - - - +
95D LYS* 1.3 59.1 + - - +
96D LEU 2.9 2.0 - - - -
97D ILE 2.6 21.3 + - - -
98D PRO* 2.7 45.6 + - + +
100D TRP 3.2 17.5 + - - +
101D GLU* 3.4 26.5 + - - +
102D PHE* 3.8 15.0 - - + +
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Residues in contact with LYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A SER 6.1 0.2 - - - -
115A ASP* 3.6 32.5 + - - +
116A ILE* 5.2 5.6 - - + -
117A THR* 6.5 0.7 - - - -
91D ALA* 3.0 22.9 + - - +
92D SER* 3.1 13.0 + - - +
94D LYS* 1.3 75.9 - - - +
96D LEU* 1.3 60.5 + - - +
98D PRO* 3.7 15.4 - - - +
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ILE* 4.6 23.8 - - + -
117A THR* 4.4 22.7 - - + -
16D VAL* 3.8 33.4 - - + -
19D PHE* 4.0 11.0 - - + -
20D VAL* 4.4 18.8 - - + +
41D LEU* 3.9 26.5 - - + -
92D SER 3.4 4.6 + - - +
93D LEU* 3.0 16.8 + - + +
94D LYS 2.9 0.6 - - - -
95D LYS* 1.3 83.2 - - + +
97D ILE* 1.3 66.1 + - + +
98D PRO* 3.8 3.4 - - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.6 30.3 - - + +
20D VAL* 4.5 12.3 - - + -
23D PHE* 3.4 43.1 - - + -
93D LEU 3.2 5.8 + - - +
94D LYS* 2.6 14.9 + - - +
96D LEU* 1.3 86.4 - - + +
98D PRO* 1.3 60.4 - - + +
99D ALA* 3.2 4.0 - - + +
100D TRP* 3.0 53.5 + - + +
102D PHE* 3.9 7.1 - - + -
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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